Advertisements
Feeds:
Posts
Comments

Archive for the ‘Congenital Heart DIsease’ Category


Individuals without angiographic CAD but with hiPRS remain at significantly elevated risk of mortality after cardiac catheterization

Reporter: Aviva Lev-Ari, PhD, RN

 

A genome-wide Polygenic risk scores (PRS) improves risk stratification when added to traditional risk factors and coronary angiography. Individuals without angiographic CAD but with hiPRS remain at significantly elevated risk of mortality.

 

Background:

Coronary artery disease (CAD) is influenced by genetic variation and traditional risk factors. Polygenic risk scores (PRS), which can be ascertained before the development of traditional risk factors, have been shown to identify individuals at elevated risk of CAD. Here, we demonstrate that a genome-wide PRS for CAD predicts all-cause mortality after accounting for not only traditional cardiovascular risk factors but also angiographic CAD itself.

Methods:

Individuals who underwent coronary angiography and were enrolled in an institutional biobank were included; those with prior myocardial infarction or heart transplant were excluded. Using a pruning-and-thresholding approach, a genome-wide PRS comprised of 139 239 variants was calculated for 1503 participants who underwent coronary angiography and genotyping. Individuals were categorized into high PRS (hiPRS) and low-PRS control groups using the maximally selected rank statistic. Stratified analysis based on angiographic findings was also performed. The primary outcome was all-cause mortality following the index coronary angiogram.

Results:

Individuals with hiPRS were younger than controls (66 years versus 69 years; P=2.1×10-5) but did not differ by sex, body mass index, or traditional risk-factor profiles. Individuals with hiPRS were at significantly increased risk of all-cause mortality after cardiac catheterization, adjusting for traditional risk factors and angiographic extent of CAD (hazard ratio, 1.6; 95% CI, 1.2–2.2; P=0.004). The strongest increase in risk of all-cause mortality conferred by hiPRS was seen among individuals without angiographic CAD (hazard ratio, 2.4; 95% CI, 1.1–5.5; P=0.04). In the overall cohort, adding hiPRS to traditional risk assessment improved prediction of 5-year all-cause mortality (area under the receiver-operating curve 0.70; 95% CI, 0.66–0.75 versus 0.66; 95% CI, 0.61–0.70; P=0.001).

Conclusions:

A genome-wide PRS improves risk stratification when added to traditional risk factors and coronary angiography. Individuals without angiographic CAD but with hiPRS remain at significantly elevated risk of mortality.

Footnotes

https://www.ahajournals.org/journal/circgen

*A list of all Regeneron Genetics Center members is given in the Data Supplement.

Guest Editor for this article was Christopher Semsarian, MBBS, PhD, MPH.

The Data Supplement is available at https://www.ahajournals.org/doi/suppl/10.1161/CIRCGEN.118.002352.

Scott M. Damrauer, MD, Department of Surgery, Hospital of the University of Pennsylvania, 3400 Spruce St, Silverstein 4, Philadelphia, PA 19104. Email 
SOURCE
Advertisements

Read Full Post »


The HFE H63D variant confers an increased risk for hypertension, no increased risk for adverse cardiovascular events or substantial left ventricular remodeling

Reporter: Aviva Lev-Ari, PhD, RN

Conclusion:

The HFE H63D variant confers an increased risk for hypertension per allele and, given its frequency, accounts for a significant number of cases of hypertension. However, there was no increased risk for adverse cardiovascular events or substantial left ventricular remodeling.

 

HFE H63D Polymorphism and the Risk for Systemic Hypertension, Myocardial Remodeling, and Adverse Cardiovascular Events in the ARIC Study

Originally publishedHypertension. 2018;0:HYPERTENSIONAHA.118.11730

H63D has been identified as a novel locus associated with the development of hypertension. The quantitative risks for hypertension, cardiac remodeling, and adverse events are not well studied. We analyzed white participants from the ARIC study (Atherosclerosis Risk in Communities) with H63D genotyping (N=10 902). We related genotype status to prevalence of hypertension at each of 5 study visits and risk for adverse cardiovascular events. Among visit 5 participants (N=4507), we related genotype status to echocardiographic features. Frequencies of wild type (WT)/WT, H63D/WT, and H63D/H63D were 73%, 24.6%, and 2.4%. The average age at baseline was 54.9±5.7 years and 47% were men. Participants carrying the H63D variant had higher systolic blood pressure (P=0.004), diastolic blood pressure (0.012), and more frequently had hypertension (P<0.001). Compared with WT/WT, H63D/WT and H63D/H63D participants had a 2% to 4% and 4% to 7% absolute increase in hypertension risk at each visit, respectively. The population attributable risk of H63D for hypertension among individuals aged 45 to 64 was 3.2% (95% CI, 1.3–5.1%) and 1.3% (95% CI, 0.0–2.4%) among individuals >65 years. After 25 years of follow-up, there was no relationship between genotype status and any outcome (P>0.05). H63D/WT and H63D/H63D genotypes were associated with small differences in cardiac remodeling. In conclusion, the HFE H63D variant confers an increased risk for hypertension per allele and, given its frequency, accounts for a significant number of cases of hypertension. However, there was no increased risk for adverse cardiovascular events or substantial left ventricular remodeling.

Footnotes

The online-only Data Supplement is available with this article at https://www.ahajournals.org/doi/suppl/10.1161/HYPERTENSIONAHA.118.11730.

Correspondence to Scott D. Solomon, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115. Email 

Read Full Post »


Aortic Stenosis (AS): Managed Surgically by Transcatheter Aortic Valve Replacement (TAVR) – Search Results for “TAVR” on NIH.GOV website, Top 16 pages

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 9/24/2018

Sapien 3, CoreValve Evolut R on Par for Aortic Stenosis

Head-to-head trial also shows local, general anesthesia outcomes similar

by Ashley Lyles, Staff Writer, MedPage Today

  • This article is a collaboration between MedPage Today® and:

    Medpage Today

SAN DIEGO — Transfemoral transcatheter aortic valve replacement (TAVR) with the balloon-expandable Edwards Sapien 3 valve yields the same early outcomes as the self-expanding CoreValve Evolut R, regardless of anesthesia strategy, a two-by-two randomized trial showed.

In the valve comparison, the primary endpoint of all-cause mortality, stroke, moderate or severe prosthetic valve regurgitation, and permanent pacemaker implantation at 30 days met criteria for equivalence, with a composite rate of 27.2% with Evolut R and 26.1% with Sapien 3, Holger Thiele, MD, of University Hospital in Leipzig, Germany, reported here at the Transcatheter Cardiovascular Therapeutics meeting.

The researchers also evaluated the effects of anesthesia used during these procedures and found no significant difference. The composite endpoint at 30 days came out 27.0% for local anesthesia and 25.5% for general anesthesia.

“The SOLVE-TAVI trial is the first adequately powered randomized trial comparing local versus general anesthesia in patients with symptomatic aortic valve stenosis undergoing TAVR,” said Thiele in a press release. “Results indicate that local anesthesia is both safe and effective and may be a good option for those patients undergoing TAVR with an intermediate or high surgical risk.”

In the majority of aortic stenosis cases, it doesn’t matter which valve you choose, although there are still some cases, like heavy calcification, when it may be better to choose one valve over the other, noted panel discussant Molly Szerlip, MD, of Baylor Scott & White The Heart Group in McKinney, Texas.

The researchers evaluated 447 patients who were receiving care at German medical centers for severe symptomatic aortic stenosis and were at an intermediate- to high-surgical risk. The patients were randomized to have the Sapien 3 valve or CoreValve Evolut R and to either receive general or local anesthesia with conscious sedation.

The individual valve strategy findings again showed equivalence without superiority between Evolut R and Sapien 3 for mortality (2.8% vs 2.3%) and moderate or severe valve regurgitation (1.9% vs 1.4%). But for stroke Evolut R came out superior (0.5% vs 4.7%), and the two didn’t meet criteria for equivalence on pacemaker implantation (22.9% vs 19.0%, P=0.06 for equivalence).

“The rate of relevant valve regurgitation was low whereas permanent pacemaker rates are still relatively high,” the researchers wrote.

The anesthesia comparison endpoints all met the criteria for equivalence without superiority of general anesthesia over local anesthesia:

  • Morality (2.3% vs 2.8%)
  • Stroke (2.8% vs 2.4%)
  • Myocardial infarction (both 0.5%)
  • Infection requiring antibiotics (both 21.0%)
  • Acute kidney injury (9.2% vs 8.9%)

SOURCE

https://www.medpagetoday.com/meetingcoverage/tct/75262?xid=nl_mpt_ACC_Reporter_2018-09-23&eun=g5099207d2r

 

The concept of transcatheter balloon expandable valves was first introduced in the 1980s by a Danish researcher by the name of H. R. Anderson who began testing this idea on pigs. In 2002, Dr. Alain Cribier performed the first successful percutaneous aortic valve replacement on an inoperable patient. The first approval of TAVR for the indication of severe AS in prohibitive risk patients came in 2011. In 2012, the FDA approved TAVR in patients at high surgical risk. In 2015 the indication was expanded to include “valve-in-valve” procedure for failed surgical bioprosthetic valves. Most recently, in 2016 the FDA approved the SAPIEN valve for use in patients with severe AS at intermediate risk.

SOURCE

https://www.ncbi.nlm.nih.gov/pubmed/28613729

 

Critical care management of patients following …

Transcatheter aortic valve replacement (TAVR) is rapidly gaining popularity as a technique to surgically manage aortic stenosis (AS) in high risk …

Imaging in Transcatheter Aortic Valve Replacement (TAVR …

Transcatheter aortic valve replacement (TAVR) is a novel technique developed in the last decade to treat severe aortic stenosis in patients who are …

TAVR and SAVR: Current Treatment of Aortic Stenosis

Transcatheter aortic valve replacement (TAVR) was approved in the United States in late 2011, providing a critically needed alternative therapy for …

Transcatheter Aortic Valve Replacement: Design, Clinical …

Transcatheter aortic valve replacement (TAVR) is a new technology that recently has been shown to improve survival and quality of life in patients …

Cost-Effectiveness Analysis of TAVR

Transcather aortic valve replacement (TAVR) has rapidly gained worldwide acceptance for treating very high-risk patients with symptomatic severe …

Clinical Studies Assessing Transcatheter Aortic Valve …

Extreme-Risk or Inoperable Patients for sAVR. Early clinical evaluation of TAVR included patients deemed unsuitable for sAVR. The logistic Euroscore …

Mitral Valve Surgery: Current Minimally Invasive and …

Minimally Invasive Mitral Valve Repair or Replacement. Most MV pathology can be treated with minimally invasive, … As we learned from the TAVR …

Transcatheter (TAVR) versus surgical (AVR) aortic valve …

The risk in the early phase was higher after TAVR than AVR, and in the TAVR arm in patients with a smaller aortic valve area index. In the late risk …

Procedure makes heart valve replacement safer for high-risk patients

4 months ago – Scientists developed a novel technique that prevents a rare but often fatal complication that can arise during a heart valve procedure called …

Sedation or general anesthesia for transcatheter aortic …

Transfemoral transcatheter aortic valve implantation (TAVI) is nowadays a routine therapy for elderly patients with severe aortic stenosis (AS) and …

Transcatheter aortic valve replacement: outcomes of …

Transcatheter aortic valve replacement: outcomes of patients with moderate or severe mitral regurgitation. Toggweiler S(1), … One year after TAVR …

Outcomes in Transcatheter Aortic Valve Replacement for …

BACKGROUND: Transcatheter aortic valve replacement (TAVR) is being increasingly performed in patients with bicuspid aortic valve stenosis (AS).

New method for performing aortic valve replacement proves …

Researchers at the National Institutes of Health have developed a new, less invasive way to perform transcatheter aortic valve replacement (TAVR), a …

Acquired Aorto-Right Ventricular Fistula following …

Transcatheter aortic valve replacement (TAVR) techniques are rapidly evolving, and results of published trials suggest that TAVR is emerging as the …

Post Transapical Aortic Valve Replacement (TAVR …

A 63-year-old female presented to the emergency department with complaints of her “heart beating out of my chest,” palpitations, and shortness of …

Surgical or Transcatheter Aortic-Valve Replacement in …

Surgical or Transcatheter Aortic-Valve Replacement in Intermediate-Risk Patients. … Although transcatheter aortic-valve replacement (TAVR) …

Transcatheter aortic valve replacement versus surgical …

Transcatheter aortic valve replacement versus surgical valve replacement in intermediate-risk patients: a propensity score analysis. Thourani VH(1) …

Transcatheter aortic valve replacement (TAVR): access …

Ramlawi B(1), Anaya-Ayala JE, Reardon MJ. Author information: (1)Methodist DeBakey Heart & Vascular Center, The Methodist Hospital, Houston, Texas …

Simulation of Transcatheter Aortic Valve Replacement in …

Simulation of Transcatheter Aortic Valve Replacement in patient-specific aortic roots: … Transcatheter aortic valve replacement (TAVR), …

Simulation of Transcatheter Aortic Valve Replacement in …

Simulation of Transcatheter Aortic Valve Replacement in patient-specific aortic roots: … Transcatheter aortic valve replacement (TAVR), …

Transcatheter Aortic Valve Replacement Versus Surgery in …

The objective of this study was to compare outcomes in women after surgical aortic valve replacement … transcatheter aortic valve replacement (TAVR) …

Lederman Lab – NHLBI Cardiovascular Intervention Program

ledermanlab.nhlbi.nih.gov/

Transcaval TAVR was developed at the NHLBI Cardiovascular Intervention Program and applied to patient care in collaboration with Dr. Adam Greenbaum at …

Functional status and quality of life after transcatheter …

Kim CA, Rasania SP, Afilalo J, Popma JJ, Lipsitz LA, Kim DH. BACKGROUND: The functional and quality-of-life benefits of transcatheter aortic valve …

One-Year Outcomes of Transcatheter Aortic Valve …

1. Ann Thorac Surg. 2017 May;103(5):1392-1398. doi: 10.1016/j.athoracsur.2016.11.061. Epub 2017 Feb 24. One-Year Outcomes of Transcatheter Aortic …

Local versus general anesthesia for transcatheter aortic …

Now randomized trials are needed for further evaluation of MAC in the setting of TAVR. PMCID: PMC4022332 PMID: 24612945 [PubMed – indexed for MEDLINE]

Predictors and clinical outcomes of permanent pacemaker …

CONCLUSIONS: PPM was required in 8.8% of patients without prior PPM who underwent TAVR with a balloon-expandable valve in the PARTNER trial and …

Transcatheter aortic valve replacement program development …

TAVR programs require data management strategies to facilitate and monitor program growth, support program evaluation, and meet the requirements for …

New technique makes heart valve replacement safer for some …

Lederman explained that during TAVR, the surgeon places a catheter inside the heart and uses a balloon to open a new valve inside the aortic valve.

Minimally invasive aortic valve replacement using the …

The term “sutureless aortic valve” (su-AV) describes a type of valve which facilitates anchoring of bioprostheses in the aortic position without use …

Use of extracorporeal membrane oxygenation in complicated …

1. Gen Thorac Cardiovasc Surg. 2017 Feb 24. doi: 10.1007/s11748-017-0757-1. [Epub ahead of print] Use of extracorporeal membrane oxygenation in …

Reoperative aortic valve replacement through upper …

Reoperative aortic valve replacement (AVR) has become increasingly common . … but who may not be considered eligible for TAVR procedure.

MRI evaluation prior to Transcatheter Aortic Valve …

MRI evaluation prior to Transcatheter Aortic Valve Implantation … Transcatheter Aortic Valve Implantation (TAVI) … imaging for TAVR assessment in …

Impact of New-Onset Left Bundle Branch Block and …

New-onset LBBB post-TAVR was associated with a higher risk of PPI (risk ratio [RR], 2.18; 95% confidence interval [CI], 1.28-3.70) and cardiac death …

Migration of the transcatheter valve into the left ventricle

Transcatheter valves can embolize into the aorta if the valve is malpositioned too high or, less commonly, migrate into the left ventricle when the …

Transcarotid Transcatheter Aortic Valve Replacement …

All patients were unsuitable for transfemoral TAVR due to severe peripheral vascular disease. An MIS was undertaken in 29.8% (n = 52) …

The transaortic approach for transcatheter aortic valve …

The transaortic approach for transcatheter aortic valve replacement: initial clinical experience in the United States. Lardizabal JA(1), O’Neill BP …

Transcatheter Aortic Valve Replacement: The New Standard …

Transcatheter Aortic Valve Replacement: The … The aim of this study was to assess how the introduction of transcatheter aortic valve replacement (TA …

Minimally invasive aortic valve surgery: state of the art …

Minimally invasive aortic valve replacement (MIAVR) is defined as an aortic valve replacement (AVR) procedure that involves a small chest wall …

Prognostic impact of pulmonary artery systolic pressure in …

Prognostic impact of pulmonary artery systolic pressure in patients undergoing transcatheter aortic valve … TAVR was associated with a decrease in …

Transcatheter Aortic Valve Replacement is Associated with …

This meta-analysis aims to assess the differential outcomes of TAVR and SAVR in patients enrolled in published randomised controlled trials (RCTs).

Aspirin Versus Aspirin Plus Clopidogrel as Antithrombotic …

There were no differences between groups in valve hemodynamic status post-TAVR. CONCLUSIONS: This small trial showed that SAPT (vs. DAPT) …

Upper gastrointestinal bleeding following transcatheter …

Upper gastrointestinal bleeding following transcatheter aortic valve replacement: A retrospective analysis. Stanger DE(1), … (TAVR). BACKGROUND: …

Computed tomography-based sizing recommendations for …

Consecutive patients (n = 120) underwent CT before TAVR with balloon-expandable valves sized by transesophageal echocardiography (TEE) …

European experience and perspectives on transcatheter …

European experience and perspectives on transcatheter aortic valve replacement. Davies WR(1), Thomas MR(2).

[PDF] Mandatory Reporting of Clinical Trial Identifier Numbers …

accrualnet.cancer.gov/sites/accrualnet.cancer.gov/files/Mandatory%20Reporting%20of%20Clinical%20Trial%20Identifier%20FAQs.pdf

Mandatory Reporting of Clinical Trial Identifier Numbers on Claims . Q: Do organizations bill Medicare for all services related to the clinical trial …

Transcatheter Aortic Valve Replacement: Imaging Techniques …

Transcatheter Aortic Valve Replacement: Imaging Techniques for Aortic Root Sizing. Wichmann JL(1), Varga-Szemes A, Suranyi P, Bayer RR 2nd, Litwin SE …

Transcatheter Aortic Valve Thrombosis: Incidence …

METHODS: Among 460 consecutive patients who underwent TAVR with the Edwards Sapien XT or Sapien 3 (Edwards Lifesciences, Irvine, California) THV, …

Sutureless aortic valve replacement – PubMed Central (PMC)

Given its recent developments, the majority of evidence regarding sutureless aortic valve replacement (SU-AVR) is limited to observational studies …

Comparison of balloon-expandable vs self-expandable valves …

Comparison of balloon-expandable vs self-expandable valves in patients undergoing transcatheter aortic valvereplacement: … (TAVR) is an effective …

Geometric changes in ventriculoaortic complex after …

Geometric changes in ventriculoaortic complex after transcatheter aortic valve replacement and its association … The post-TAVR AoA area/pre-TAVR AoA …

Acute and 30-Day Outcomes in Women After TAVR: Results …

Randomized assessment of TAVR versus surgical aortic valve replacement in intermediate risk women is warranted to determine the optimal strategy.

Should We Perform Carotid Doppler Screening Before …

Should We Perform Carotid Doppler Screening Before Surgical or Transcatheter Aortic Valve Replacement? … (TAVR) between January 2007 and August …

Transcatheter Versus Surgical Aortic Valve Replacement in …

BACKGROUND: Transcatheter aortic valve replacement (TAVR) is an option in certain high-risk surgical patients with severe aortic valve stenosis.

Risk stratification and clinical pathways to optimize …

Risk stratification and clinical pathways to optimize length of stay after … We evaluated standardized TAVRoutcomes and length of stay according to …

Use of imaging for procedural guidance during …

1. Curr Opin Cardiol. 2013 Sep;28(5):512-7. doi: 10.1097/HCO.0b013e3283632b5e. Use of imaging for procedural guidance during transcatheter aortic …

Serial Changes in Cognitive Function Following …

Serial Changes in Cognitive Function Following Transcatheter Aortic Valve Replacement. Auffret V(1), Campelo-Parada F(1), Regueiro A(1), …

Acute kidney injury after transcatheter aortic valve …

Acute kidney injury after transcatheter aortic valve replacement: a systematic review and meta-analysis. Thongprayoon C(1), Cheungpasitporn W, Srivali …

Aortic valve replacement – PubMed Health

Transcatheter aortic valve replacement (TAVR), sometimes called transcatheter aortic valve implantation (TAVI), was developed as an alternative for …

Costs of periprocedural complications in patients treated …

Costs of periprocedural complications in patients treated with transcatheter aortic valve replacement: … Renal failure and the need for repeat TAVR …

Trial design: Rivaroxaban for the prevention of major …

The direct factor Xa inhibitor rivaroxaban may potentially reduce TAVR-related thrombotic complications and premature valve failure. DESIGN: GALILEO …

Expandable sheath for transfemoral transcatheter aortic …

Expandable sheath for transfemoral transcatheter aortic valve replacement: procedural outcomes and complications. Borz B(1), Durand E, Tron C, …

Direct Aortic Access Transcatheter Aortic Valve …

Direct Aortic Access Transcatheter Aortic Valve Replacement: Three-Dimensional Computed Tomography Planning and Real … was selected for DA-TAVR …

The impact of frailty on outcomes after cardiac surgery: a …

1. J Thorac Cardiovasc Surg. 2014 Dec;148(6):3110-7. doi: 10.1016/j.jtcvs.2014.07.087. Epub 2014 Aug 7. The impact of frailty on outcomes after …

Establishment of a transcatheter aortic valve program and …

Establishment of a transcatheter aortic valve program and heart valve team at a Veterans Affairs facility. … (TAVR) program.

Echocardiographic determinants of LV functional …

Echocardiographic determinants of LV functional improvement after transcatheter aortic valve replacement. … Transcatheter aortic valve replacement ( …

CT in transcatheter aortic valve replacement.

CT in transcatheter aortic valve replacement. … the rapidly emerging role of CT in the context of transcatheter aortic valve replacement will be …

Transcatheter Aortic Valve Replacement for the Treatment …

Transcatheter Aortic Valve Replacement for the … This study sought to summarize available evidence on transcatheter aortic valve replacement (TAVR) …

Valvular performance and aortic regurgitation following …

End points were post-TAVR moderate to severe AR and paravalvular AR, effective orifice area (EOA), mean trans-aortic pressure gradient (MPG), …

Annual Outcomes With Transcatheter Valve Therapy: From the …

Annual Outcomes With Transcatheter Valve Therapy: From the STS/ACC TVT Registry. Holmes DR Jr, Nishimura RA, Grover FL, Brindis RG, Carroll JD …

The impact of live case transmission on patient outcomes …

The impact of live case transmission on patient outcomes during transcatheter aortic valve replacement: … Data support the notion that live …

Review of Major Registries and Clinical Trials of Late …

Review of Major Registries and Clinical Trials of Late Outcomes After Transcatheter … Final studies were selected irrespective of the type of TAVR …

Trans-subclavian aortic valve replacement with various …

Trans-subclavian aortic valve replacement with various bioprosthetic valves: Single-center experience. Kasapkara HA(1), Aslan AN(2), Ayhan H(1), …

Vascular complications post-transcatheter aortic valve …

Vascular complications post-transcatheter aortic valve procedures. Mangla A(1), Gupta S(2). Author information: (1)Division of Cardiology, Department …

[Monitoring of haemodynamics and function of the aortic …

[Monitoring of haemodynamics and function of the aortic prosthesis during transcatheter aortic valve replacement]. [Article in Russian]

Midregional Proadrenomedullin Improves Risk Stratification …

Midregional Proadrenomedullin Improves Risk Stratification beyond Surgical Risk Scores in Patients Undergoing Transcatheter Aortic Valve … (TAVR …

Midregional Proadrenomedullin Improves Risk Stratification …

Midregional Proadrenomedullin Improves Risk Stratification beyond Surgical Risk Scores in Patients Undergoing Transcatheter Aortic Valve … (TAVR …

Dual Versus Single Antiplatelet Regimen With or Without …

Dual Versus Single Antiplatelet Regimen With or Without Anticoagulation in Transcatheter Aortic Valve … (TAVR), with dual antiplatelet therapy …

Impact of baseline mitral regurgitation on short- and long …

Impact of baseline mitral regurgitation on short- and long-term outcomes following transcatheter aortic … before the index TAVR procedure was …

TAVRassociated prosthetic valve infective endocarditis …

TAVRassociated prosthetic valve infective endocarditis: results of a large, multicenter registry. Latib A, Naim C, De Bonis M, Sinning JM, …

Mechanisms of Heart Block after Transcatheter Aortic Valve …

Consequently, patients undergoing TAVR are prone to peri-procedural complications including cardiac conduction disturbances, which is the focus of …

JACC. Cardiovascular Imaging – Journals – NCBI

JACC. Cardiovascular Imaging journal page at PubMed Journals. Published by Elsevier

Short-Term Outcomes with Direct Aortic Access for …

Short-Term Outcomes with Direct Aortic Access for Transcatheter Aortic Valve Replacement. Ramlawi B, Abu Saleh WK, Jabbari OA, Barker C, Lin C, … (T …

Impact of patient-prosthesis mismatch after transcatheter …

Impact of patient-prosthesis mismatch after transcatheter aortic valve-in-valve implantation in degenerated bioprostheses. Seiffert M(1), Conradi L …

Extent and distribution of calcification of both the …

AR grade 2 to 4 assessed by the method of Sellers immediately after TAVR device implantation was observed in 55 patients (31%). Multivariate …

Safety, Feasibility, and Hemodynamic Effects of Mild …

Safety, Feasibility, and Hemodynamic Effects of Mild Hypothermia in Transcatheter Aortic Valve Replacement: The TAVR … feasibility, and hemodynamic …

Transcatheter aortic valve implantation: anesthetic …

Transcatheter aortic valve implantation: anesthetic considerations. Billings FT 4th(1), Kodali SK, Shanewise JS. Author information: (1)Departments of …

RFA-HL-19-009: Cardiothoracic Surgical Trials Network …

grants.nih.gov/grants/guide/rfa-files/RFA-HL-19-009.html

Bicuspid aortic valve disease has been excluded from TAVR pivotal trials, but TAVR is increasingly used in this population, despite …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Outcome comparison of African-American and Caucasian …

METHODS: Consecutive patients who underwent TAVR were included in this analysis. Patients’ baseline characteristics, procedural data, …

Incidence and predictors of permanent pacemaker …

Incidence and predictors of permanent pacemaker implantation following treatment with the repositionable Lotus™ transcatheter aortic valve.

Effect of Hospital Volume on Outcomes of Transcatheter …

Effect of Hospital Volume on Outcomes of Transcatheter Aortic Valve Implantation. Badheka AO(1), Patel NJ(2), Panaich SS(3), Patel SV(4), …

Aortic valve sizer for TAVR | NIH 3D Print Exchange

3dprint.nih.gov/discover/3dpx-007958

This sizer is designed to simulate the insertion of heart valve prosthetics into 3d printed patient phantoms. It is loosely based on the size …

Health Topics | National Heart, Lung, and Blood Institute …

Materials for patients and health professionals on health topics related to overweight and obesity, heart, lung, blood, and sleep disorders.

DailyMed – ASPIRIN 81MG ADULT LOW DOSE- aspirin tablet …

dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=14d010fb-c4a1-4c3d-942f-58719727bfc0

ASPIRIN 81MG ADULT LOW DOSE- aspirin tablet, delayed release . To receive this label RSS feed. Copy the URL below and paste it into your RSS Reader …

Incidence and predictors of permanent pacemaker …

Incidence and predictors of permanent pacemaker implantation following treatment with the repositionable Lotus™ transcatheter aortic valve.

Aortic valve sizer for TAVR | NIH 3D Print Exchange

3dprint.nih.gov/discover/3dpx-007958

This sizer is designed to simulate the insertion of heart valve prosthetics into 3d printed patient phantoms. It is loosely based on the size …

Transcatheter Aortic Valve Replacement in Severe Aortic …

1. Transcatheter Aortic Valve Replacement in Severe Aortic Stenosis: A Review of Comparative Durability and Clinical Effectiveness Beyond 12 Months …

Sigmoid Septum and Balloon-Expandable Transcatheter Aortic …

de Biasi AR, Worku B, Skubas NJ, Salemi A. Transcatheter aortic valve replacement (TAVR) continues to garner considerable attention, especially as the …

Intra- and Inter-Observer Reproducibility of Transcatheter …

Intra- and Inter-Observer Reproducibility of Transcatheter Aortic Valve Replacement Planning Measurements by Multidetector … of the pre-TAVR …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Transthoracic Echocardiography to Assess Aortic …

Transthoracic Echocardiography to Assess Aortic Regurgitation after TAVRA Comparison with Periprocedural Transesophageal Echocardiography.

Procedural Experience for Transcatheter Aortic Valve …

Procedural Experience for Transcatheter Aortic Valve Replacement and Relation to Outcomes: The STS/ACC TVT Registry. Carroll JD(1), Vemulapalli S(2) …

A comprehensive review of the PARTNER trial.

Svensson LG(1), Tuzcu M, Kapadia S, Blackstone EH, Roselli EE, Gillinov AM, Sabik JF 3rd, Lytle BW. Author information: (1)Department of Thoracic and …

TCT-697 Comparison of Outcomes of Transcatheter Aortic …

TCT-697 Comparison of Outcomes of Transcatheter Aortic Valve Replacement plus Percutaneous Coronary Intervention versus Transcatheter Aortic Valve …

Combined rotational atherectomy and aortic balloon …

Combined rotational atherectomy and aortic balloon valvuloplasty as a bridge to transcatheter aortic valve replacement. Ali O(1), Marmagkiolis K(2) …

Updated standardized endpoint definitions for …

1. Eur J Cardiothorac Surg. 2012 Nov;42(5):S45-60. doi: 10.1093/ejcts/ezs533. Epub 2012 Oct 1. Updated standardized endpoint definitions for …

Clinical outcomes after transcatheter aortic valve …

CONCLUSIONS: VARC definitions have already been used by the TAVR clinical research community, establishing a new standard for reporting clinical …

2012 ACCF/AATS/SCAI/STS expert consensus document on …

2012 ACCF/AATS/SCAI/STS expert consensus document on transcatheter aortic valve replacement. Holmes DR Jr, Mack MJ, Kaul S, Agnihotri A, Alexander KP …

Combined rotational atherectomy and aortic balloon …

Combined rotational atherectomy and aortic balloon valvuloplasty as a bridge to transcatheter aortic valve replacement. Ali O(1), Marmagkiolis K(2) …

Clinical outcomes after transcatheter aortic valve …

CONCLUSIONS: VARC definitions have already been used by the TAVR clinical research community, establishing a new standard for reporting clinical …

TAVR MVR – PubMed Result – ncbi.nlm.nih.gov

1: Grover FL, Vemulapalli S, Carroll JD, Edwards FH, Mack MJ, Thourani VH, Brindis RG, Shahian DM, Ruiz CE, Jacobs JP, Hanzel G, Bavaria JE, Tuzcu EM …

Aortic valve calcium scoring is a predictor of …

Aortic valve calcium scoring is a predictor of paravalvular aortic regurgitation after transcatheter aortic valve implantation

Transcatheter Aortic Valve-in-Valve Replacement Instead of …

Díez JG, Schechter M, Dougherty KG, Preventza O, Coselli JS. Transcatheter aortic valve replacement (TAVR) is a well-established method for replacing …

Coronary Calcium Scan | National Heart, Lung, and Blood …

Buildup of calcium, or calcifications, are a sign of atherosclerosis, coronary heart disease, or coronary microvascular disease. A coronary calcium …

An update on transcatheter aortic valve replacement.

An update on transcatheter aortic valve replacement. … Before the development of transcatheter aortic valve replacement (TAVR … and noninferiority …

The Iowa Model of Evidence-Based Practice to Promote …

The Iowa Model of Evidence-Based Practice to Promote Quality Care: an illustrated example in oncology nursing. Brown CG(1). Author information: …

Two-Year Outcomes in Patients With Severe Aortic Valve …

There was no difference in all-cause mortality at 2 years between TAVR and SAVR (8.0% versus 9.8%, respectively; P=0.54) or cardiovascular mortality …

Home – PubMed – NCBI

PubMed comprises more than 28 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include …

Integrated 3D Echo-X-Ray navigation to predict optimal …

Integrated 3D Echo-X-Ray navigation to predict optimal angiographic deployment projections for TAVR. Kim MS, Bracken J, Nijhof N, Salcedo EE, Quaife …

Cardiac rehabilitation after transcatheter aortic valve …

Cardiac rehabilitation after transcatheter aortic valve implantation compared to patients after valve replacement. Tarro Genta F(1), Tidu M, Bouslenko …

TAVR | NIH 3D Print Exchange

3dprint.nih.gov/discover/tavr

TAVR. Discover > TAVR. 3DPX-007958 Aortic valve sizer for TAVR ahmedhosny. TAVR, aortic valve, sapienXT, heart valve, sizer, Prosthetic. Discover 3D …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Imaging Pandora’s Box: incidental findings in elderly …

Imaging Pandora’s Box: incidental findings in elderly patients evaluated for transcatheter aortic valve replacement. Orme NM(1), Wright TC(2), Harmon …

fascia iliaca compartment block – PubMed – NCBI

TCT-753 Fascia Iliaca Compartment Block (FICB) and None to Light Sedation as an Alternative Minimalist Approach to Sedation for Patients Undergoing …

Stents | National Heart, Lung, and Blood Institute (NHLBI)

For the Coronary Arteries. Doctors may use stents to treat coronary heart disease (CHD). CHD is a disease in which a waxy substance called plaque …

TAVR | NIH 3D Print Exchange

3dprint.nih.gov/discover/tavr

TAVR. Discover > TAVR. 3DPX-007958 Aortic valve sizer for TAVR ahmedhosny. TAVR, aortic valve, sapienXT, heart valve, sizer, Prosthetic. Discover 3D …

Imaging Pandora’s Box: incidental findings in elderly …

Imaging Pandora’s Box: incidental findings in elderly patients evaluated for transcatheter aortic valve replacement. Orme NM(1), Wright TC(2), Harmon …

Transcatheter Aortic Valve Implantation Within Degenerated …

Transcatheter Aortic Valve Implantation Within Degenerated Aortic Surgical Bioprostheses: PARTNER 2 Valve-in-Valve Registry. Webb JG(1), Mack MJ(2) …

[PDF] Transmural” catheter interventions for congenital and …

demystifyingmedicine.od.nih.gov/dm16/m03d22/DM-LedermanRJ.pdf

Transmural” catheter interventions for congenital and structural heart disease … For TAVR, TEVAR, pVAD, etc, when 6-9 mm femoral artery sheaths …

Leaflet Thrombosis in Surgically Explanted or Post-Mortem …

1. JACC Cardiovasc Imaging. 2017 Jan;10(1):82-85. doi: 10.1016/j.jcmg.2016.11.009. Leaflet Thrombosis in Surgically Explanted or Post-Mortem TAVR Valv …

Diagnostic accuracy of multidetector computed tomography …

Diagnostic accuracy of multidetector computed tomography coronary angiography in 325 consecutive patients referred for transcatheter aortic valve …

Transcatheter aortic valve implantation in bicuspid anatomy.

Zhao ZG(1), Jilaihawi H(2), Feng Y(1), Chen M(1). Author information: (1)Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Platelet activation is less enhanced in the new balloon …

Stroke and thromboembolic events after transfemoral aortic valve replacement (TAVR) continue to be a problem. The aim of our study was to compare …

Discover 3D Models | NIH 3D Print Exchange

3dprint.nih.gov/discover?terms=&field_model_category_tag_tid%5B0%5D=93&field_model_license_nid=All&sort_by=created&sort_order=DESC&items_per_page=24&page=2

Discover 3D Models . Back To Top. Search . Enter terms, … 3DPX-007958 Aortic valve sizer for TAVR. ahmedhosny. 3DPX-007884 Fly Pad. Joyner Cruz …

Beyond PARTNER: appraising the evolving trends and …

Beyond PARTNER: appraising the evolving trends and outcomes in transcatheter aortic valve replacement. … TAVR may become an alternative to surgical …

1-Year Outcomes With the Fully Repositionable and …

1. JACC Cardiovasc Interv. 2016 Feb 22;9(4):376-384. doi: 10.1016/j.jcin.2015.10.024. 1-Year Outcomes With the Fully Repositionable and Retrievable …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Beyond PARTNER: appraising the evolving trends and …

Beyond PARTNER: appraising the evolving trends and outcomes in transcatheter aortic valve replacement. … TAVR may become an alternative to surgical …

Echocardiographic imaging of procedural complications …

Echocardiographic imaging of procedural complications during self-expandable transcatheter aortic valve replacement. Hahn RT(1), Gillam LD(2), Little …

Digest – The NIH Record – November 18, 2016

nihrecord.nih.gov/newsletters/2016/11_18_2016/digest.htm

For about 85 percent of patients with this condition, doctors typically perform TAVR through the femoral artery in the leg. But for the other 15 …

Electrocardiographic changes and clinical outcomes after …

Gutiérrez M(1), Rodés-Cabau J, Bagur R, Doyle D, DeLarochellière R, Bergeron S, Lemieux J, Villeneuve J, Côté M, Bertrand OF, Poirier P, Clavel MA …

Coronary Artery Bypass Grafting | National Heart, Lung …

Coronary artery bypass grafting (CABG) is a type of surgery that improves blood flow to the heart. Surgeons use CABG to treat people who have severe …

Heart Surgery | National Heart, Lung, and Blood Institute …

Heart surgery is done to correct problems with the heart. Many heart surgeries are done each year in the United States for various heart problems. The …

Aspirin-clopidogrel no better than aspirin alone for …

NIH study also shows that overall stroke risk is down from 10 years ago. Aspirin combined with the antiplatelet drug clopidogrel is no better than asp …

Heart Valve Disease | National Heart, Lung, and Blood …

Heart valve disease occurs if one or more of your heart valves don’t work well. The heart has four valves: the tricuspid, … (TAVR). For this …

The Odyssey of TAVR from concept to clinical reality.

1. Tex Heart Inst J. 2014 Apr 1;41(2):125-30. doi: 10.14503/THIJ-14-4137. eCollection 2014. The Odyssey of TAVR from concept to clinical reality.

Echo Doppler Estimation of Pulmonary Capillary Wedge …

Echo Doppler Estimation of Pulmonary Capillary Wedge Pressure in Patients with … (TAVR) has become a … Noninvasive quantification of pulmonary …

Aspirin-clopidogrel no better than aspirin alone for …

NIH study also shows that overall stroke risk is down from 10 years ago. Aspirin combined with the antiplatelet drug clopidogrel is no better than asp …

Could late enhancement and need for permanent pacemaker …

Could late enhancement and need for permanent pacemaker implantation in patients undergoing TAVR be explained by undiagnosed transthyretin cardiac …

Diabetes mellitus is associated with increased acute …

However, there are conflicting data on the impact of DM on outcomes of transcatheter aortic valve replacement (TAVR). HYPOTHESIS: …

Cardiac Catheterization | National Heart, Lung, and Blood …

Cardiac catheterization (KATH-eh-ter-ih-ZA-shun) is a medical procedure used to diagnose and treat some heart conditions. A long, thin, flexible tube …

The National Institutes of Health (NIH) Consensus …

consensus.nih.gov/1984/1984FrozenPlasma045html.htm

Fresh Frozen Plasma: Indications and Risks. National Institutes of Health Consensus Development Conference Statement September 24-26, 1984

Successful repair of aortic annulus rupture during …

Successful repair of aortic annulus rupture during transcatheter aortic valve replacement using extracorporeal membrane oxygenation support. Negi …

Pathology of balloon-expandable and self-expanding stents …

1. J Heart Valve Dis. 2015 Mar;24(2):139-47. Pathology of balloon-expandable and self-expandingstents following MRI-guided transapical aortic valve …

Fluoroscopy-guided aortic root imaging for TAVR: “follow …

Fluoroscopy-guided aortic root imaging for TAVR: “follow the right cusp” rule. Kasel AM, Cassese S, Leber AW, von Scheidt W, Kastrati A.

Reply: Aortic Stiffness: Complex Evaluation But Major …

Reply: Aortic Stiffness: Complex Evaluation But Major Prognostic Significance Before TAVR. Yotti R, Bermejo J, Gutiérrez-Ibañes E, …

Ventricular Assist Device | National Heart, Lung, and …

ventricular assist device (VAD) is a mechanical pump that supports heart function and blood flow in people who have weakened hearts.

Severe Symptomatic Aortic Stenosis in Older Adults …

Severe Symptomatic Aortic Stenosis in Older Adults: Pathophysiology, Clinical Manifestations, Treatment Guidelines, and Transcatheter Aortic Valve …

Aortic Stiffness: Complex Evaluation But Major Prognostic …

Aortic Stiffness: Complex Evaluation But Major Prognostic Significance Before TAVR. Harbaoui B, Courand PY, Girerd N, Lantelme P.

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Home – MeSH – NCBI

MeSH (Medical Subject Headings) is the NLM controlled vocabulary thesaurus used for indexing articles for PubMed.

Cohen M[author] – PubMed – NCBI

TCT-712 “Cusp Overlap” View Facilitates Accurate Fluoro-Guided Implantation of Self-Expanding Valve in TAVR. Zaid S, Raza A, Michev I, Ahmad H, Kaple …

Incidence and risk factors of hemolysis after …

1. Am J Cardiol. 2015 Jun 1;115(11):1574-9. doi: 10.1016/j.amjcard.2015.02.059. Epub 2015 Mar 12. Incidence and risk factors of hemolysis after …

Insurance Coverage and Clinical Trials – National Cancer …

Insurance Coverage and Clinical Trials. Federal law requires most health insurance plans to cover routine patient care costs in clinical … National …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

PARTNER trial data showing superior outcomes from TAVI …

openi.nlm.nih.gov/detailedresult.php?img=PMC3431975_cmc-6-2012-125f4&req=4

PARTNER trial data showing superior outcomes from TAVI vs. standard therapy for death at 1 and 2 years for: (A) death from any cause, and (B) death …

Transthoracic echocardiography guidance for TAVR under …

Transthoracic echocardiography guidance for TAVR under monitored anesthesia care. Sengupta PP, Wiley BM, Basnet S, Rajamanickman A, Kovacic JC …

Incidence and risk factors of hemolysis after …

1. Am J Cardiol. 2015 Jun 1;115(11):1574-9. doi: 10.1016/j.amjcard.2015.02.059. Epub 2015 Mar 12. Incidence and risk factors of hemolysis after …

A year in the life of a cardiologist: an interview with Dr …

Dr Manoharan is the clinical lead for the TAVR programme in Northern Ireland and functions as a Clinical Proctor for the Medtronic CoreValve and the …

Insurance Coverage and Clinical Trials – National Cancer …

Insurance Coverage and Clinical Trials. Federal law requires most health insurance plans to cover routine patient care costs in clinical … National …

Transcatheter aortic valve replacement (TAVR) in patients …

Transcatheter aortic valve replacement (TAVR) in patients with systemic autoimmune diseases. Fuentes-Alexandro S(1), Escarcega R, Garcia-Carrasco M …

Transcatheter versus surgical aortic-valve replacement in …

Transcatheter versus surgical aortic-valve replacement in high-risk patients. Smith CR(1), Leon MB, Mack MJ, Miller DC, Moses JW, Svensson LG, …

Transapical Transcatheter Valve-in-Valve Implantation for …

Transapical Transcatheter Valve-in-Valve Implantation for Failed Mitral Valve Bioprosthesis. … Transcatheter valve-in- valve implantation has been …

Echocardiography – Journals – NCBI

Echocardiography journal page at PubMed Journals. Published by Wiley-Blackwell

Transapical Transcatheter Valve-in-Valve Implantation for …

Transapical Transcatheter Valve-in-Valve Implantation for Failed Mitral Valve Bioprosthesis. … Transcatheter valve-in- valve implantation has been …

Impact of Interaction of Diabetes Mellitus and Impaired …

Impact of Interaction of Diabetes Mellitus and Impaired Renal Function on Prognosis and the Incidence of Acute Kidney Injury in Patients Undergoing …

Frequency of and Prognostic Significance of Atrial …

Frequency of and Prognostic Significance of Atrial Fibrillation in Patients Undergoing Transcatheter Aortic Valve Implantation. Sannino A(1), …

Timing, predictive factors, and prognostic value of …

1. Circulation. 2012 Dec 18;126(25):3041-53. doi: 10.1161/CIRCULATIONAHA.112.110981. Epub 2012 Nov 13. Timing, predictive factors, and prognostic …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

AccessGUDID – DEVICE: NA (00643169368873)

accessgudid.nlm.nih.gov/devices/00643169368873

accessgudid – na (00643169368873)- custom pack cb8a42r 2pk tavr pack

Balloon expandable sheath for transfemoral aortic valve …

Balloon expandable sheath for transfemoral aortic valve implantation: a viable option for patients with challenging access. Dimitriadis Z(1), Scholtz …

Staged High-Risk Percutaneous Coronary Intervention with …

The management of concomitant obstructive coronary artery disease and severe aortic stenosis in poor surgical candidates is an evolving topic …

TAVR BMI – PubMed Result

1: Arsalan M, Filardo G, Kim WK, Squiers JJ, Pollock B, Liebetrau C, Blumenstein J, Kempfert J, Van Linden A, Arsalan-Werner A, Hamm C, Mack MJ …

Aortic valve replacement: is porcine or bovine valve better?

Comment in Interact Cardiovasc Thorac Surg. 2013 Mar;16(3):373-4. Interact Cardiovasc Thorac Surg. 2013 Mar;16(3):374. A best evidence topic in …

Can TAVR Make Me Smarter?

Author information: (1)Hôpital du Sacré-Coeur de Montréal, Montréal, Québec, Canada; Morristown Medical Center, Morristown, New Jersey; Cardiovascular …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Transthoracic echocardiography guidance for TAVR under …

Transthoracic echocardiography guidance for TAVR under monitored anesthesia care. Sengupta PP, Wiley BM, Basnet S, Rajamanickman A, Kovacic JC …

Intravenous Adenosine-Based Fractional Flow Reserve in Pre …

1. J Invasive Cardiol. 2016 Sep;28(9):362-3. Intravenous Adenosine-Based Fractional Flow Reserve in Pre-TAVR Assessment of Severe AS: Finally Some …

Intraprocedural TAVR Annulus Sizing Using 3D TEE and the …

Intraprocedural TAVR Annulus Sizing Using 3D TEE and the “Turnaround Rule”. Wiley BM, Kovacic JC, Basnet S, Makoto A, Chaudhry FA, Kini AS, Sharma SK …

Transcatheter versus surgical aortic-valve replacement in …

Transcatheter versus surgical aortic-valve replacement in high-risk patients. Smith CR(1), Leon MB, Mack MJ, Miller DC, Moses JW, Svensson LG, …

Timing, predictive factors, and prognostic value of …

1. Circulation. 2012 Dec 18;126(25):3041-53. doi: 10.1161/CIRCULATIONAHA.112.110981. Epub 2012 Nov 13. Timing, predictive factors, and prognostic …

Reply: Antithrombotic Regimen in Post-TAVR Atrial …

Reply: Antithrombotic Regimen in Post-TAVR Atrial Fibrillation: Not an Easy Decision. Abdul-Jawad Altisent O, Durand E, Muñoz-García AJ, …

A meta-analysis of transfemoral versus transapical …

Zhao A(1), Minhui H(2), Li X(1), Zhiyun X(1). Author information: (1)Department of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical …

Initial Single-Center Experience With the Fully …

Initial Single-Center Experience With the Fully Repositionable Transfemoral Lotus Aortic Valve System. Jarr KU, Leuschner F, Meder B, Katus HA, …

Predictors for Paravalvular Regurgitation After TAVR With …

Predictors for Paravalvular Regurgitation After TAVR With the Self-Expanding Prosthesis: Quantitative Measurement of MDCT Analysis. Yoon SH, Ahn JM …

Native valve endocarditis due to Streptococcus …

Native valve endocarditis due to Streptococcus vestibularis and Streptococcus oralis. Doyuk E(1), Ormerod OJ, Bowler IC.

Dobutamine stress echocardiography for risk stratification …

Dobutamine stress echocardiography for risk stratification of patients with low-gradient severe aortic stenosis undergoing TAVR. Hayek S, Pibarot P …

www.ncbi.nlm.nih.gov

Moved Permanently. The document has moved here.

Intravenous Adenosine-Based Fractional Flow Reserve in Pre …

1. J Invasive Cardiol. 2016 Sep;28(9):362-3. Intravenous Adenosine-Based Fractional Flow Reserve in Pre-TAVR Assessment of Severe AS: Finally Some …

Postprocedural management of patients after transcatheter …

Postprocedural management of patients after transcatheter aortic valve implantation procedure with self-expanding bioprosthesis. Ussia GP(1), …

diastolic dysfunction – PubMed – NCBI

PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include …

SOURCE

Read Full Post »


cvd-series-a-volume-iii


Series A: e-Books on Cardiovascular Diseases
 

Series A Content Consultant: Justin D Pearlman, MD, PhD, FACC

VOLUME THREE

Etiologies of Cardiovascular Diseases:

Epigenetics, Genetics and Genomics

http://www.amazon.com/dp/B018PNHJ84

 

by  

Larry H Bernstein, MD, FCAP, Senior Editor, Author and Curator

and

Aviva Lev-Ari, PhD, RN, Editor and Curator

Introduction to Volume Three 

PART 1
Genomics and Medicine

1.1  Genomics and Medicine: The Physician’s View

1.2  Ribozymes and RNA Machines – Work of Jennifer A. Doudna

1.3  Genomics and Medicine: Contributions of Genetics and Genomics to Cardiovascular Disease Diagnoses

1.4 Genomics Orientations for Individualized Medicine, Volume One

1.4.1 CVD Epidemiology, Ethnic subtypes Classification, and Medication Response Variability: Cardiology, Genomics and Individualized Heart Care: Framingham Heart Study (65 y-o study) & Jackson Heart Study (15 y-o study)

1.4.2 What comes after finishing the Euchromatic Sequence of the Human Genome?

1.5  Genomics in Medicine – Establishing a Patient-Centric View of Genomic Data

 

PART 2
Epigenetics – Modifiable Factors Causing Cardiovascular Diseases

2.1 Diseases Etiology

2.1.1 Environmental Contributors Implicated as Causing Cardiovascular Diseases

2.1.2 Diet: Solids, Fluid Intake and Nutraceuticals

2.1.3 Physical Activity and Prevention of Cardiovascular Diseases

2.1.4 Psychological Stress and Mental Health: Risk for Cardiovascular Diseases

2.1.5 Correlation between Cancer and Cardiovascular Diseases

2.1.6 Medical Etiologies for Cardiovascular Diseases: Evidence-based Medicine – Leading DIAGNOSES of Cardiovascular Diseases, Risk Biomarkers and Therapies

2.1.7 Signaling Pathways

2.1.8 Proteomics and Metabolomics

2.1.9 Sleep and Cardiovascular Diseases

2.2 Assessing Cardiovascular Disease with Biomarkers

2.2.1 Issues in Genomics of Cardiovascular Diseases

2.2.2 Endothelium, Angiogenesis, and Disordered Coagulation

2.2.3 Hypertension BioMarkers

2.2.4 Inflammatory, Atherosclerotic and Heart Failure Markers

2.2.5 Myocardial Markers

2.3  Therapeutic Implications: Focus on Ca(2+) signaling, platelets, endothelium

2.3.1 The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia, Similarities and Differences, and Pharmaceutical Targets

2.3.2 EMRE in the Mitochondrial Calcium Uniporter Complex

2.3.3 Platelets in Translational Research ­ 2: Discovery of Potential Anti-platelet Targets

2.3.4 The Final Considerations of the Role of Platelets and Platelet Endothelial Reactions in Atherosclerosis and Novel Treatments

2.3.5 Nitric Oxide Synthase Inhibitors (NOS-I)

2.3.6 Resistance to Receptor of Tyrosine Kinase

2.3.7 Oxidized Calcium Calmodulin Kinase and Atrial Fibrillation

2.3.8 Advanced Topics in Sepsis and the Cardiovascular System at its End Stage

2.4 Comorbidity of Diabetes and Aging

2.4.1 Heart and Aging Research in Genomic Epidemiology: 1700 MIs and 2300 coronary heart disease events among about 29 000 eligible patients

2.4.2 Pathophysiological Effects of Diabetes on Ischemic-Cardiovascular Disease and on Chronic Obstructive Pulmonary Disease (COPD)

2.4.3 Risks of Hypoglycemia in Diabetics with Chronic Kidney Disease (CKD)

2.4.4  Mitochondrial Mechanisms of Disease in Diabetes Mellitus

2.4.5 Mitochondria: More than just the “powerhouse of the cell”

2.4.6  Pathophysiology of GLP-1 in Type 2 Diabetes

2.4.7 Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

2.4.8 CaKMII Inhibition in Obese, Diabetic Mice leads to Lower Blood Glucose Levels

2.4.9 Protein Target for Controlling Diabetes, Fractalkine: Mediator cell-to-cell Adhesion though CX3CR1 Receptor, Released from cells Stimulate Insulin Secretion

2.4.10 Peroxisome proliferator-activated receptor (PPAR-gamma) Receptors Activation: PPARγ transrepression for Angiogenesis in Cardiovascular Disease and PPARγ transactivation for Treatment of Diabetes

2.4.11 CABG or PCI: Patients with Diabetes – CABG Rein Supreme

2.4.12 Reversal of Cardiac Mitochondrial Dysfunction

2.4.13  BARI 2D Trial Outcomes

2.4.14 Overview of new strategy for treatment of T2DM: SGLT2 inhibiting oral antidiabetic agents

2.5 Drug Toxicity and Cardiovascular Diseases

2.5.1 Predicting Drug Toxicity for Acute Cardiac Events

2.5.2 Cardiotoxicity and Cardiomyopathy Related to Drugs Adverse Effects

2.5.3 Decoding myocardial Ca2+ signals across multiple spatial scales: A role for sensitivity analysis

2.5.4. Leveraging Mathematical Models to Understand Population Variability in Response to Cardiac Drugs: Eric Sobie, PhD

2.5.5 Exploiting mathematical models to illuminate electrophysiological variability between individuals.

2.5.6 Clinical Effects and Cardiac Complications of Recreational Drug Use: Blood pressure changes, Myocardial ischemia and infarction, Aortic dissection, Valvular damage, and Endocarditis, Cardiomyopathy, Pulmonary edema and Pulmonary hypertension, Arrhythmias, Pneumothorax and Pneumopericardium

 

2.6 Male and Female Hormonal Replacement Therapy: The Benefits and the Deleterious Effects on Cardiovascular Diseases

2.6.1  Testosterone Therapy for Idiopathic Hypogonadotrophic Hypogonadism has Beneficial and Deleterious Effects on Cardiovascular Risk Factors

2.6.2 Heart Risks and Hormones (HRT) in Menopause: Contradiction or Clarification?

2.6.3 Calcium Dependent NOS Induction by Sex Hormones: Estrogen

2.6.4 Role of Progesterone in Breast Cancer Progression

PART 3
Determinants of Cardiovascular Diseases Genetics, Heredity and Genomics Discoveries

Introduction

3.1 Why cancer cells contain abnormal numbers of chromosomes (Aneuploidy)

3.1.1 Aneuploidy and Carcinogenesis

3.2 Functional Characterization of Cardiovascular Genomics: Disease Case Studies @ 2013 ASHG

3.3 Leading DIAGNOSES of Cardiovascular Diseases covered in Circulation: Cardiovascular Genetics, 3/2010 – 3/2013

3.3.1: Heredity of Cardiovascular Disorders

3.3.2: Myocardial Damage

3.3.3: Hypertention and Atherosclerosis

3.3.4: Ethnic Variation in Cardiac Structure and Systolic Function

3.3.5: Aging: Heart and Genetics

3.3.6: Genetics of Heart Rhythm

3.3.7: Hyperlipidemia, Hyper Cholesterolemia, Metabolic Syndrome

3.3.8: Stroke and Ischemic Stroke

3.3.9: Genetics and Vascular Pathologies and Platelet Aggregation, Cardiac Troponin T in Serum

3.3.10: Genomics and Valvular Disease

3.4  Commentary on Biomarkers for Genetics and Genomics of Cardiovascular Disease

PART 4
Individualized Medicine Guided by Genetics and Genomics Discoveries

4.1 Preventive Medicine: Cardiovascular Diseases

4.1.1 Personal Genomics for Preventive Cardiology Randomized Trial Design and Challenges

4.2 Gene-Therapy for Cardiovascular Diseases

4.2.1 Genetic Basis of Cardiomyopathy

4.3 Congenital Heart Disease/Defects

4.4 Cardiac Repair: Regenerative Medicine

4.4.1 A Powerful Tool For Repairing Damaged Hearts

4.4.2 Modified RNA Induces Vascular Regeneration After a Heart

4.5 Pharmacogenomics for Cardiovascular Diseases

4.5.1 Blood Pressure Response to Antihypertensives: Hypertension Susceptibility Loci Study

4.5.2 Statin-Induced Low-Density Lipoprotein Cholesterol Reduction: Genetic Determinants in the Response to Rosuvastatin

4.5.3 SNPs in apoE are found to influence statin response significantly. Less frequent variants in PCSK9 and smaller effect sizes in SNPs in HMGCR

4.5.4 Voltage-Gated Calcium Channel and Pharmacogenetic Association with Adverse Cardiovascular Outcomes: Hypertension Treatment with Verapamil SR (CCB) vs Atenolol (BB) or Trandolapril (ACE)

4.5.5 Response to Rosuvastatin in Patients With Acute Myocardial Infarction: Hepatic Metabolism and Transporter Gene Variants Effect

4.5.6 Helping Physicians identify Gene-Drug Interactions for Treatment Decisions: New ‘CLIPMERGE’ program – Personalized Medicine @ The Mount Sinai Medical Center

4.5.7 Is Pharmacogenetic-based Dosing of Warfarin Superior for Anticoagulation Control?

Summary & Epilogue to Volume Three

 

 

Read Full Post »


Lysyl Oxidase (LOX) gene missense mutation causes Thoracic Aortic Aneurysm and Dissection (TAAD) in Humans because of inadequate cross-linking of collagen and elastin in the aortic wall

Mutation carriers may be predisposed to vascular diseases because of weakened vessel walls under stress conditions.

 

Reporter: Aviva Lev-Ari, PhD, RN

 

Loss of function mutation in LOX causes thoracic aortic aneurysm and dissection in humans

  1. Vivian S. Leea,
  2. Carmen M. Halabia,b,
  3. Erin P. Hoffmanc,1,
  4. Nikkola Carmichaelc,d,
  5. Ignaty Leshchinerc,d,
  6. Christine G. Liand,e,
  7. Andrew J. Bierhalsf,
  8. Dana Vuzmanc,d,
  9. Brigham Genomic Medicine2,
  10. Robert P. Mechama,
  11. Natasha Y. Frankc,d,g,3, and
  12. Nathan O. Stitzielh,i,j,3

Edited by J. G. Seidman, Harvard Medical School, Boston, MA, and approved June 7, 2016 (received for review January 27, 2016)

  • Author contributions: V.S.L., R.P.M., N.Y.F., and N.O.S. designed research; V.S.L., C.M.H., and N.O.S. performed research; E.P.H., N.C., C.G.L., D.V., B.G.M.P., R.P.M., and N.Y.F. contributed new reagents/analytic tools; V.S.L., C.M.

Significance

The mechanical integrity of the arterial wall is dependent on a properly structured ECM. Elastin and collagen are key structural components of the ECM, contributing to the stability and elasticity of normal arteries. Lysyl oxidase (LOX) normally cross-links collagen and elastin molecules in the process of forming proper collagen fibers and elastic lamellae. Here, using whole-genome sequencing in humans and genome engineering in mice, we show that a missense mutation in LOX causes aortic aneurysm and dissection because of insufficient elastin and collagen cross-linking in the aortic wall. These findings confirm mutations in LOX as a cause of aortic disease in humans and identify LOX as a diagnostic and potentially therapeutic target.

Abstract

Thoracic aortic aneurysms and dissections (TAAD) represent a substantial cause of morbidity and mortality worldwide. Many individuals presenting with an inherited form of TAAD do not have causal mutations in the set of genes known to underlie disease. Using whole-genome sequencing in two first cousins with TAAD, we identified a missense mutation in the lysyl oxidase (LOX) gene (c.893T > G encoding p.Met298Arg) that cosegregated with disease in the family. Using clustered regularly interspaced short palindromic repeats (CRISPR)/clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease (Cas9) genome engineering tools, we introduced the human mutation into the homologous position in the mouse genome, creating mice that were heterozygous and homozygous for the human allele. Mutant mice that were heterozygous for the human allele displayed disorganized ultrastructural properties of the aortic wall characterized by fragmented elastic lamellae, whereas mice homozygous for the human allele died shortly after parturition from ascending aortic aneurysm and spontaneous hemorrhage. These data suggest that a missense mutation in LOX is associated with aortic disease in humans, likely through insufficient cross-linking of elastin and collagen in the aortic wall. Mutation carriers may be predisposed to vascular diseases because of weakened vessel walls under stress conditions. LOX sequencing for clinical TAAD may identify additional mutation carriers in the future. Additional studies using our mouse model of LOX-associated TAAD have the potential to clarify the mechanism of disease and identify novel therapeutics specific to this genetic cause.

SOURCE

http://www.pnas.org/content/early/2016/07/15/1601442113.abstract

Missense LOX Mutation Linked to Aortic Rupture, Aneurysm

NEW YORK (GenomeWeb) – Researchers from Washington University School of Medicine have linked a LOX gene variant with aortic rupture and aneurysm.

As they reported in the online early edition of the Proceedings of the National Academy of Sciences yesterday, the researchers sequenced two first cousins from a family with a history of aortic ruptures and aneurysms to uncover a missense mutation in the lysyl oxidase (LOX) gene, which encodes a protein that cross-links elastin and collagen. When they used CRISPR/Cas9 genome engineering to introduce the mutation into a mouse model, mice heterogeneous for the mutation had disorganized aortic walls, while mice homozygous for the mutation died shortly after birth of ascending aneurysm and spontaneous hemorrhage, suggesting that the LOX variant might be causal.

Read more @ the Source

SOURCE

https://www.genomeweb.com/sequencing/missense-lox-mutation-linked-aortic-rupture-aneurysm

Read Full Post »


Human Genetics and Childhood Diseases

Curator: Larry H. Bernstein, MD, FCAP

 

 

 

Publication Roundup: HGMD

HGMD®, the Human Gene Mutation Database is used by scientists around the world to find information on reported genetic mutations. The papers below use the database to advance our understanding of disease, DNA dynamics, and more.

https://www.qiagenbioinformatics.com/blog/translational/publication-roundup-hgmd

Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes
First author: Albino Bacolla

Scientists in the US and UK published results in Nucleic Acids Research of a detailed analysis of single-base substitutions and indels in the human genome. Their findings show that certain base positions are more susceptible to mutagenesis than others. They used HGMD Professional to find mutations in specific genomic regions for analysis; the paper includes charts showing mutation patterns, germline SNPs, and more from HGMD data.

High prevalence of CDH23 mutations in patients with congenital high-frequency sporadic or recessively inherited hearing loss
First author: Kunio Mizutari

This Orphanet Journal of Rare Diseases paper from scientists in Japan sequenced 72 patients with unexplained hearing loss, finding several CDH23 mutations, some of which were novel. Mutations in the gene have been linked to Usher syndrome and other forms of hereditary hearing loss. The scientists used HGMD to find all known CDH23 mutations within nearly 70 coding regions.

Mutation analyses and prenatal diagnosis in families of X-linked severe combined immunodeficiency caused by IL2Rγ gene novel mutation
First author: Q.L. Bai

In Genetics and Molecular Research, scientists report the utility of mutation analysis of the interleukin-2 receptor gamma gene to assess carrier status and perform prenatal diagnosis for X-linked severe combined immunodeficiency. They studied two high-risk families, along with 100 controls, to evaluate the approach. Sequence variation was determined using HGMD Professional and an X-SCID database, and a new mutation was discovered in the project.

Impact of glucocerebrosidase mutations on motor and nonmotor complications in Parkinson’s disease
First author: Tomoko Oeda

Researchers from three hospitals in Japan published this Neurobiology of Aging report that may help stratify Parkinson’s disease patients by prognosis. They sequenced mutations in the GBA gene in 215 patients, finding that those who had mutations associated with Gaucher disease suffered dementia and psychosis much earlier than those who didn’t. The team found previously reported GBA mutations using HGMD Professional.

Comprehensive Genetic Characterization of a Spanish Brugada Syndrome Cohort
First author: Elisabet Selga

In this PLoS One publication, scientists from a number of institutions in Spain examined genetic variation among patients with Brugada syndrome, a rare genetic cardiac arrhythmia. They sequenced 14 genes in 55 patients, identifying 61 variants and finding the subset that appear pathogenic. Variants were filtered against a number of databases, including HGMD.

 

 

Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes

Albino Bacolla1Xiao Zhu2Hanning Chen3Katy Howells4David N. Cooper4 and Karen M. Vasquez1

Nucl. Acids Res. (26 May 2015) 43(10): 5065-5080.   http://dx.doi.org:/10.1093/nar/gkv364

Single base substitutions (SBSs) and insertions/deletions are critical for generating population diversity and can lead both to inherited disease and cancer. Whereas on a genome-wide scale SBSs are influenced by cellular factors, on a fine scale SBSs are influenced by the local DNA sequence-context, although the role of flanking sequence is often unclear. Herein, we used bioinformatics, molecular dynamics and hybrid quantum mechanics/molecular mechanics to analyze sequence context-dependent mutagenesis at mononucleotide repeats (A-tracts and G-tracts) in human population variation and in cancer genomes. SBSs and insertions/deletions occur predominantly at the first and last base-pairs of A-tracts, whereas they are concentrated at the second and third base-pairs in G-tracts. These positions correspond to the most flexible sites along A-tracts, and to sites where a ‘hole’, generated by the loss of an electron through oxidation, is most likely to be localized in G-tracts. For A-tracts, most SBSs occur in the direction of the base-pair flanking the tracts. We conclude that intrinsic features of local DNA structure, i.e. base-pair flexibility and charge transfer, render specific nucleotides along mononucleotide runs susceptible to base modification, which then yields mutations. Thus, local DNA dynamics contributes to phenotypic variation and disease in the human population.

INTRODUCTION

Changes in human genomic DNA in the form of base substitutions and insertions/deletions (indels) are essential to ensure population diversity, adaptation to the environment, defense from pathogens and self-recognition; they are also a critical source of human inherited disease and cancer. On a genome-wide scale, base substitutions result from the combined action of several factors, including replication fidelity, lagging versus leading strand DNA synthesis, repair, recombination, replication timing, transcription, nucleosome occupancy, etc., both in the germline and in cancer (14). On a much finer scale [(over a few base pairs (bp)], rates of base substitutions may be strongly influenced by interrelationships between base–protein and base–base interactions. For example, the mutator role of activation-induced deaminase (AID) in B-cells during class-switch recombination and somatic hypermutation (5) targets preferentially cytosines within WRC (W: A|T; R: A|G) sequences (6), whereas apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) overexpression displays a preference for base substitutions at cytosines in TCW contexts (7). Other examples, such as the induction of C→T transitions at CG:CG dinucleotides by cytosine-5-methylation and the role of UV light in promoting base substitutions at pyrimidine dimers have been well documented (reviewed in (4,8)). More recently, complex patterns of base substitution at guanosines in cancer genomes have been found to correlate with changes in guanosine ionization potentials as a result of electronic interactions with flanking bases (9), suggesting a role for electron transfer and oxidation reactions in sequence-dependent mutagenesis. However, despite these advances, the increasing number of sequence-dependent patterns of mutation noted in genome-wide sequencing studies has met with a lack of understanding of most of the underlying mechanisms (10). Thus, a picture is emerging in which mutations are often heavily dependent on sequence-context, but for which our comprehension is limited.

Mononucleotide repeats comprise blocks of identical base pairs (A|T or C|G; hereafter referred to as A-tracts and G-tracts) and display distinct features: they are abundant in vertebrate genomes; mutations within the tracts occur more frequently than the genome-wide average; mutations generally increase with increasing tract length; length instability is a hallmark of mismatch repair-deficiency in cancers; and sequence polymorphism within the general population has been linked to phenotypic diversity (1115). Thus, mononucleotide repeats appear ideal for addressing the question of sequence-dependent mutagenesis since base pairs within the tracts are flanked by identical neighbors. Both historic and recent investigations concur with the conclusion that a major source of mononucleotide repeat polymorphism is the occurrence of slippage (i.e. repeat misalignment) during semiconservative DNA replication, which gives rise to the addition or deletion of repeat units (11,12). An additional and equally important source of mutation has recently been suggested to arise from errors in DNA replication by translesion synthesis DNA polymerases, such as pol η and pol κ (13), also on slipped intermediates, leading to single base substitutions.

A key question that remains unanswered in these studies and which is relevant to the issue of sequence context-dependent mutagenesis is whether all base pairs within mononucleotide repeats display identical susceptibility to single base changes and whether indels (which are consequent to DNA breakage) occur randomly within the tracts.

Herein, we combine bioinformatics analyses on mononucleotide repeat variants from the 1000 Genomes Project and cancer genomes with molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations to address the question of sequence-dependent mutagenesis within these tracts. We show that mutations along both A-tracts and G-tracts are highly non-uniform. Specifically, both base substitutions and indels occur preferentially at the first and last bp of A-tracts, whereas they are concentrated between the second and third G:C base pairs in G-tracts. These positions coincide with the most flexible base pairs for A-tracts and with the preferential localization of a ‘hole’ that results when one electron is lost due to an oxidation reaction anywhere along G-tracts. Thus, despite the uniformity of sequence composition, mutations occur in a sequence-dependent context at homopolymeric runs according to a hierarchy that is imposed by both local DNA structural features and long-range base–base interactions. We also show that the repair processes leading to base substitution must differ between A- and G-tracts, since in the former, but not in the latter, base substitutions occur predominantly in the direction of the base immediately flanking the tracts. Additional sequence-dependent patterns of mutation are likely to arise from studies of more heterogeneous sequence combinations, possibly involving other aspects intrinsic to the structure of DNA.

 

RESULTS

Mononucleotide repeat variation is defined by tract length and flanking base composition

We define mononucleotide repeats in the GRCh37/hg19 (hg19) human genome assembly as uninterrupted runs of A:T and G:C base pairs (hereafter referred to as A-tracts and G-tracts, respectively) from 4 to 13 base pairs in length (Figure 1A). We retrieved a total of 48,767,945 A-tracts and 13,633,781 G-tracts, both of which displayed a biphasic distribution with an inflection point between tract lengths of 8 and 9 (bp) and with the number of runs declining with length more dramatically for G-tracts than for A-tracts (Figure 1B), as noted previously (29). Both the number of short tracts and the extent of decline varied with flanking base composition, TA[n]T runs being two- to three-fold more abundant than CA[n]Cs (Supplementary Figure S1A) and AG[n]As declining the most rapidly (Supplementary Figure S1B). Thus, mononucleotide runs exist as a collection of separate pools of sequences in extant human genomes, each maintained at distinctive rates of sequence stability, as determined by factors such as bp composition (A:T versus G:C), tract length and flanking sequence composition.

Figure 1.

Mononucleotide repeat variation, evolutionary conservation and association with transcription. (A) The search algorithm was designed to retrieve runs of As or Ts (A-tracts) and Gs or Cs (G-tracts) length n (n = 4 to 13), along with their 5′ (n = 0) and 3′ (n = n + 1) nearest neighbors from hg19. Tract bases were numbered 5′ to 3′ with respect to the purine-rich sequence. The panel exemplifies the nomenclature for A- and G-tracts of length 4. (B) Logarithmic plot of the number of A-tracts (closed circles) and G-tracts (open circles) in hg19 as a function of length. (C) Normalized fractions of polymorphic tracts (F SNV) (number of SNVs divided by both hg19 number of tracts and n) from the 1KGP for A-tracts (closed circles) and G-tracts (open circles). (D) Radial plot of SNVs in the 1KGP at the 5′ and 3′ nearest neighbors of A-tracts. Periphery, tract length; horizontal axis, scale for the fraction of SNVs (F SNV). (E) Radial plot of SNVs in the 1KGP at the 5′ and 3′ nearest neighbors of G-tracts. (F) Percent difference in the numbers of A-tracts (closed circles) and G-tracts (open circles) between syntenic regions of hg19 and HN genomes. (G) The exponents of Benjamini-corrected P-values for A-tract-containing genes enriched in transcription-factor binding sites plotted as a function of A-tract length (triangles); each value represents the median of the top 11 USCS_TFBS terms. The percent A-tracts (closed circles) and G-tracts (open circles) intersecting genomic regions pulled-down by chromatin immunoprecipitation using antibodies against transcription factors are plotted as a function of tract length. (H) List of gene enrichment terms with a Benjamini-corrected P-value of <0.05 in common between genes containing A- and G-tracts of lengths 4–13, excluding the UCSC_TFBS terms.

 We examined the extent of sequence variation in the human population by mapping 38,878,546 single nucleotide variants (SNVs) from 1092 haplotype-resolved genomes (the 1000 Genomes Project, 1KGP) (30) to the hg19 A- and G-tracts. The normalized fractions of polymorphic tracts (F SNV) were greater for G-tracts than A-tracts and both displayed Gaussian-type distributions, with maxima of 0.067 for G-tracts of length 8 and 0.017 for A-tracts of length 9 (Figure 1C). CA[n]C and AG[n]A runs displayed the highest F SNV values for A- and G-tracts, respectively (Supplementary Figure S1C and D), with F SNV values for AG[n]As attaining ∼0.10 at length 8. We conclude that flanking base composition influences the rates of SNV within mononucleotide runs and, as a consequence, their representation in the reference human genome.

F SNV values at the flanking 5′ and 3′ bp were similar between A- and G-tracts, except for minor differences for the least represented (i.e. longest) tracts and did not exceed 0.02 (Supplementary Figure S1E). These fractions are expected to be greater than at more distant positions from the tracts, based on previous data (29). SNVs at G-tracts, but not at A-tracts, were more frequent than at flanking base pairs. F SNVs for base pairs flanking short (≤8 bp) tracts were at least twice as high as those flanking long tracts; F SNVs also displayed distinct sequence preference with most (∼0.1) variants occurring at Ts 3′ of G-tracts (Figure 1D and E). In summary, SNVs at mononucleotide runs do not increase monotonically with length but peak at 8–9 bp. This behavior mirrors the genomic distributions, both with respect to the total number of tracts (Figure 1B) and the subsets flanked by specific-sequence combinations (Supplementary Figure S1A–D). Variation at flanking base pairs also displayed a biphasic pattern centered at a length of 8–9 bp, with a greater chance of variation adjacent to G- than A-tracts and with characteristic sequence preferences.

Long tracts are evolutionarily conserved and associated with high transcription

To assess whether more variable monosatellite runs (Figure 1C) might have undergone a greater reduction in number in extant humans relative to extinct hominids, we compared the number of A- and G-tracts between syntenic regions of five individuals comprising hg19 and three Neanderthal (HN) specimens (31). The difference between hg19 and HN was very small (<±2%) for the short tracts, but it displayed more negative values in hg19 with increasing tract length, which reached a maximum of −11.8 and −32.7% for A- and G-tracts, respectively, of length 9. Beyond this threshold, the numbers of tracts converged for A-tracts, whereas they were more abundant in hg19 for G-tracts >11 bp (Figure 1F). In summary, the largest difference in the number of mononucleotide runs between hg19 and HN sequences was centered at 9 bp for both A- and G-tracts, suggesting that the length distributions (Figure 1A and Supplementary Figure S1A and B) reflect distinct rates of evolutionary gains and losses due to differential sequence mutability (Figure 1C) as a function of length and flanking sequence composition (12).

The fact that long (>9 bp) mononucleotide runs display low variability in the human population (Figure 1C) and sequence conservation during evolutionary divergence (Figure 1F) raises the possibility that they might serve functional roles. Through gene enrichment analyses, we found that genes containing A- and G-tracts were enriched for genes associated with the term ‘UCSC_TFBS’, which pertains to transcripts harboring frequent transcription factor binding sites (32,33). For A-tract-containing genes, the median P-values for the top 11 UCSC_TFBS terms decreased from 2.95E-26 for tracts of length 4 to 5.22E-241 for tracts of length 13 (Figure 1G). The percent of A-tracts intersecting genomic fragments amplified from chromatin immunoprecipitation using transcription-factor binding antibodies (32,33) also increased from 8.7 to 9.9 from length 6 to 13, whereas it was constant (mean ± SD, 22.4 ± 1.1) for G-tracts (Figure1G). For gene classes excluding ‘UCSC_TFBS’, a search for categories enriched at P < 0.05 and common to all A- and G-tract-containing genes returned a set of 25 terms, 22 of which were associated with high levels of tissue-specific gene expression (Figure 1H). In summary, these analyses extend prior work (14) supporting a role for mononucleotide tracts in enhancing gene expression, a function that for A-tracts appears to increase with increasing tract length.

Repeat variability is highly skewed

Next we addressed whether bp along A- and G-tracts display equal probability and type of variation. In the 1KGP dataset, the number of SNVs at each position along both A- and G-tracts of length 4 was within a two-fold difference (144,000–240,000); for both types of sequence, transitions (i.e. A→G and G→A) were the predominant (51–78%) type of base substitution (Supplementary Figure S2A and B). However, with increasing length, the number of SNVs decreased up to 30-fold more drastically for G-tracts than for A-tracts, with increasing numbers of transversions (A→T and G→C|T) being predominant. Normalizing the data for the number of tracts genome-wide revealed that the extent of SNV varied by up to 10-fold, depending upon tract length and bp position. Specifically, the highest degree of variation was observed at the first and last A within the A-tracts (i.e. A1 and An), which underwent up to 61% A→T and 43% A→C transversions, respectively, at length 9 (Figure 2A). Likewise, for G-tracts, the most polymorphic sites were G3, followed by G2, for mid-size tracts of 8–10 bp, with 44% G→C transversions at G3 for tracts of length 8 (Figure2B). Thus, the extent of SNV at mononucleotide runs is grossly skewed in human genomes, both along the sequence itself and across tract length, which must account for the bell-shape behavior in F SNV for the tracts as a whole (Figure 1C).

Figure 2.

Population variation spectra. (A) Variation spectra of A-tracts. Percent (number of SNVs at each position divided by the number of tracts in hg19 × 100) of A→T (black), A→C (red) and A→G (green) SNVs in the 1KGP dataset (left). Percent SNVs at A1 as a function of tract length (right). (B) Variation spectra of G-tracts. As in panel A with G→T (black), G→C (red) and G→A (cyan) (left). Percent SNVs at G3 as a function of tract length (right). (C) Percent A→T, A→C and A→G transitions at each position along A-tracts (stars) preceded and followed by a T (TA[n]T, left), C (CA[n]C), center) and G (GA[n]G, right) as a function of tract length. (D) Percent G→T, G→C and G→A transitions at each position along G-tracts (stars) preceded and followed by a T (TG[n]T, left), C (CG[n]C), center) and A (AG[n]A, right) as a function of tract length. (E) Percent transitions at base pairs (stars) preceding or following A-tracts (left) and G-tracts (right) as a function of tract length (n). *, mutated position.

We assessed whether SNV hypervariability was associated with specific combinations of nearest neighbors. For A-tracts flanked 5′ by a T, C or G, the highest percentage of SNVs was observed at A1 when preceded by a T, which reached 7.9% for TA[n] tracts of length 9 (Supplementary Figure S2C). By contrast, for 3′ T, C or G, the greatest effect was elicited by a C, with the highest percentage (7.1%) of SNVs at An for A[n]C tracts of length 9 (Supplementary Figure S2D). Therefore, flanking base pairs play a critical role both in the spectra and frequencies of SNVs at A-tracts. More detailed plots along A-tracts either preceded (Supplementary Figure S2E), followed (Supplementary Figure S2F) or preceded and followed (Figure 2C) by a T, C or G revealed the dramatic and long-range (up to 9–10 bp for the longest tracts, higher than the value of 4 bp predicted by mathematical models of slippage (11)) influence of flanking base pairs on variation spectra, in which up to 95% of the changes were in the direction of the base flanking the tract. Because the number of A-tracts preceded or followed by a specific base varies by up to three-fold (Supplementary Figure S2G), we conclude that for A-tracts, the overall mutation fractions and spectra are the result of at least three variables; length, position along the tract, and base composition of the 5′ and 3′ nearest-neighbors.

For G-tracts flanked 5′ by a T, C or A, high percentages (10–12%) of SNVs were observed at G1 for tracts preceded by a C, an effect that decreased with increasing tract length (Supplementary Figure S3A). This result, together with an exceedingly low number of G→A transitions at G1 for tracts not preceded by a C (Supplementary Figure S3C) relative to all tracts (Supplementary Figure S2B), is consistent with the known high mutability of CG:CG dinucleotides as a result of cytosine-5 methylation (9). The hypermutability at G2 was observed preferentially for tracts preceded by an A, and to a lesser extent T, whereas that at G3 was insensitive to flanking sequence composition. Likewise, G-tracts flanked 3′ by a T, C or A did not display marked sequence-dependent effects (Supplementary Figure S3B). Detailed plots of the SNV spectra along G-tracts either preceded (Supplementary Figure S3D), followed (Supplementary Figure S3E), or preceded and followed (Figure 2D) by a T, C or A revealed a noticeable effect only for 5′ T in association with G→T substitutions at G1for tracts of length ≥8. Thus, despite a consistent over-representation of G-tracts flanked 5′ by a T (Supplementary Figures S3F and S1B), which must account for the high absolute number of SNVs at G1 for TG[n] relative to AG[n] and CG[n] (Supplementary Figure S3G), nearest-neighbor base composition seems to play a lesser role in SNV spectra at G-tracts than at A-tracts.

With respect to SNVs at the flanking 5′ and 3′ nearest positions, no B→A or H→G substitutions (Figure 1A) were found above a length threshold of 9 for A-tracts and 8 for G-tracts (Figure 2E, gray shading) out of 5969 SNVs, implying that tract expansion by recruiting flanking base pairs is disfavored at these lengths. In summary, base substitution along mononucleotide repeats is strongly skewed towards the edges of A-tracts and within the 5′ half of G-tracts, with frequencies that peak at midsize lengths (8–9 bp). For A-tracts ≥7 bp, base substitution occurred almost exclusively in the direction of the flanking nearest-neighbors. Finally, base substitution at flanking bases did not contribute to tract expansion for mononucleotide runs longer than 8–9 bp.

Insertions and deletions display length and positional preference

In addition to SNVs, mononucleotide runs are polymorphic in length as a result of indels. Herein, we consider separately two types of indels: one in which tract length changes by ±1 and flanking bp composition is not altered (slippage); the other comprising all other cases involving the addition or removal of 1–200 bp (indels). Slippage is a widely accepted mutational mechanism (1112,34), whereby DNA replication errors at reiterated DNA motifs cause changes in the number of motifs (most often +/−1). The normalized fractions of slippage in the 1KGP dataset peaked at lengths of 8 bp for A-tracts and 9 bp for G-tracts (Figure 3A), generating bell-shaped curves similar to those observed for SNVs (Figure1C) and with no differences in the highest fraction of ‘slipped’ tracts, which peaked at ∼0.02. By contrast, +1 slippage occurred more frequently than −1 slippage at A-tracts (Figure 3B). These results support recent studies on microsatellite repeats (12) and contrast with previous conclusions that slippage increases monotonically with tract length, and that the extent of slippage differs between A- and G-tracts (35,36).

Figure 3.

Population insertions and deletions. (A) Normalized fractions of A-tracts (closed circles) and G-tracts (open circles) displaying +/−1 bp slippage in the 1KGP dataset as a function of tract length. Data were obtained by dividing the number of events by both the number of hg19 tracts and tract length (n). (B) Ratio of the number of +1 to −1 slippage for A-tracts (closed circles) and G-tracts (open circles). (C) Indels at A-tracts. For positions along the tracts (‘Tract’), ‘F Indel’ is the ratio between the number of indels and the number of tracts in hg19 multiplied by tract length. For the positions immediately flanking the tracts genomic coordinates (‘Before tract’ and ‘After tract’), ‘F Indel’ is the ratio between the number of indels and the number of tracts in hg19. (D) Indels at G-tracts, calculated as described in panel C. (E) Heatmap representation of insertions along A-tracts. The percent insertions (i.e. the number of insertions at each position divided by the number of tracts in hg19) (y-axis) plotted as a function of location (x-axis) from position 0 (insertion between the bp 5′ to the tract and the first bp of the tract) to position n + 1 (insertion between the bp 3′ to the last bp of the tract and the following bp) (see Figure 1A) and as a function of tract length (z-axis). (F) Heatmap representation of insertions along G-tracts.

With respect to indels, the normalized fractions were low (<1 × 10−3) along short (4–6 bp) A- and G-tracts, but rose to a plateau for longer tracts as reported earlier (11); this plateau was 10-fold higher for G-tracts (∼0.03) than for A-tracts (∼0.003) (Figure 3C and D). Indels also occurred more frequently (up to six-fold for A-tracts of length 11) at nearest-neighboring base pairs (‘Before tract’ and ‘After tract’ in Figure 3C and D) than along the tracts. Thus, contrary to SNVs and slippage, indels increased to a plateau with mononucleotide tract length.

We analyzed in detail the locations of insertions along the tracts and the flanking positions with respect to the 5′ to 3′ orientation of the tracts (Figure 1A). The normalized fractions demonstrated that insertions peaked at the 3′, and to a lesser extent 5′, ends of the longest A-tracts (Figure 3E), but remained low. For G-tracts, insertions occurred most efficiently at two locations (G2–3 and G5) (Figure 3F), they increased with tract length (up to ∼0.04), and attained ∼10-fold higher values than for A-tracts. In conclusion, insertion sites at A- and G-tracts followed the patterns observed for SNVs (Figure 2A and B), suggesting that factors associated with local DNA dynamics sensitize specific bases along the tracts to genetic alteration, inducing both SBS and indels.

Base pair flexibility and charge localization map to sites of sequence changes

To elucidate elements of intrinsic DNA dynamics that may be responsible for the biases in SNV and insertion sites, we performed molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations on model A[6], A[9], G[6] and G[9] duplex DNA fragments. We focused on water bridge coordination (Figure 4A), bp step flexibility, and for the G[6] and G[9], charge localization, as these properties are known to impact the susceptibility of DNA to base damage, repair and mutation. The fractions of one water coordination increased along the A[9] and A[6] structures in a 5′ to 3′ direction, irrespective of flanking sequence composition, in concert with a decrease in minor groove width (Figure 4B and Supplementary Figure S4A) as predicted (37). Vstep, a measure of bp structural fluctuation, displayed a prominent peak of ∼40 Å3deg3 at the 5′-TA-3′ step for both structures (Figure 4C and Supplementary Figure S4B), which together with low water occupancy points to 5′-TA-3′ being a preferred location for base modification and mutation. In the G[9] and G[6] structures water coordination involved mostly two-water bridges due to wide (∼14 Å) minor grooves (Figure 4Dand Supplementary Figure S4C), whereas flexibility was modest (∼20–22 Å3deg3, Figure 4E and Supplementary Figure S4D). Thus, bp dynamics are likely to impact mutations at A-tracts to a greater extent than at G-tracts. Guanine has the lowest ionization potential (IP) of all four bases and IP further decreases at guanine runs, rendering them targets for electron loss, charge localization, oxidation and eventually mutation (4,38). Because after electron loss the ensuing charge (hole) can migrate along the DNA double-helix and relocalize at specific guanines, we addressed whether the preferred sites of mutation along G-tracts, i.e. G2–3 and G5, would also be preferred sites for charge localization. The QM/MM determinations indicated that whereas for the short G[6] fragment the difference in the density-derived atomic partial charges (DDAPC) (i.e. the hole) localized most often (∼50%) to the first position (Figure 4F), for the long G[9] fragment charge localization shifted downstream (mostly to the second, but also to positions 6–7, Figure 4G). Importantly, the charge was found exclusively around the guanine rings (Figure 4H). Thus, the two main sites of sequence change along G-tracts, i.e. G2–3 and G5, coincide with positions where charge localization and hence one-electron oxidation reactions is predicted to occur most frequently. In summary, bp flexibility at A-tracts and charge transfer at G-tracts likely represent intrinsic DNA features underlying the bias in SNV and insertions at mononucleotide runs in human genomes.

Figure 4.

MD and QM/MM simulations. (A) Molecular modeling of one (left) and two (right) minor groove water bridge coordination. (B) Fraction of one-water bridge occupancy (left axis) at A[9] DNA sequences flanked 5′ and 3′ by a T (black circles), C (red circles) or G (green circles). Minor groove widths (right axis), as determined from intrastrand phosphate-to-phosphate distances. (C) Vstep for A[9] DNA sequences, determined as the product of the square root of the eigenvalues (λi) described by the six bp step parameters shift, slide, rise, tilt, roll and twist; i.e. Vstep=6i=1λi−−√. (D) Fraction of one- (black circles) and two-water (red circles) bridge occupancy (left axis) at G[9] DNA sequences. Minor groove widths (right axis), as assessed from intrastrand phosphate-to-phosphate distances. (E) Vstep for G9 DNA sequences. (F) Average charge redistribution (open circles and right axis) for G[6] DNA structures upon vertical ionization, examined by calculating the difference on the density-derived atomic partial charges (DDAPC) for the neutral and negatively charged states. Histogram of the number of instances (left axis) in which the largest charge redistribution occurred at a specific position along the G[6] structures. (G) DDAPC for G[9] DNA structures (open circles and right axis) and histogram of the number of instances (left axis) in which the largest charge redistribution occurred at a specific position. (H) VMD rendering of a G[9] DNA structure displaying hole localization at G2. Capped base pairs were removed for clarity.

Position and orientation along nucleosome core particles modulate sequence variation

DNA wrapped around histones in nucleosomes is subject to local deformation (39), which may impact mutation. Thus, we analyzed the 1KGP SNVs at A- and G-tracts predicted to overlap with well-positioned nucleosome core particles (NCPs) (16). In hg19, the percentage of tracts that overlap with NCPs decreased moderately from ∼90% at length of 4 to 81% and 71% for A- and G-tracts of length 13, respectively (Figure 5A), suggesting that mononucleotide runs are not depleted in NCPs in human genomes as previously proposed (40). A-tracts of lengths 4–8 base pairs displayed distinctive peaks along the NCP surface in phase with the helical repeat of DNA (10.5 bp) and with minor grooves facing toward the inner protein core (lengths 4–5) (16) (Figure 5B and Supplementary Figure S5A). A-tracts of length of 9–13 bp exhibited only half (six) the peaks evident for the shorter tracts. For the G-tracts, only small peaks with no clear minor groove-inward-facing regions were detected (Supplementary Figure S5B).

Figure 5.

Positioning along nucleosome core particles. (A) Percent of A-tract (open circles) and G-tract (closed circles) base pairs in hg19 overlapping with well-positioned NCP genomic coordinates as a function of tract length. (B) Counts of base pairs in hg19 A-tracts of length 5 overlapping with NCPs genomic regions as a function of distance from the histone octamer dyad axis. Minor groove-inward-facing regions (gray) were derived from the X-ray crystal structure of NCP147 (41). (C) Percent SNVs in the 1KGP dataset (left axis) at every bp along A-tracts of length 5 for tracts centered at maxima (black) and minima (gray) along NCPs (Figure 5B). Percent increase (right axis) of SNVs at minima relative to maxima (green). P-values for paired t-tests: 0.013 (*), 0.002 (**) and 4.7 × 10−6 (***). (D) Whisker plots of%SNVs (left axis) at A1 for A-tracts of length 5 centered at maxima and minima (black) along NCPs (Figure 5B). Percent difference (right axis) in the number of A-tracts of length 5 in hg19 preceded by C, T or G (red) between those centered at minima and those centered at maxima (Figure5B). (E) C-containing/G-containing ratios (see text) for G-tracts of length 5 in hg19 as a function of distance from the NCP dyad axis (black) and location of core histones (maroon and green). Peaks correspond to negative iSAT (i.e. tilt parameters multiplied by the corresponding sin θ) values (gray) (39). Ratios of%SNV at G1 (upshifted by 0.5 for clarity) between C-containing (5′-CCCCCG-3′ sequences on the hg19 forward strand) and G-containing (5′-CGGGGG-3′ sequences on the hg19 forward strand) (Figure 1A) CG[5] tracts mapping NCP Chip-seq genomic intervals (red) fitted by a non-parametric local regression (loess; sampling proportion, 0.100; polynomial degree, 3). (F) VMD rendering (top) of TATTT residues 34–38 (yellow) and the complementary AAATA residues 672–753 (pink) from the 1EQZ pdb nucleosomal crystal structure, corresponding to peak area from −40 to −36 in Figure 5E. The switch in G-tract (lengths of 5 and 7) orientation along NCPs (bottom) serves to position the C-containing strand on the outside (yellow) and, correspondingly, the G-containing strand on the inside (pink).

 To assess if tract-positioning along NCPs influences SNVs, we selected A-tracts of lengths 5, 7 and 9 bp and G-tracts of lengths 5 and 7 bp whose central positions coincided with either the maxima or minima (41) (Figure 5B and Supplementary Figure S5A and B) and conducted pair-wiset-tests (330 total) between permutations of ‘categories’, including ‘tracts centered at maxima versus minima’, ‘position along the tracts’, ‘flanking sequence composition’, ‘specific NCP locations’ and ‘tract orientation’. For A-tracts, 79/207 (38%) significant pairs were found, 68 (86%) of which were related to differences between tracts centered at maxima versus minima, with a preponderance (63%) of tests displaying increased %SNVs at minima (Supplementary Figure S5C and E). For example, %SNVs at length 5 bp were greater at minima than at maxima at each position along the A-tracts (Figure 5C). A→C substitutions at A1 were more abundant at maxima than at minima (mean ± SD, 18.7 ± 0.7% at max and 17.6 ± 0.8% at min; P-value 0.001), whereas A→T substitutions at the same position displayed the opposite trend (mean ± SD, 18.4 ± 0.5% at max and 19.8 ± 1.1% at min; P-value 0.0005) (Figure 5D). A-tracts of length 7 also exhibited a similar pattern at A7 (Supplementary Figure S5H). The percentages of CA[5] and A[7]C tracts in hg19 centered at maxima were greater than at minima and the reverse was observed for the TA[5] and A[7T] tracts (Figure 5D and Supplementary Figure S5H). Thus, we conclude that positioning along the NCP surface of both the double-helical grooves and junctions with flanking base pairs influence SNVs along A-tracts. However, this influence is complex and for the most part, difficult to predict.

For G-tracts, most pairwise comparisons (18/34, 53%) indicated SNV variation according to sequence orientation (Supplementary Figure S5F and G). In hg19, the ratio of the numbers of G-tracts of lengths 5 and 7 for which the C-containing strand coincided with the forward sequence (downstream example sequence in Figure 1A) to the numbers of G-tracts for which the G-containing strand coincided with the forward sequence (upstream example sequence in Figure 1A) (C-containing/G-containing ratios) displayed a prominent 10.5-bp oscillation in phase with iSAT (Figure 5E), a measure of ‘inside’ and ‘outside’ bases, according to the bp step tilt parameter (39). Analysis of the helical path of a 146-bp DNA fragment wrapped around histones showed that the oscillation in the C-containing/G-containing ratios corresponds to a preference for guanine bases to face the protein core (Figure 5F). We analyzed the subset of G-tracts preceded by a 5′ C (i.e. CG[5]) to assess whether SNVs at G1, the position known to be mutable due to CpG methylation also oscillated with the C-containing/G-containing ratios. Oscillation in SNV-C-containing/SNV-G-containing values was evident, with peaks aligning to the hg19 troughs (Figure 5E) implying that the cytosines facing the protein surface harbor more variants than those facing away. We conclude that A- and G-tracts display preferential positioning (the former) and orientation (the latter) along NCPs, which in turn modulate the rate of sequence variation.

Mutations associated with human disease

Knowing that the first and last As of long A-tracts and G2–3 in G-tracts are the major sites of SNV in the human population, we addressed whether these features are also discernible in mutated mononucleotide tracts associated with human genetic disease. We collected 9,450,456 unique SBSs (both SBSs and SNVs refer to single base changes) from sequenced cancer genomes and normalized the percent mutations along A- and G-tracts to enable a direct comparison with the 1KGP dataset. For A-tracts (Figure 6A and Supplementary Figure S6A), SBSs displayed the same trend as the 1KGP data (Figure 2A) with respect to the bell-shape increase in mutations at A1 and An and the mutation spectra, although the susceptibility to mutation as a function of tract length attained greater values (6.36% for length 11 in cancer versus 4.15% for length 9 in the 1KGP datasets at A1). The first and last 3 bp also harbored more SBSs than in the 1KGP dataset for tracts >7 bp, a feature that we found to be due exclusively to a large cancer dataset (42) containing high-level microsatellite instability (MSI) samples (Supplementary Figure S6B and C), which are known to result from mismatch-repair deficiency (15). Thus, A-tracts display similar patterns of base substitution between the germline and somatic cancer tissues. For G-tracts, mutation spectra were characterized by G→T transversions at tract lengths >7, particularly at G1, the most frequently mutated position for tracts lengths up to 11 bp (Figure 6B and Supplementary Figure S6D). This trend persisted even when the high rates of methylation-mediated deamination mutations at the CG dinucleotide were removed (Supplementary Figure S6E). Thus, mutation patterns in cancer genomes contrast with those observed in the germline, both with respect to the most mutable position (G1 versus G2–3) and the types of base substitution (G→T in cancer genomes versus G→T and G→C in the germline).

Figure 6.

Mutation patterns in cancer genomes. (A) Mutation spectra for SBSs at A-tracts. Percent values were obtained by dividing the total number of SBSs at each position by the number of tracts in hg19 and then multiplying by 3.2516 to equalize the percentage of A-tracts of length 4 between the cancer genomes and the 1KGP datasets. (B) Mutation spectra for SBSs at G-tracts in cancer genomes. Percent values were obtained as in (A) using a multiplication factor of 3.7419. (C) Normalized fractions of A-tracts (closed circles) and G-tracts (open circles) displaying +/−1 bp slippage, obtained by dividing the number of events by both the number of tracts in hg19 and tract length. (D) Indels at A-tracts, calculated as described in Figure 3C. (E) Indels at G-tracts, calculated as described in Figure3C. (F) Heatmap representation of insertions along G-tracts, as described in Figure 3E.

 With respect to slippage, the fractions for A-tracts elicited an excess at lengths 9 and 10 bp relative to the 1KGP dataset, which was also due to the MSI-containing dataset. For G-tracts, the fractions peaked at length 8, as for the 1KGP dataset (Figures 3A and 6C), implying that the propensity to undergo slippage is indistinguishable between the germline and soma. Indels were also more abundant at flanking base pairs than along the tracts (Figure 6D and E), particularly for G-tracts of length >7, similar to the 1KGP dataset (Figure 3C and D). Detailed analyses of insertions revealed that both G1 and the preceding position were the most significant sites of mutation (F-values up to 0.08 at G1 for tracts of length 8) (Figure 6F). Thus, the 5′ end of long G-tracts is the most susceptible site for both SBSs and insertions in cancer genomes, in contrast to the germline where these occur within the runs, typically at G2–3.

We also extracted the mutated A- and G-tracts from the Human Gene Mutation Database (HGMD), a collection of >150,000 germline gene mutations associated with human inherited disease. A total of 1519 genes were mutated at A- or G-tracts out of a total of 3972 (38%); 3480 SBSs and 2866 slippage events were noted within these tracts, 85 and 46% of which were predicted to be disease-causing, respectively (Figure 7A and Supplementary Table S1). Ranking genes by the number of literature reports indicated that among the top 10 entries three were associated with cancer (BRCA1, BRCA2 and APC), two with hemophilia (F8 and F9), four with debilitating lesions of the skin (COL71A), muscle (DMD), lung (CFTR) and kidney (PKD1), with one causing hypercholesterolemia (LDLR) (Figure 7B). Thus, mutations within A- and G-tracts carry a high social burden by contributing to some of the most common human pathological conditions.

Figure 7.

Mutation patterns in HGMD and model for sequence context-dependent changes. (A) Number of germline SBSs and slippage events (Slip.) at A- and G-tracts in HGMD. Gene alterations were classified as disease-causing mutation (DM), likely disease-causing mutation (DM?), disease-associated and putatively functional polymorphism (DFP), disease-associated polymorphism with additional supporting functional evidence (DP) and invitro/laboratory orinvivo functional polymorphism (FP). Codon changes (SIFT predictor) were classified as damaging (d), null (n), tolerated (t) and low-confidence prediction (l). (B) The 10 most commonly reported genes in HGMD with mutations at A- and G-tracts. Various mutated tracts were generally reported for the same gene in different reports. (C) Mutation spectra for SBSs at A- (left) and G-tracts (right) in HGMD. Percent values were obtained by dividing the total number of SBSs at each position by the number of tracts in hg19 exons. A|G→T (black), A|G→C (red), A→G (green), G→A (cyan). (D) Normalized fractions of A-tracts (closed circles) and G-tracts (open circles) displaying +/−1 bp slippage, obtained by dividing the total number of events by the number of tracts in hg19 exons and by tract length. (E) Model for sequence context-dependent changes at A-tracts (left) and G-tracts (right). *, site of base modification.

 For both A- and G-tracts, SBSs occurred mostly at tract lengths of 4–7, with patterns more similar to those in the 1KGP than in the cancer datasets, both with respect to the location of the most mutable positions (first and last As and first/second Gs) and the types of base substitution (A→T and G→H) (Figure 7C and Supplementary Figure S6F). Likewise, slippage events peaked at tract lengths of 7–9 as observed in the 1KGP dataset (Figure 7D). In summary, the patterns of both SBSs and slippage in the HGMD dataset followed the trend observed in the 1KGP dataset, suggesting that germline variants at mononucleotide repeats leading to either population variation or human inherited disease may have arisen through similar mechanisms.
DISCUSSION

Why are specific A:T and G:C base pairs within A- and G-tracts more susceptible to sequence changes than their identical neighbors? For A-tracts, bp flexibility may play a role. Chemical damage to DNA, such as by hydroxyl radicals has been shown to be proportional to the geometrical solvent-accessible surface of the atomic groups, which increases with DNA flexibility (43). Along A-tracts flexibility is restricted, but it is high at both the 5′ and 3′ junctions. Thus, the fact that the highest rates of mutation coincide with the highest degree of flexibility at the 5′-TA-3′ bp step is consistent with the view that this position may be susceptible to DNA damage as a result of flexibility. Other sources of DNA dynamics are also likely to be relevant, such as sugar flexibility at the junctions, which increases with tract length (44). Chemical modification at these junctions may then lead to base substitution and indels, the latter as a result of strand breaks.

With respect to SNV mutation spectra, these were found mostly in the direction of flanking base composition above a length of 7–8 bp. We interpret this behavior in terms of DNA slippage along A-tracts when attempts are made during translesion synthesis (TLS) to bypass a damaged site (Figure 7Ei). Two scenarios may be considered to account for A→T transitions at A1. In the first, the last tract-template base would loop out into the polymerase active site permitting base-pairing and strand elongation (Figure 7Eii) using the tract-flanking base as a template (34,4546). In the second (Figure 7Eiii), slippage would occur behind the polymerase, prompting extension past the newly created A*:T mispair generated by primer/template misalignment. Either pathway would yield a common intermediate (Figure 7Eiv) that contains the base complementary to the junction across from the damaged site upon slippage resolution (34). Following DNA synthesis (S) and/or repair (R) (Figure 7Ev and vi), this mispair will generate a base change that is always identical to the tract-flanking base.

For G-tracts, the high rates of G→T transversions at G1 in cancer genomes are also consistent with preferred chemical attack at this site due to high flexibility (Figure 7F top). Direct chemical attack at a guanine is known to result in stable products, such as 8-oxo-G and Fapy-G, both of which are known to yield G→T transversions (4750). Thus, G1 may be the most susceptible site for such reactions for G-tracts of lengths ≥7 (Figure 7Fright), which in cancer genomes would become a mutation hotspot. In the germline, SNVs peaked inside G-tract base pairs, while mutational spectra were insensitive to flanking base composition; these events are inconsistent with a role for template misalignment and slippage as noted for A-tracts. Rather, the correspondence between hotspot mutations at G2–3 and G5 and the QM/MM simulations suggest a role for charge transfer. A large body of work during the past 20 years using computational, theoretical chemistry and biophysical techniques on short oligonucleotides, has shown that guanine is the most easily oxidizable base in DNA and that indeed a guanine radical cation can be generated through long-range hole transfer from an oxidant via one-electron oxidation mechanisms (5155). GGG triplets were found to act as the most effective traps in hole transfer by both experimental and theoretical work (5659), demonstrating that the resulting guanine radical cation (or its neutral deprotonated form) became rather delocalized, but it preferentially centered at the first and second G. These well-established patterns of chemical reactivity are consistent with our experimental observation of high mutation frequencies at G1 for short G-tracts and the results from QM/MM simulations on G6. For longer tracts, the downstream shift in mutation hotspots, i.e., G2–3 and G5, also correlate well with the charge localization predicted from QM/MM simulations, which explicitly included solvent effects and structural fluctuations. Thus, in conjunction with the constrained density functional theory (60), both the neutral and oxidized forms of a guanine nucleobase can be reliably constructed to infer the accurate determination of mutational patterns of mononucleotide repeats in human genomic DNA.

The compact organization of the sperm genome (61), and presumably low levels of oxidative stress in the germline, may enable guanine oxidization through one-electron oxidation reactions rather than by direct chemical attack, thereby favoring the formation of radical cations. A charge injected at G1 by electron loss would then migrate to neighboring guanines and localize at sites of low IP, such as G2 (Figure 7F left). Guanine radical cations are known to readily undergo further chemical modification leading to products such as 8-oxo-G, oxazolone, imidazolone, guanidinohydantoin, and spiroiminodyhydantoin (62) (M in Figure 7F), to yield G→T, G→C and G→A substitutions (4,63). Our model is in line with recent observations in which mutations at guanines within short G-runs (1–4 bp) correlate with sequence-dependent IPs at the target guanine in cancer genomes (9). Interestingly, these correlations were not observed in the germline (9). We interpret these composite observations as follows. The IP values for G-runs have been shown to decrease asymptotically with tract length, although the absolute values vary according to the methods and assumptions used (we obtained a value of 5.43 eV for both G[6] and G[9]) (64,65). We suggest that short G-runs with high IPs undergo one-electron oxidation reactions in the oxidative environment of cancer cells but would be refractory to such a mechanism in the germline (Figure 7Fright yellow and left white sectors). As length increases and IP values fall, G-runs would be attacked directly by oxidants abundant in tumor cells (Figure 7F orange sector), whereas oxidation will be limited to electron loss in the germline environment (Figure 7F left yellow sector).

These models (template misalignment for A-tracts and charge transfer for G-tracts) suggest a more complex scenario for mechanisms underlying mononucleotide repeat polymorphism in the human population than recently proposed (13), in which nucleotide misincorporation by error-prone polymerases is proposed as a primary source of mutations at both A- and G-tracts. As already stated, the directionality of SNVs toward tract-flanking bases in A-tracts and the hotspot mutations at G2–3, supports multiple and distinct mechanisms of base substitution at mononucleotide repeats.

Our analyses highlight additional information, including the lack of mutations in the direction of tract-base composition for base pairs flanking long tracts, the association with gene expression and the preference of guanines for the inner NCP surface, and extend prior observations (12) such as the bell-shape character of base substitution and slippage, whose mechanisms remain to be fully clarified. Finally, we document the contribution of mononucleotide mutagenesis to key aspects of human pathology beyond the well-established MSI instability in cancer (15), including hemophilia and tissue degeneration. Our collective work supports the conclusion that as the human genome undergoes evolutionary diversification and along the way suffers disease-associated mutations, oxidation reactions including charge transfer may play a prominent role.

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online.

 

 

Mutation analyses and prenatal diagnosis in families of X-linked severe combined immunodeficiency caused by IL2Rγ gene novel mutation

, , , ,

Genet. Mol. Res. 14 (2): 6164 – 6172   DOI: 10.4238/2015.June.9.2
Severe combined immunodeficiency diseases (SCIDs) are a group of primary immunodeficiency diseases characterized by a severe lack of T cells (or T cell dysfunction) caused by various gene abnormalities and accompanied by B cell dysfunction (WHO, 1992; Buckley et al., 1997). The incidence rates in infants were 1/75,000-1/10,0000 (WHO, 1992), but no morbidity statistics are available in China. The 2 genetic modes of SCID include X-linked recessive and autosomal recessive genetic inheritance. X-linked severe combined immunodeficiency (X-SCID) is the most common form, accounting for 50-60% of SCID cases (Noguchi et al., 1993). Immune system abnormalities in patients with X-SCID include T-B+NK-, in which T cells (CD3+) and natural killer (NK) cells (CD16+/CD56+) are absent or significantly reduced, and the number of B cells (CD19+) is normal or increased, causing reduced immunoglobulin production and class switching disorder (Buckley, 2004; Fischer et al., 2005). The IL- 2Rg gene mutation has been confirmed to be a major cause of X-SCID (Noguchi et al., 1993). In recent years, great progress has been made in understanding the pathogenesis of primary immunodeficiency disease and its application in clinical treatment, particularly regarding the development of critical care medicine and immune reconstruction technology. With timely control of infection and early bone marrow or stem cell transplantation, X-SCID patients can be treated, prolonging survival time. Therefore, early diagnosis of X-SCID is very important for patient treatment. Gene diagnosis has become a better early diagnosis or differential diagnosis method. In addition, familial X-SCID brings a great psychological burden to the relatives of patients. Ordinary chromosome analysis and immunological evaluation cannot be used for female carrier identification and fetal diagnosis, and gene diagnosis is the most effective method of carrier detection and prenatal diagnosis. In this study, we detected mutations in 2 families with X-SCID and identified 2 novel mutations, confirming the X-SCID pedigrees. Prenatal diagnosis was performed for the pregnant fetus in the mother of one of the probands based on gene diagnosis. Female individuals in this family were subjected to carrier detection.
IL2Rg gene mutation test Direct sequencing of 1-8 exons and the flanking region of the IL2Rg gene by PCR in family 1 showed that the 3rd exon of the proband contained the c.361-363delGAG heterozygous deletion mutation, which led to deletion of the 121st amino acid glutamate (p.E121del) in its coding product. There were no sequence variations in other coding regions or in the shear zone. The proband’s mother carried the same heterozygous mutation, while his father did not carry the mutation site (Figure 2a, b, c). This mutation was not observed in any cases of the control group, and this family was identified as an X-SCID family. The c.510-511insGAACT insertion heterozygous mutation was present in the 4th exon of the proband’s mother in family 2. This mutation was a 5-base repeat of GAACT, resulting in a change in amino acid 173 from tryptophan into a stop codon (p.W173X). While there were no sequence variations in other coding regions or in the shear zone, the patient’s father did not carry the mutation (see Figure 2d, e). We did not find this mutation in the healthy control group. We presumed that the 4th exon of the deceased child in family 2 contained the c.510-511insGAACT insertion mutation, leading to X-SCID symptoms, and thus we speculated that this family was an X-SCID pedigree. Prenatal diagnosis We verified the chorionic villus status of the fetus in family 1 using the PowerPlex 16 HS System kit. The results of prenatal diagnosis showed that the fetal tissue contained no maternal contamination and that this fetus was female. The results of prenatal diagnosis showed that there was no c.361-363delGAG (p.E121del) heterozygous mutation in the female fetus of family 1.
Figure 2. Sequencing graph of IL2Rg gene in 2 pedigrees with X-chain severe combined immunodeficiency. a.-c. Family 1. a. Normal control (rectangle indicates 3 edentulous bases of this patient). b. Proband carrying the c.361- 363delGAG (p.E121del) mutation (arrow indicates deletion of fragment connection sites). c. The proband’s mother contained a c.361-363delGAG (p.E121del) heterozygous mutation (arrow). d.-e. Family 2. d. The proband’s mother carried the c.510-511insGAACT (p.W173X) heterozygous mutation (arrow indicates that the reverse sequencing graph was positive). e. Normal control (rectangular box indicates 2 normal copies of GAACT (the mutation fragment was 3 copies). Carrier detection results For the c.361-363delGAG (p.E121del) site, the gene analysis results of the female individual in family 1 showed that I2 (proband’s grandmother) was a heterozygous carrier and that II3 (proband’s aunt) was a non-carrier and had no mutations.
IL-2 can combine with the IL-2 receptor (IL-2R) of the immune cell membrane. IL-2R is composed of 3 subunits, including the IL-2Ra chain (CD25), IL-2Rb chain (CD122), and IL- 2Rg chain (CD132). IL-2Rg functional units in common with IL-4, IL-7, IL-9, IL-15, IL-21, and other cytokine receptors, and these regions are referred to as the total chain (Li et al., 2000). The IL-2Rg chain can maintain the integrity of the IL-2R complex and is required for the internalization of the IL-2/IL-2R complex; it is also the link that contacts the cell membrane surface factor region and downstream cell signal transduction molecules. Therefore, the integrity of the IL-2Rg chain is vital for the immune function of an organism (Malka et al., 2008; Shi et al., 2009).
Mutations in the IL2Rg gene, which encodes IL-2Rg, were identified to be a major cause of X-SCID in 1993 (Noguchi et al., 1993). The IL2Rg gene is located on chromosome X q21.3-22, is 37.5 kb length, and contains 8 exons, which encode 369 IL-2Rg amino acids. The IL2Rg chain exhibits varying structural regions, such as the signal peptide [amino acids (AA) 1-22], extracellular domain (AA 23-262), transmembrane region (AA 263-283), and intracellular region (AA 284-369). The WSXWS motif is located in the extracellular region (AA 237-241), while Box 1 is located in the intracellular region (AA 286-294).
By the end of 2013, the Human Gene Mutation Database contained a total of 200 mutations in the IL2Rg gene (HGMD Professional 2013.4). The most common mutation types in the IL2Rg gene were the missense or nonsense mutations, which result from single base changes. A total of 100 missense or nonsense mutations have been identified, followed by insertion or deletion mutations in a total of 50 species. The 3rd most common type of mutations includes shear mutations in approximately 30 species. Eight exons contained mutations, and mutations in 3rd or 4th exons were the highest, accounting for a total mutation rate of 43% (86/200). According to the X-SCID gene database (IL2RGbase) (http://research.nhgri. nih.gov/scid/), the gene mutations in IL2Rg mainly occurred in the extracellular region of the IL2Rg chain (Fugmann et al., 1998). Zhang et al. (2013) reported that the IL2Rg gene mutations in 10 patients with X-SCID in China were located in the extracellular region. Two mutations reported in our study were also located in the extracellular region. The mutation of IL2Rg gene in family 1 was a codon mutation in the 3rd exon, resulting in a 3-base deletion. The c.361-363delGAG (p.E121del) mutation was located in the extracellular area of the IL- 2Rg subunit, and we inferred that the 121 glutamate deletion caused by the mutation would lead to changes in the structure of the peptide chain, affecting signal transmission and resulting in serious symptoms. The mutation of family 2 was a GAACT repeat of ILR2g gene; this repeat of 5 bases resulted in 173 codon changes from tryptophan into a stop codon. Generation of the peptide chain with the mutation lacked 196 amino acids compared to the normal chain, including the intracellular, transmembrane, and some extracellular regions, directly affecting the structure and function of receptors and causing disease. No studies have been reported regarding these 2 mutations. We combined with the mutation characteristics and clinical manifestations and diagnosed family 1 as X-SCID pedigrees. Although the patient in family 2 was deceased, it can be speculated that the 2 deceased patients in family 2 were X-SCID pedigrees caused by c.510-511insGAACT (W173X).
Prenatal diagnosis can accurately identify fetal situations and be used to avoid birth defects, which can also ease the anxiety of the pregnant mother. Gene diagnosis for pedigrees of patients based on DNA samples has advanced recently, particularly with the application of high-throughput sequencing technology (Alsina et al., 2013). We can now perform gene analysis for varied clinical infectious diseases for differential diagnosis. However, the effectiveness of prenatal diagnosis for pedigrees in which the proband is dead remains unclear. Because the gene mutations in the proband is unknown in these cases, the patient’s situation was only inferred by his mother’s genotypes. However, we considered that for the deceased, if we can define the mother was a pathogenic gene carrier, even if the proband is not X-SCID, the woman also has a risk of having X-SCID children and this pedigree may be X-linked recessive inheritance. Prenatal diagnosis may provide a choice for preventing the birth of patients in these families in the premise of informed consent.
Gene diagnosis of IL2Rg can also be used for carrier detection of suspected females in the family.
In the present study, we performed carrier detection of the patient’s grandmother and aunt in family 1 and determined that the patient’s pathogenic mutations were from his grandmother. His aunt did not inherit the pathogenic gene, and thus she was a non-carrier and her fertility will not be affected. In this study, we used direct sequencing of PCR products and identified IL2Rg gene mutations in 2 pedigrees with X-SCID. We found 2 unreported mutations in the IL2Rg gene, and prenatal diagnosis and carrier detection were conducted in 1 X-SCID family. Because the incidence rate of X-SCID is extremely low, it is difficult to promote the widespread use and application of genetic diagnosis. However, this study may provide some implications for the diagnosis of infants with immunodeficiency, and gene diagnosis techniques such as conventional or high-throughput sequencing should be used as soon as possible during pregnancy, which can be used to guide treatment. This method can also provide reliable prenatal diagnosis and carrier detection service for these families.
MEF2A gene mutations and susceptibility to coronary artery disease in the Chinese population
J. Li1 , H.-X. Chen2 , J.-G. Yang3 , W. Li3 , R. Du3 and L. Tian3       DOI http://dx.doi.org/10.4238/2014.October.20.15
Coronary artery disease (CAD) has high morbidity and mortality rates worldwide. Thus, the pathogenesis of CAD has long been the focus of medical studies. Myocyte enhancer factor 2A (MEF2A) was first discovered as a CAD-related gene by Wang (2005) and Wang et al. (2003, 2005). Three mutation points in exon 7 of MEF2A were subsequently identified by Bhagavatula et al. (2004); however, Altshuler and Hirschhorn (2005) and Weng et al. (2005) predicted that the MEF2A gene lacked mutations. Zhou et al. (2006a,b) analyzed the mutations and polymorphisms in exons 7 and 11 of the MEF2A gene in the Han population in Beijing, and various rare mutations were found in exon 11 rather than in exon 7. The clinical significance of specific 21-bp deletions in MEF2A was also explored, and previous studies have shown mixed results. In this study, polymerase chain reaction-singlestrand conformation polymorphism (PCR-SSCP) and DNA sequencing were used to detect exon 11 of the MEF2A gene in samples collected from 210 CAD patients and 190 healthy controls and to investigate the function of the MEF2A gene in CAD pathogenesis and their correlation.
CAD, a common disease in China, is induced by multiple factors, such as genetics, the environment, and lifestyle. Thus, a multi-faceted approach is necessary in the study of CAD pathogenesis, particularly in molecular biology research, which is important for developing comprehensive treatment of CAD based on gene therapy. The MEF2A gene was first identified as a CAD-related gene through linkage analysis of a large family with CAD (9 of 13 patients developed MI) in 2003.
In this study, we found the following mutations: 1) codon 451G/T (147191) heterozygous or homozygous mutation; 2) loss of 1 (Q), 2 (QQ), 3 (QQP), 6 (425QQQQQQ430), and 7 (424QQQQQQQ430) amino acids (147108-147131); and 3) codon 435G/A (147143) heterozygous mutation. Among these mutations, the synonymous mutation at locus 147191 was confirmed by reference to the National Center for Biotechnology Information (NCBI) database to be a single nucleotide polymorphism, which was also demonstrated in our study by the extensive presence of this polymorphism in healthy controls. However, the heterozygous mutation at locus 147143 was only found in the genomes of CAD patients, and was therefore identified as a mutation.
Given that MEF2A is a CAD-related gene, the results of various studies are controversial among several countries. Weng et al. (2005) screened gene mutations in exon 11 of the MEF2A gene from 300 CAD patients and 1500 healthy controls. They hypothesized that the changes in 5-12 CAG repeats are genetic polymorphisms and that the 21-base deletion in exon 11 of the MEF2A gene did not induce autosomal dominant genetic CAD. Gonzalez et al. (2006) suggested that the CAG repeat polymorphism was independent of MI susceptibility in Spanish patients. Kajimoto et al. (2005) reported that the CAG repeat sequence was not correlated with MI susceptibility in Japanese patients. Horan et al. (2006) also found that the CAG repeat sequence was not associated with the susceptibility to early-onset familial CAD in an Irish population. Hsu et al. (2010) identified no correlation between the CAG repeat sequence and CAD susceptibility in the Taiwanese population. Dai et al. (2010) found that the structural change in exon 11 was not related to CAD in the Chinese Han population. Lieb et al. (2008) and Guella et al. (2009) hypothesized that MEF2A was independent of CAD. However, Yuan et al. (2006) and Han et al. (2007) suggested that the CAG repeat sequence was correlated with CAD because 9 CAG repeats was an independent predictor of CAD. Elhawari et al. (2010) and Maiolino et al. (2011) suggested that MEF2A is a susceptibility gene for CAD. Dai et al. (2013) showed that mutations in exon 12 are associated with the early onset of CAD in the Chinese population. Liu et al. (2012) failed to demonstrate a correlation between the CAG repeat sequence and CAD through case-control analysis, systematic review, and meta-analysis, but found that the 21- base deletion in exon 11 was strongly associated with CAD, and that genetic variations in MEF2A may be a relatively rare, but specific, pathogenic gene for CAD/MI. Kajimoto et al. (2005) reported 4-15 CAG repeats. However, only 4-11 CAG repeats were observed in our study, possibly because of genetic differences in patients in this study. Eleven CAG repeats were observed in most samples from the control group, and the proportion of 10, 9, and 8 repeats exceeded 1%. The heterozygous mutation at 147143, as well as the 4 and 5 CAG repeats, was only observed in CAD patients. Thus, we speculated that the CAG repeat sequence is correlated with CAD susceptibility, and the presence of 4 or 5 repeats may be a risk factor for CAD, which was inconsistent with the results obtained by Han et al. (2007). The inconsistency in these results may be explained by the differences in subjects and sample sizes among studies.
Impact of glucocerebrosidase mutations on motor and nonmotor complications in Parkinson’s disease

Homozygous and compound heterozygous mutations in GBA encoding glucocerebrosidase lead to Gaucher disease (GD). A link between heterozygous GBAmutations and Parkinson’s disease (PD) has been suggested ( Bembi et al., 2003,Goker-Alpan et al., 2004, Halperin et al., 2006, Machaczka et al., 1999, Neudorfer et al., 1996, Tayebi et al., 2001 and Tayebi et al., 2003). In 2009, a 16-center worldwide analysis of GBA revealed that heterozygous GBA mutation carriers have a strong risk of PD ( Sidransky et al., 2009).

In addition, heterozygote GBA mutations not only carry a risk for PD development but also the possibility of some risk burden on the progression of PD clinical course. In cross-sectional analyses of GBA mutations in PD patients, earlier disease onset, increased cognitive impairment, a greater family history of PD, and more frequent pain were reported in patients with mutations, compared with no mutations ( Chahine et al., 2013,Clark et al., 2007, Gan-Or et al., 2008, Kresojevic et al., 2015, Lwin et al., 2004, Malec-Litwinowicz et al., 2014, Mitsui et al., 2009, Neumann et al., 2009, Nichols et al., 2009,Seto-Salvia et al., 2012, Sidransky et al., 2009, Swan and Saunders-Pullman, 2013 and Wang et al., 2012). Recently, a few prospective studies have investigated clinical features of PD with GBA and showed a more rapid progression of motor impairment and cognitive decline in GBA mutation cases than in PD controls ( Beavan et al., 2015, Brockmann et al., 2015 and Winder-Rhodes et al., 2013). However, in terms of motor complications such as wearing-off and dyskinesia, no studies exist in the longitudinal course of PD with GBA mutations.

Here, we conducted a multicenter retrospective cohort analysis, and the data were investigated by survival time analysis to show the impact of GBA mutations on PD clinical course. We also investigated regional cerebral blood flow (rCBF) and cardiac sympathetic nerve degeneration of subjects with GBA mutations, compared with matched PD controls.

3.1. Subjects

Among the 224 eligible PD patients (the subjects were not related to each other), 9 subjects were excluded from the analysis (4 due to multiple system atrophy findings on subsequent brain MRI and 5 because of insufficient clinical information). Therefore, 215 PD patients [female, 52.1%; age, 66.7 ± 10.8 (mean ± standard deviation)] were analyzed. For non-PD healthy controls, 126 patients’ spouses (female, 58.7%; age, 67.3 ± 10.3) without a family history of PD or GD were enrolled.

3.2. GBA mutations and risk ratios for PD

In the PD subjects, we identified 10 nonsynonymous and 2 synonymous GBA variants. Within the nonsynonymous variants, 7 mutations were previously reported in GD [R120W, L444P-A456P-V460 (RecNciI), L444P, D409H, A384D, D380N, and444L(1447-1466 del 20, insTG)] as GD-associated mutations. Three nonsynonymous mutations have never been reported in GD patients [I(-20)V, I489V, and there was one novel mutation (Y11H)].

GD-associated GBA mutations were found in 19 of the 215 (8.8%) PD patients but none in the healthy controls. The risk of PD development relative to these GD-associated mutations was estimated as an OR of 25.1 [95% confidence interval (CI), 1.50–420,p = 0.0001] with 0-cell correction. The nonsynonymous mutations that were not reported in GD patients had no association with PD development (p = 0.506; OR, 1.3; 95% CI, 0.7–2.6) ( Table 1). Four subjects had double mutations. For subsequent analyses, 2 subjects with double mutations of I (-20)V and K466K were adopted to the group of mutations unreported in GD, and 2 subjects with double mutations of R120W and I(-20)V, and of R120W and L336L were adopted to the group of GD-associated mutations.

Table 1.Frequency of glucocerebrosidase gene allele in Parkinson’s disease patients and controls

Allele name PD (n = 215) Controls (n = 126) p Odds ratio (95% CI)
GD-associated mutations
 R120W 7a 0 0.050 9.1 (0.5–160.8)
 RecNciI (L444P-A456P-V460) 4 0
 L444P 4 0
 D409H 1 0
 A384D 1 0
 D380N 1 0
444L(1447-1466 del 20, insTG) 1 0
 Subtotal, n (%) 19 (8.8%) 0 (0%) <0.001 25.1 (1.5–419.8)b
Nonsynonymous mutations not reported in GD
 I(-20)V 27a 13 0.603 1.3 (0.6–2.5)
 I489V 3 0
 Y11Hc 0 1
 Subtotal, n (%) 30 (14.0%) 14 (11.1%) 0.506 1.3 (0.7–2.6)
Synonymous, n
 K466K 2a 1
 L336L 1a 0
Allele names refer to the processed protein (excluding the 39-residue signal peptide).

Key: CI, confidence interval; GD, Gaucher disease; PD, Parkinson’s disease.

a Four subjects had double mutations; 2 of I(-20)V and K466K, 1 of I(-20)V and R120W, and 1 of R120W and L336L.
b Odds ratio was calculated by adding 0.5 to each value.
c Novel mutation.
3.3. Clinical features of PD patients by GBA mutation groups

The clinical features of PD patients with GD-associated mutations, those with mutations unreported in GD, and those without mutations are shown in Table 2. In the GD-associated mutation group, females, those with a family history and those with dementia (DSM IV) were significantly more frequent than those in the no-mutation group (p = 0.047, 0.012, and 0.020, respectively). The age of PD onset was lower in patients with GD-associated mutations (55.2 ± 9.9 years ± standard deviation), compared with those without mutations (59.3 ± 11.5), although the statistical difference was not significant. There were no differences in clinical manifestations between subjects with mutations unreported in GD and those without mutations, except for dopamine agonist dosage (p = 0.026) ( Table 2).

Table 2.Epidemiological and clinical features of PD patients with Gaucher disease–associated GBA mutations, those with mutations previously unreported in GD and those without mutations

Variables Total n = 215 Mutation (-) GD-associated mutations


Mutations unreported in GD


167 19a pb 29c pd
Sex Female, n (%) 83 (49.7) 14 (73.7) 0.047 15 (51.7) ns
Age Mean (SD) 67.0 (10.8) 62.2 (10.7) 0.063e 67.5 (11.2) nsf
Disease duration (y) Mean (SD) 7.7 (5.5) 6.9 (4.6) nsf 7.2 (4.9) nsf
Onset age Mean (SD) 59.3 (11.5) 55.2 (9.9) ns 60.3 (11.8) ns
Family history Yes, n (%) 17 (11.0)g 6 (31.6) 0.012 0 (0.0) ns
Dementia (DSM-IV) Yes, n (%) 29 (17.4) 9 (47.4) 0.020 5 (17.2) ns
MMSE Mean (SD) 25.8 (5.4)h 23.3 (7.7) nsf 27.0 (3.4)i nsf
Onset symptom (tremor vs. others) Tremor, n (%) 78 (46.8) 9 (47.4) ns 15 (51.7) ns
Modified H-Y on (<3 vs. ≥3) ≥3, n (%) 82 (49.1) 14 (73.7) 0.042 16 (55.2) ns
UPDRS part 3 Mean (SD) 23.6 (12.2)j 28.5 (13.8) nsf 21.9 (8.7) nsf
Wearing off Yes, n (%) 70 (41.9) 9 (47.4) ns 13 (44.8) ns
Dyskinesia Yes, n (%) 49 (29.3) 8 (42.1) ns 8 (27.6) ns
Mood disorder Yes, n (%) 43 (25.7) 8 (42.1) ns 7 (24.1) ns
Orthostatic hypotension symptom Yes, n (%) 21 (12.6) 5 (26.3) ns 7 (24.1) ns
Psychosis history Yes, n (%) 59 (35.3) 10 (52.6) ns 7 (24.1) ns
ICD history Yes, n (%) 8 (4.8) 1 (5.3) ns 1 (3.4) ns
Stereotactic brain surgery for PD Yes, n (%) 4 (2.4) 0 (0.0) ns 0 (0.0) ns
Agonist LED mg/d Mean (SD) 92.8 (114.2) 72.1 (137.7) nse 163.7 (155.6) 0.026e
Levodopa LED mg/d Mean (SD) 400.7 (184.2) 456.7 (206.9) nsf 369.2 (230.3) nse
Total LED mg/d Mean (SD) 496.4 (233.7) 537.9 (258.9) nsf 525.7 (287.4) nsf
Categorical data were examined by Fisher’s exact test.

Key: DSM-IV, Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition; GBA, glucocerebrosidase gene; GD, Gaucher disease; H-Y, Hoehn and Yahr; ICD, impulse control disorder; LED, levodopa equivalent dose; ns, not significant; MMSE, Mini-Mental State Examination; PD, Parkinson’s disease; SD, standard deviation; UPDRS, Unified Parkinson’s Disease Rating Scale.

a Including a double-mutation subject (with a mutation unreported in GD).
b GD-associated mutations versus mutation (-).
c Two subjects with double mutation, including GD-associated mutations, were assigned to GD-associated mutation group.
d Other mutations versus mutation (-).
e Examined by Student t test after Levene’s test for equality of variances.
f Examined by Mann-Whitney U-test because of non-Gaussian distribution.
g    n = 155 due to 10 missing data.
h    n = 164 due to 3 missing data.
i     n = 28 due to 1 missing datum.
j     n = 165 due to 2 missing data.

3.4. Survival time analyses to develop dementia, psychosis, dyskinesia, and wearing-off

Time to develop clinical outcomes (dementia, psychosis, dyskinesia, and wearing-off) was compared in 19 subjects with GD-associated mutations, 29 with mutations unreported in GD, and 167 without mutation. The median observation time was 6.0 years. The subjects with GD-associated mutations showed a significantly earlier development of dementia and psychosis, compared with subjects without mutation (p < 0.001 and p = 0.017) ( Supplementary Table e-1, Fig. 1A and B). We rereviewed the clinical record of the subject who showed early dementia (defined by DSM IV) ( Fig. 1A) and made sure it did not satisfy the criteria of DLB ( McKeith et al., 2005).

Kaplan–Meier curves of dementia and psychosis in Parkinson's disease (PD) ...

Fig. 1.

Kaplan–Meier curves of dementia and psychosis in Parkinson’s disease (PD) patients with Gaucher disease (GD)-associated glucocerebrosidase gene (GBA) mutations and those without mutations. PD patients with GD-associated GBA mutations and those without GBA mutations were compared to investigate the time taken to develop dementia (A) and psychosis (B). Because of insufficient information in several patients, the numbers in each analysis were different. The patients with and without mutations were 17 and 165 (A), 18 and 165 (B) against a total of 19 and 167. DSM IV, Diagnostic and Statistical Manual of Mental Disorders, revised fourth edition. p-Values were calculated by log-rank tests.

The associations of GBA mutations and these symptoms were estimated as HRs, adjusting for sex and age at PD onset. HRs were 8.3 for dementia (95% CI, 3.3–20.9; p < 0.001) and 3.1 for psychosis (95% CI, 1.5–6.4; p = 0.002). The time until development of wearing-off and dyskinesia complications was not statistically significant, with HRs of 1.5 (95% CI, 0.8–3.1; p = 0.219) and 1.9 (95% CI, 0.9–4.1; p = 0.086) ( Table 3).

Table 3.Hazard ratios of GBA pathogenic mutations for clinical symptoms

Model Clinical feature Hazard ratio 95% CI p
1 Dementia (DSM-IV) 8.3 3.3–20.9 <0.001
2 Psychosis 3.1 1.5–6.4 0.002
3 Wearing-off 1.5 0.8–3.1 0.219
4 Dyskinesia 1.9 0.9–4.1 0.086
Each model was adjusted for sex and age at onset.

Key: CI, confidence interval; DSM-IV; The Diagnostic and Statistical Manual of Mental Disorders part 1IV; GBA, glucocerebrosidase.

Subjects with mutations unreported in GD did not show significant differences in time to develop all 4 outcomes, compared with no mutation subjects. Therefore, subjects with GD-unreported mutations were regarded as subjects without GBA mutations in further analyses.

3.5. rCBF on SPECT in patients with GD-associated GBA mutations

We conducted pixel-by-pixel comparisons of rCBF on SPECT between PD subjects with mutations (cases) and sex-, age-, and disease duration-matched PD subjects without any mutations in GBA (controls). Four controls were adopted for each case (except for a 34-year-old female case who was matched to a control), and in total 12 cases (female 50%, age at SPECT mean ± standard error (SE); 58.9 ± 3.3 years, disease duration at SPECT 7.3 ± 1.5 years) and 45 controls (female 64.4%, age at SPECT mean ± SE; 61.0 ± 1.3 years, disease duration at SPECT 7.1 ± 0.7 years) were analyzed. As a result, a significantly lower rCBF was seen in the cases compared to the controls in the bilateral parietal cortex, including the precuneus ( Fig. 2).

Regional cerebral blood flow in the group with GD-associated mutations compared ...

Fig. 2.

Regional cerebral blood flow in the group with GD-associated mutations compared with the matched Parkinson’s disease group without mutations. Regions with lower regional cerebral blood flow in the group with GD-associated mutations displayed on an anatomic reference map. Abbreviation: GD, Gaucher disease.

3.6. H/M ratios on MIBG scintigraphy in patients with GD-associated GBA mutations

Cardiac MIBG scintigraphy visualizes catecholaminergic terminals in vivo that are reduced as well as brain dopaminergic neurons in PD patients. We also investigated MIBG scintigraphy between 16 cases (female 68.8%, age at examination mean ± SE; 60.2 ± 2.6 years, disease duration at examination 6.2 ± 1.2 years) and sex-, age- and disease duration-matched 61 controls [(63.8 %, age 62.0 ± 1.1 years, disease duration 5.5 ± 0.6 years) (1:4 except for 1 young 34-year-old female case who was matched to a control)]. In the results, both early and late H/M ratios declined in both groups and did not show any significant differences (p = 0.309 and 0.244) ( Supplementary Table e-2).

4. Discussion

4.1. Contributions of GD-associated GBA mutations to the development of PD

In the analysis of 215 PD patients and 126 non-PD controls, we identified 10 nonsynonymous heterozygous GBA mutations, including 1 novel mutation. Among these mutations, 7 were GD-associated, and the patients carrying these mutations represented 8.8% of the PD cohort. No significant association was found between the GD-unreported mutations and PD development, which suggests that only the GD-associated mutations are a genetic risk for PD. According to a worldwide multicenter analysis of 1883 fully sequenced PD patients, 7% of the GD-associated mutations are found in non-Ashkenazi Jewish PD patients ( Sidransky et al., 2009). Although the mutation frequency in the present study was similar to previous results, the OR of GD-associated heterozygous mutations (25.1) was significantly greater than the OR (5.43) of other ethnic cohorts (Sidransky et al., 2009) and was consistent with an OR of 28.0 from a previous Japanese report ( Mitsui et al., 2009). These results, taken together, suggest the possibility thatGBA mutations are at a distinct risk for PD in the Japanese population. However, a larger Japanese cohort study is required to confirm this.

4.2. Cross-sectional clinical figures of PD with GBA mutations

Before the survival time analyses, we investigated clinical features at enrollment between mutation groups. The lower onset age, more frequent family history and dementia, and worse disease severity of PD in patients with GBA mutations, compared with those without mutations, were consistent with previous cross-sectional case-control reports ( Anheim et al., 2012, Brockmann et al., 2011, Chahine et al., 2013, Lesage et al., 2011, Li et al., 2013, Mitsui et al., 2009, Neumann et al., 2009, Seto-Salvia et al., 2012 and Sidransky et al., 2009). In contrast, female-predominance (73.7%, p = 0.047) in patients with mutations observed in the present study is inconsistent ( Neumann et al., 2009 and Seto-Salvia et al., 2012).

4.3. Impact of GBA mutations on the clinical course of PD

To investigate the impact of GBA mutations on the clinical course of PD, a prospective-designed study over a long period is preferred. Although there has been a few longitudinally designed study to date, follow-up clinical data for a median of 6 years of 121 PD cases from a community-based incident cohort was recently reanalyzed; results demonstrate that progression to dementia defined by DSM IV (HR 5.7) and Hoehn and Yahr stage 3 (HR 3.2) are significantly earlier in 4 GBA mutation-carrier patients compared with 117 patients with wild-type GBA ( Winder-Rhodes et al., 2013). A 2-year follow-up clinical report of 28 heterozygous GBA carriers who were recruited from relatives of GD-patients shows slight but significant deterioration of cognition and smelling, compared to healthy controls ( Beavan et al., 2015). Brockmann et al. (2015)assessed motor and nonmotor symptoms including cognitive and mood disturbances for 3 years in 20 PD patients with GBA mutations and showed a more rapid disease progression of motor impairment and cognitive decline in GBA mutation cases comparing to sporadic PD controls. The current long-term retrospective cohort study up to 12 years reinforced these results. It revealed that dementia and psychosis developed significantly earlier in subjects with GD-associated mutations compared with those without mutation, and the HRs of GBA mutations were estimated at 8.3 for dementia and 23.1 for psychosis, with adjustments for sex and PD onset age. In contrast, the results showed no significant difference in developing wearing-off and dyskinesia.

In this study, we also investigated whether GD-unreported mutations affected the clinical course of PD. In both cross-sectional and survival time analyses, the mutations unreported in GD carried no increased burden on clinical symptoms such as dementia, psychosis, wearing-off, and dyskinesia.

4.4. Reduced rCBF in PD with GBA mutations compared with matched PD controls

We found a significantly decreased rCBF, reflecting decreased synaptic activity, in the bilateral parietal cortex including the precuneus, in subjects with GD-associated mutations compared with matched subjects without mutations. The pattern of reduced rCBF was very similar to the pattern of H215O positron-emission tomography that Goker-Alpan et.al. (2012) reported, showing decreased resting rCBF in the lateral parietal association cortex and the precuneus bilaterally in GD subjects with parkinsonism (7 subjects with homozygous or compound heterozygous GBA mutations), compared with 11 PD without GBA mutations. Results suggest that PD with heterozygous GBAmutations and GD patients presenting parkinsonism had a common reduced pattern of rCBF. Interestingly, in their study, rCBF in the precuneus—but not in the lateral parietal cortex—correlated with IQ, suggesting that the involvement of the precuneus is critical for defining GBA-associated patterns.

4.5. Reduced cardiac MIBG H/M ratios as well as matched PD controls

We also showed that cardiac MIBG H/M ratios in subjects with GD-associated mutations were lower than the cutoff point for PD discrimination (Sawada et al., 2009), suggesting that postganglionic sympathetic nerve terminals to the epicardium were denervated, as well as in PD without mutations.

4.6. Mechanisms of impact on PD clinical course by GD-associated GBA mutations

Experimental studies suggesting a bidirectional pathogenic loop between α-synuclein and glucocerebrosidase have been accumulated (Fishbein et al., 2014, Gegg et al., 2012, Mazzulli et al., 2011, Noelker et al., 2015, Schondorf et al., 2014 and Uemura et al., 2015). Loss of glucocerebrosidase function compromises α-synuclein degradation in lysosome, whereas aggregated α-synuclein inhibits normal lysosomal function of glucocerebrosidase. The pathogenic loop may facilitate neurodegeneration in GD-associated PD brain, resulting in early development of dementia or psychosis as shown in the present study. Several recent researches propose the possibility that the similar mechanism as in PD with GBA mutations exists even in idiopathic PD brain ( Alcalay et al., 2015, Chiasserini et al., 2015, Gegg et al., 2012 and Murphy et al., 2014). On the other hand, the impacts of GD-associated GBA mutations for the development of motor complications such as wearing-off and dyskinesia were not statistically significant, suggesting other pathophysiological mechanisms in the striatal circuit brought out after long-term therapy especially by l-dopa.

4.7. Limitations

Our study has several limitations. In the design of the study, we assumed that the sample size was 215 (PD patients) for survival time analyses and investigated 224 PD patients. We assumed that the mutation prevalence would be 9.4%, and in fact, we found 19 patients with mutations (8.5%) of the 224 patients. Based on these figures, we estimated the risk ratios of heterozygous GBA mutations for the risk of PD development and PD clinical symptoms as ORs in the cross-sectional multivariate analyses, although the 95% CIs were broad. More of subject numbers will be needed to determine robust risk ratios.

Comprehensive Genetic Characterization of a Spanish Brugada Syndrome Cohort

PLOS   Published: July 14, 2015   DOI: http://dx.doi.org:/10.1371/journal.pone.0132888

Brugada syndrome (BrS) was identified as a new clinical entity in 1992 [1]. Six years later, the first genetic basis for the disease was identified, with the discovery of genetic variations inSCN5A [2]. Nowadays, more than 300 pathogenic variations in this first gene are known to be associated with BrS [3]. SCN5A encodes for the α subunit of the cardiac voltage-dependent sodium channel (Nav1.5), which is responsible for inward sodium current (INa), and thus plays an essential role in phase 0 of the cardiac action potential (AP). Genetic variations in this gene can explain around 20–25% of BrS cases [3].

Since BrS was classified as a genetic disease, several other genes have been described to confer BrS-susceptibility [47]. Pathogenic variations have been mainly described in: 1) genes encoding proteins that modulate Nav1.5 function, and 2) other calcium and potassium channels and their regulatory subunits. All these proteins participate, either directly or indirectly, in the development of the cardiac AP. Although the incidence of pathogenic variations in these BrS-associated genes is low [6], it is considered that, among all of them, they could provide a genetic diagnosis for up to an extra 5–10% of BrS cases. Hence, altogether, a genetic diagnosis can be achieved approximately in 35% of clinically diagnosed BrS patients.
Other types of genetic abnormalities have been suggested to explain the remaining percentage of undiagnosed patients. Indeed, multiplex ligation-dependent probe amplification (MLPA) has allowed the detection of large-scale gene rearrangements involving one or several exons ofSCN5A in BrS cases. However, the low proportion of BrS patients carrying large genetic imbalances identified to date suggests that this type of rearrangements will provide a genetic diagnosis for a modest percentage of BrS cases [810].
BrS has been associated with an increased risk of sudden cardiac death (SCD), despite the reported variability in disease penetrance and expressivity [11]. The prevalence of BrS is estimated at about 1.34 cases per 100 000 individuals per year, with a higher incidence in Asia than in the United States and Europe [12]. However, the dynamic nature of the typical electrocardiogram (ECG) and the fact that it is often concealed, hinder the diagnosis of BrS. Therefore, an exhaustive genetic testing and subsequent family screening may prove to be crucial in identifying silent carriers. A large percentage of these pathogenic variation carriers are clinically asymptomatic, and may be at risk of SCD, which is, sometimes, the first manifestation of the disease [13].
In the present work, we aimed to determine the spectrum and prevalence of genetic variations in BrS-susceptibility genes in a Spanish cohort diagnosed with BrS, and to identify variation carriers among relatives, which would enable the adoption of preventive measures to avoid SCD in their families.

Results  
Study population 

thumbnail

Table 1. Demographics of the 55 Spanish BrS patients included in the study.

The table shows the demographic characteristics of all the patients included in the study. Numbers in parentheses represent the relative percentages for each condition. T1 ECG refers to Type 1 BrS diagnostic electrocardiogram (ECG), obtained either spontaneously, or after drug challenge. The information regarding both the electrophysiological studies (EPS) and the treatment was not available for all the patients. Two of the patients that didn’t receive any treatment died, and were not taken into account for the calculations of percentages (+2 dead). ICD, intracardiac cardioverter defibrillator.

http://dx.doi.org:/10.1371/journal.pone.0132888.t001

thumbnail

Table 2. Characteristics of the Spanish BrS patients carrying rare genetic variations.

The table shows the clinical characteristics of the probands who carried rare genetic variations in SCN5A, SCN2B, or RANGRF. All of them are potentially pathogenic except that found in RANGRF, which is of unknown significance (see discussion). All the potentially pathogenic variations (PPVs) that had been previously reported, except p.P1725L and p.R1898C, had been identified in BrS patients. p.P1725L had been associated with Long QT Syndrome and p.R1898C was found in Exome Variant Server with a MAF of 0.0079%. No rare variations were identified in the control population. Patient’s age is expressed in years. Bold identifies the patients carrying variations that had not been described previously. M, male; F, female; S, syncope; ICD, intracardiac cardioverter defibrillator; UK, unknown; EPS, electrophysiological studies (+, positive response;-, negative response; N/P, not performed). The two patients who carried two PPVs each are identified by a and b, respectively.

http://dx.doi.org:/10.1371/journal.pone.0132888.t002

Sequencing of genes associated with BrS

We performed a genetic screening of 14 genes (SCN5A, CACNA1C, CACNB2, GPD1L,SCN1B, SCN2B, SCN3B, SCN4B, KCNE3, RANGRF, HCN4, KCNJ8, KCND3, and KCNE1L), which allowed the identification of 61 genetic variations in our cohort. Of these, 20 were classified as potentially pathogenic variations (PPVs), one variation of unknown significance, and 40 common or synonymous variants considered benign.

The 20 PPVs were found in 18 of the 55 patients (32.7% of the patients, 83.3% males; Table 2). Sixteen patients (88.9%) carried one PPV, and two patients (11.1%) carried two different PPVs each. Nineteen out of the 20 PPVs identified were localized in SCN5A and one in SCN2B.

The vast majority of the PPVs identified were missense (70%). We also detected 2 nonsense variations (10%), 3 insertions or deletions causing frameshifts (15%), and one splicing variation (5%). The three frameshifts (p.R569Pfs*151, p.E625Rfs*95 and p.R1623Efs*7) were identified in SCN5A. These were not found in any of the databases consulted (see Methods), and were thus considered potentially pathogenic (see below). The other 16 rare variations identified inSCN5A had been previously described, and hence were also considered potentially pathogenic. Fourteen of them had been identified in BrS patients. Of these, 6 had also been identified in individuals diagnosed with other cardiac electric diseases (i.e. Sick Sinus Syndrome, Long QT Syndrome, Sudden Unexplained Nocturnal Death Syndrome or Idiopathic Ventricular Fibrillation [2,15,16,20,21,25]). The other 2, p.P1725L and p.R1898C, had only been associated with Long QT Syndrome or found in Exome Variant Server with a MAF of 0.0079%, respectively. Furthermore, we identified a variation in SCN2B (c.632A>G in exon 4 of the gene, resulting in p.D211G) which was considered pathogenic. This patient was included within our cohort, but the functional characterization of channels expressing SCN2B p.D211G was object of a previous study from our group [7]. We also identified a nonsense variation in RANGRFwhich has been formerly reported as rare genetic variation of unknown significance [29].

Additionally, we screened the relatives of those probands carrying a PPV. We analysed a total of 129 relatives, 69 of which (53.5%) were variation carriers. Genotype-phenotype correlations evidenced that 8 of the families displayed complete penetrance (S3 Table). Additionally, no relatives were available for one of the probands carrying a PPV, thus hampering genotype-phenotype correlation assessment. The other 12 families showed incomplete penetrance.

 

MLPA analysis

The 37 patients with negative results after the genetic screening of the 14 BrS-associated genes underwent MLPA analyses of SCN5A. This technique did not reveal any large exon deletion or duplication in this gene for any of the patients.

 

SCN5A p.R569Pfs*151 (c.1705dupC), a novel PPV

A 41-year-old asymptomatic male presented a type 3 BrS ECG which was suggestive of BrS. Flecainide challenge unmasked a type 1 BrS ECG (Fig 1A, left), which was also spontaneously observed sometimes during medical follow up. Sequencing of SCN5A revealed a duplication of a cytosine at position 1705 (c.1705dupC; Fig 1A, right), which originated a frameshift that lead to a truncated Nav1.5 channel (p.R569Pfs*151). The proband’s sister also carried this duplication, but had never presented signs of arrhythmogenesis. The proband’s twin daughters were also variation carriers, displayed normal ECGs and, to date, are asymptomatic (Fig 1A, middle). Thus, p.R569Pfs*151 represents a novel genetic alteration in the Nav1.5 channel that could potentially lead to BrS, but with incomplete penetrance.

thumbnail

Fig 1. Characteristics of the probands carrying non-reported potentially pathogenic variations (PPVs) in SCN5A and their families.

Left: Electrocardiograms of the probands: (A) patient carrying the p.R569Pfs*151 variation, showing the ST elevation characteristic of BrS in V1 at the time of the flecainide test; (B) patient carrying the p.E625Rfs*95 variation, showing the spontaneous ST elevation characteristic of BrS in V1 and V2; and (C) patient carrying the p.R1623Efs*7 variation, showing the spontaneous ST elevation characteristic of BrS in V1 and V2. Middle: Family pedigrees. Open symbols designate clinically normal subjects, filled symbols mark clinically affected individuals and question marks identify subjects without an available clinical diagnosis. Plus signs indicate the carriers of the PPVs and minus signs, non-carriers. The crosses mark deceased individuals and arrows identify the proband. Right: Detail of the electropherograms obtained after SCN5Asequence analysis of a control subject (left panels) and of the probands (right panels).

http://dx.doi.org:/10.1371/journal.pone.0132888.g001

SCN5A p.E625Rfs*95 (c.1872dupA), a novel PPV

A 51-year-old asymptomatic male was diagnosed with BrS since he presented a spontaneous ST segment elevation in leads V1 and V2 characteristic of type 1 BrS ECG (Fig 1B, left). The sequencing of SCN5A evidenced an adenine duplication at position 1872 (c.1872dupA, Fig 1B, right). This genetic variation results in a truncated Nav1.5 channel (p.E625Rfs*95). The genetic analysis of the proband’s relatives proved that only her mother carried the variation (Fig 1B, middle). She was asymptomatic, but a BrS ECG was unmasked upon ajmaline challenge. The proband’s sister was found dead in her crib at 6 months of age, which suggests that her death might be compatible with BrS. Therefore, the p.E625Rfs*95 variation in the Nav1.5 channel represents a novel genetic alteration potentially causing BrS.

SCN5A p.R1623Efs*7 (c.4867delC), a novel PPV

The proband, a 31-year-old male, was admitted to hospital after suffering a syncope. His baseline 12-lead ECG showed a ST segment elevation in leads V1 and V2 that strongly suggested BrS type 1 (Fig 1C, left). A deletion of the cytosine at position 4867 (c.4867delC) was observed upon SCN5A sequencing (Fig 1C, right). This base deletion leads to a frameshift that originates a truncated Nav1.5 channel (p.R1623Efs*7). Genetic screening of his parents and sisters evidenced that none of them carried this novel variation (Fig 1C, middle). None of them had presented any signs of arrhythmogenicity, nor had a BrS ECG. Nevertheless, in uterogenetic analysis of one of his daughters proved that she had inherited the variation. She died when she was 1 year of age of non-arrhythmogenic causes. Hence, the p.R1623Efs*7 variation in the Nav1.5 channel is a novel genetic alteration originated de novo in the proband that could potentially lead to BrS.

Synonymous and common genetic variations portrayal

In our cohort, we identified 40 single nucleotide variations which were common genetic variants and/or synonymous variants (S2 Table). Twenty-nine had a minor allele frequency (MAF) over 1%, and were thus considered common genetic variants.

We also identified 11 variants with MAF less than 1%. Of them, 9 were synonymous variants, what made us assume that they were not disease-causing. Four of these synonymous variants were not found in any of the databases consulted, and thus their MAF was considered to be less than 1%. Each of these synonymous variations was identified in 1 patient of the cohort. A similar proportion of individuals carrying these novel variations was detected upon sequencing of 300 healthy Spanish individuals (600 alleles). The remaining 2 variants were missense, and although they had either a MAF of less than 1% or an unknown MAF according to the Exome Variant Server and dbSNP websites, they were common in our cohort (29.2 and 50%, respectively; S2 Table), and a similar MAF was detected in a Spanish cohort of healthy individuals (26.7% and 48.8%, respectively).

Influence of phenotype and age on PPV discovery

To assess if a connection existed between the probands’ phenotype and the PPV detection yield, we classified the patients in our cohort according to their ECG (spontaneous or induced type 1), the presence of BrS cases within their families, and the presence/absence of symptoms. Even though the overall PPV detection yield was 32.7%, it was even higher for symptomatic patients (Fig 2). Indeed, in this group of patients, having a family history of BrS was identified as a factor for increased PPV discovery yield. In the case of absence of BrS in the family, the variation discovery yield was almost double for those patients having a spontaneous type 1 BrS ECG than for patients with drug-induced type 1 ECG (45.5% vs 25%, respectively). In addition, we identified a PPV in 44.4% of the asymptomatic patients who presented family history of BrS and a spontaneous type 1 BrS ECG. When the patient presented drug-induced type 1 ECG or in the absence of family history of BrS, the PPV discovery yield was of around 15%.

thumbnail

Fig 2. Influence of the phenotype on PPV discovery yield.

Bar graph comparing the PPV detection yield in 8 different clinical categories (stated below the graph). Each bar shows the total number of patients for each clinical category divided in those with a PPV (black) and those without an identified PPV (white). The number of patients (in brackets) and percentages are given. Pos, positive; Neg, negative; Spont, spontaneous type 1 BrS ECG; Drug, drug-induced type 1 BrS ECG; n, number of patients.

http://dx.doi.org/:10.1371/journal.pone.0132888.g002

We also investigated the role of age on the PPV occurrence. No significant age differences were observed between variation carriers and non-carriers (38.6±10.3 and 43.5±14.4, respectively, p = 0.16). However, the PPV discovery yield was higher for patients with ages between 30 and 50 years: out of the total of patients carrying a PPV, 83.3% of the patients were in this age range, while 11.1% were younger and 5.6% were older patients (Fig 3A, upper panel). The PPV discovery yield was significantly higher for symptomatic than for asymptomatic patients (42.3% vs 24.1%, respectively; Fig 3A, lower panels).

thumbnail

Fig 3. Influence of the age on PPVs discovery yield.

(A) Pie charts showing the distribution of patients in the overall population as well as in the categories of symptomatic and asymptomatic patients regarding PPV discovery. The percentage and the number of patients (in brackets) are given for each group. The small pie charts correspond to the age distribution of patients with an identified PPV. (B) Bar graphs of the PPV detection yields obtained for each of the age groups (< 30 years, 30–50 years and > 50 years). Numbers inside each bar correspond to the number of patients carrying a PPV for each category and the percentages represent the variation detection yield.

http://dx.doi.org:/10.1371/journal.pone.0132888.g003

Noteworthy, in the 30–50 age range, 52.9% (9/17) of the symptomatic patients and 35.3% (6/17) of asymptomatic patients carried one PPV (Fig 3B, middle). Additionally, 40% (2/5) of the symptomatic young patients (< 30 years) were variation carriers, while no PPVs were identified in asymptomatic patients within this age range.

Overall, 55 unrelated Spanish patients clinically diagnosed with BrS were included in our study.Table 1 shows the demographics of this cohort, and Table 2 and S1 Table show the clinical and genetic characteristics of all the patients included in the study. The mean age at clinical diagnosis was of 41.9±13.3 years. Although the majority of patients were males (74.5%), their age at diagnosis was not different than that of females (41.8±12.1 years and 42.3±16.3 years, respectively; p = 0.92). A type 1 BrS ECG was present spontaneously in 37 patients (67.3%), and drug challenge revealed a type 1 BrS ECG for the remaining 18 patients (32.7%). Almost half of the patients had experienced symptoms, including 2 SCD and 4 aborted SCD. Patients who had not previously experienced any signs of arrhythmogenicity despite having a BrS ECG were considered asymptomatic. Comparison of symptomatic vs asymptomatic patients evidenced a similar percentage of males (73.1% and 75.9%, respectively). However, the mean age at diagnosis was different between the two groups of patients (37.7±14.3 and 45.7±11.4, respectively; p<0.05).

Discussion

To the best of our knowledge, this is the first comprehensive genetic evaluation of 14 BrS-susceptibility genes and MLPA of SCN5A in a Spanish cohort. Well delimited BrS cohorts from Japan, China, Greece and even Spain have been genetically studied [24,3032]. Additionally, an international compendium of BrS genetic variations identified in more than 2100 unrelated patients from different countries was published in 2010 [3]. However, all these studies screenedSCN5A exclusively. In 2012, Crotti et al. reported the spectrum and prevalence of genetic variations in 12 BrS-susceptibility genes in a BrS cohort [5]. However, this study included patients of different ethnicity. Here, we report the analysis of 14 genes which has been conducted on a well-defined BrS cohort of the same ethnicity.

Our results confirm that SCN5A is still the most prevalent gene associated with BrS. Indeed,SCN5A-mediated BrS in our cohort (30.9%) is higher than the proportion described in other European reports [3,23], where a potentially causative variation is identified in only 20–25% of BrS patients. The reason for this discrepancy is unclear but could point towards a higher prevalence of SCN5A PPVs in the Spanish population or to selection bias. Additionally, we identified a genetic variation in SCN2B (c.632A>G, which results in p.D211G). We have formerly published the comprehensive electrophysiological characterization of this variation, and showed that indeed this variation could be responsible of the phenotype of the patient, thus linking SCN2B with BrS for the first time [7]. Also, we identified a variation in RANGRF. This variation (c.181G>T leading to p.E61X) had been previously reported in a Danish atrial fibrillation cohort [33]. Surprisingly, the authors reported an incidence of 0.4% for this variation in the healthy Danish population, which brought into question its pathogenicity. Our finding of this variation in an asymptomatic patient displaying a type 2 BrS ECG also points toward considering it as a rare genetic variation with a potential modifier effect on the phenotype but not clearly responsible for the disease [29].

No PPVs were identified in the other genes tested. Certainly, it is well accepted that the contribution of these genes to the disease is minor, and thus should only be considered under special circumstances [13,34]. In addition, recent studies have questioned the causality of variations identified in some of these minority genes [35].

We also used the MLPA technique for the detection of large exon duplications and/or deletions in SCN5A in patients without PPVs, and no large rearrangements were identified. This is in accordance with previous reports, which revealed that such imbalances are uncommon [810].

Kapplinger et al. [3] reported a predominance of PPVs in transmembrane regions of Nav1.5. Indeed, it has been proposed that most rare genetic variations in interdomain linkers may be considered as non-pathogenic [36]. In contrast, PPVs identified in this study are mainly located in extracellular loops and cytosolic linker regions of Nav1.5 (Fig 4). Additionally, 2 of our non-previously reported frameshifts are located in the DI-DII linker. These 2 genetic variations lead to truncated proteins, which would lack around 75% of the protein sequence, and thus are presupposed to be pathogenic.

thumbnail

Fig 4. Nav1.5 channel scheme showing the relative position of the SCN5A PPVs identified in our cohort.

Open symbols indicate already described variations and closed symbols locate novel variations reported in this study. DI to DIV designate the 4 domains of the protein, and numbers 1–6 identify the different segments within each domain. Crosses mark the voltage sensor.

http://dx.doi.org:/10.1371/journal.pone.0132888.g004

In our cohort, we have identified 40 synonymous or common genetic variations, 4 of which have not been previously reported. These variations are gradually becoming more and more important in the explanation of certain phenotypes of genetic diseases. Only a few common variations identified here are already published as phenotypic modifiers [37,38]. The effect of these and other common variants identified in our cohort on BrS phenotype should be further studied.

Unexpectedly, almost 40% (7/18) of the PPV carriers did not present signs of arrhythmogenicity. We also performed genotype-phenotype correlations of the PPVs identified in the families (S3 Table). These studies uncovered relatives, most of whom were young individuals, who carried a familial variation but had never exhibited any clinical manifestations of the disease. This is in agreement with Crotti et al. and Priori et al. [5,23], who postulated that a positive genetic testing result is not always associated with the presence of symptoms. Indeed, the existence of asymptomatic patients carrying genetic variations described to cause a severe Nav1.5 channel dysfunction has been reported [39]. The identification of silent carriers is of paramount importance since it allows the adoption of preventive measures before any lethal episode takes place. Unknown environmental factors, medication and modifier genes have been suggested to influence and/or predispose to arrhythmogenesis [11]. Hence, this group of patients has to be cautiously followed in order to avoid fatal events.

Our studies on the connection between patients’ phenotype and the PPV detection yield highlighted the presence of symptoms as a factor for an increased variation discovery yield. Within the group of symptomatic individuals, a PPV was identified in a higher proportion of patients displaying a spontaneous type 1 BrS ECG than for patients showing a drug-induced ECG. Likewise, within the asymptomatic patients with family history of BrS, those who presented spontaneous type 1 BrS ECG carried a PPV more often than those with a drug-induced ECG (Fig 2). Referring to age, the vast majority (17/20, 85%) of the PPVs were identified in patients around their fourth decade of age (30–50 years). This is in accordance with the accepted mean age of disease manifestation. Moreover, in this age range, more than 50% of the patients who presented symptoms carried a variation that could be pathogenic (Fig 3). Importantly, 35.3% of asymptomatic patients of around 40 years of age also carried one of such variations. These data highlight the importance of performing a genetic test even in the absence of clinical manifestations of the disease, and particularly when in the 30–50 years range, which is in accordance with consensus recommendations [13,34].

In conclusion, we have analysed for the first time 14 BrS-susceptibility genes and performed MLPA of SCN5A in a Spanish BrS cohort. Our cohort showed male prevalence with a mean age of disease manifestation around 40 years. BrS in this cohort was almost exclusivelySCN5A-mediated. The mean PPV discovery yield in our Spanish BrS patients is higher than that described for other BrS cohorts (32.7% vs 20–25%, respectively), and is even higher for patients in the 30–50 years age range (up to 53% for symptomatic patients). All these evidences support the genetic testing, at least of SCN5A, in all clinically well diagnosed BrS patients.

 

Study Limitations

First of all, drug challenge tests were not performed for all the relatives who were asymptomatic variation carriers. This fact hampered their clinical diagnosis and represents an impediment to definitely assess the link between PPVs and BrS. These patients are nowadays under follow-up.

New PPVs have been identified in our cohort. The clinical information available for the families suggests that these new variations could be pathogenic. Still, in vitro studies of these variations are required in order to evaluate their functional effects and verify their pathogenic role. Additionally, genotyping in an independent cohort would help reduce the likelihood of type I (false positive) error in genetic variant discovery.

We have to acknowledge that the study set is relatively small. Consequently, the classification of patients according to the different clinical categories rendered rather small sub-groups, which may lead to over-interpretation of the results. Future studies will be directed to the genetic screening of additional Spanish BrS patients, which will probably reinforce the significance of the tendencies observed here.

Read Full Post »


Sets of co-expressed Genes influence Blood Pressure Regulation: Genome-wide Association and mRNA expression @US National Heart, Lung, and Blood Institute

Reporter: Aviva Lev-Ari, PhD, RN

 

 

NHLBI-led Team Untangles Gene Networks Involved in Blood Pressure Regulation

Apr 16, 2015

 

a GenomeWeb staff reporter

NEW YORK (GenomeWeb) – Using network approaches, researchers from the US National Heart, Lung, and Blood Institute and their colleagues combined genome-wide association and mRNA expression data to home in on sets of co-expressed genes that appear to influence blood pressure regulation.

As they reported in Molecular Systems Biology today, the NHLBI-led team drew on data from more than 3,600 people participating in the Framingham Heart Study to identify four potentially causal gene modules and key driver genes contained within them.

“Our work was able to pinpoint several gene networks closely linked to the regulation of blood pressure,” first author Tianxiao Huan from NHLBI said in a statement.

In addition, Huan and her colleagues traced the function of one key driver gene — SH2B3 — to response to angiotensin II infusion in a mouse model, indicating that this approach may help identify new treatment targets.

For this study, Huan and her colleagues examined the gene expression profiles of 3,679 Framingham Heart Study participants of European descent who were not taking an antihypertensive drug. They correlated gene expression changes they observed in this cohort with systolic blood pressure, diastolic blood pressure, and hypertension and, after accounting for age, BMI, gender, and other factors, came up with 83 associated genes.

At the same time, the researchers constructed gene co-expression networks from that gene expression data to develop gene co-expression network modules that they then also correlated to blood pressure phenotypes. Of these 27 gene co-expression network modules, seven were significantly associated with either systolic or diastolic blood pressure, the researchers said.

While that set of 83 blood pressure-related genes wasn’t significantly enriched for any gene ontology terms, the seven gene co-expression network modules were linked to a variety of functions, including chromatin modification, immune cell-mediated cytotoxicity, inflammatory response, and more. This suggested to the researchers that genes involved in a range of biological processes are tightly co-regulated with respect to blood pressure.

Using a SNP set enrichment analysis approach, the researchers found that four of the gene co-expression network modules appeared to be potentially causal and that more than a dozen genes in those modules appeared to contribute to their association with blood pressure regulation.

For instance, one SNP, dubbed rs3184504, had been linked with blood pressure through a genome-wide association study, and it is linked with the expression of four genes in the set of genetically inferred causal blood pressure genes.

Using blood Bayesian networks and protein-protein interaction networks other groups had developed, Huan and her colleagues further zoomed in on key driver genes by testing whether the surrounding region of each gene in those four gene co-expression network modules was enriched for other potentially causal blood pressure genes.

These top key driver genes, they noted, were involved in subnetworks that appeared to regulate blood pressure-related genes.

For example, a missense SNP in an exon of SH2B3 has been associated with blood pressure and hypertension in a GWAS and is linked to expression changes in 10 other genes the researchers identified. These genes, Huan and her colleagues said, were enriched for activity in the intracellular signaling cascade, T-cell activation, and T-cell differentiation. This SH2B3-subnework was also enriched for genes known to be linked to blood pressure.

Previous work had linked SH2B3 to blood pressure regulation, Huan and her colleagues said, but how it had its effect wasn’t clear.

Mice lacking the SH2B3 gene, they noted, had normal baseline blood pressure, though it became elevated in response to a low dose of angiotensin II, an effect not seen in wild-type mice.

In addition, RNA sequencing of the whole-blood transcriptomes from wild-type and Sh2b3-/- mice indicated that more than 2,240 genes were differentially expressed between the two, especially ones involved in immune and inflammatory response. These genes significantly overlapped with the SH2B3 genetic subnetwork, and those overlapping genes were enriched for ones involved in the intracellular signaling cascade and T-cell activation, the researchers reported.

“Moving forward, it should be possible to study additional key driver genes in this way, which should help in our efforts to identify novel targets for the prevention and treatment of hypertension,” Huan added.

 

Related Articles

Mar 10, 2015

Researchers Link Innate Immune Function to PTSD Development Risk

Mar 20, 2015

Gene Expression Meta-analysis Leads to Blood Pressure Signature

Jan 23, 2015

Imperial College London-led Team Uncovers Regulator of Epilepsy Gene Network

Mar 05, 2015

Study Links Regulatory Changes during Development to Human Cerebral Cortex Evolution

May 01, 2014

Comparative Genomic Study Underscores Distinct Properties of Specialized Metabolites in Plants

Nov 06, 2014

Tools & Techniques: RNAi Delivery Tech, RNA-seq Co-expression Database

Premium

 

SOURCE

https://www.genomeweb.com/cardiovascular-disease/nhlbi-led-team-untangles-gene-networks-involved-blood-pressure-regulation

 

 

Read Full Post »

Older Posts »