Snyder, Michael

SUMMARY Neurodegenerative diseases are often accompanied by systemic comorbidities, including changes in bone health, but the molecular relationship between neurodegeneration, skeletal decline, and cellular senescence remains poorly understood. In this study, we investigated sex-specific changes in circulating bone- and senescence-related proteins across the spectrum of Alzheimer’s disease(AD), Lewbody dementia(LB) and Parkinson’s disease(PD). Plasma proteomic profiling was performed on samples from 408 participants deeply phenotyped for neurodegenerative diseases, followed by differential protein and pathway analyses. This study reveals sex-dependent alterations in bone and senescence-related circulating proteins in AD-related, PD and LB-related neurodegenerative diseases, providing insights into the complex relationship between neurodegeneration and bone health. Several candidate proteins were also associated with established plasma neurodegeneration biomarkers, particularly pTau181. Pathway analyses revealed shared mitochondrial and metabolic dysfunction across neurodegenerative diseases, with disease-specific features including vesicle trafficking disruption in AD and inflammatory-senescence pathways in LB, plus sex-divergent patterns in inflammatory signaling and bone-related pathways.

Sharing research code in an open access version-controlled repository offers significant benefits for both science as a whole and for individual researchers. In this article, we focus on this practice, which is fully aligned with the NIH’s Gold Standard Science (GSS) program as well as FAIR (findable, accessible, interoperable, reusable) and TRUST (transparency, responsibility, user focus, sustainability, technology) principles. Gold Standard Science supports open science by emphasizing transparency, reproducibility, and the use of best practices that enable others to verify and extend research. Pairing a research article’s cited data snapshot with a versioned, environment-specific code release, deposited in a companion code repository, ensures that, upon submission to a medical journal, readers and reviewers can directly verify results. An executable and updatable companion code repository complements, rather than replaces, established research data repositories. When code underlying medical research results is made openly available, then other scientists can inspect, run, and validate analyses. These activities enhance reproducibility, which is a core aim of GSS. Shared code also facilitates collaborative innovation by allowing researchers to extend the utility of the code to new datasets and applications. For researchers, code sharing can increase visibility, credibility, and citation impact. Demonstrating transparency through shared executable and updatable code builds trust with journal readers, peer reviewers, funders, and peers. Shared code in an open access repository signals adherence to high standards of scientific integrity and attracts opportunities for collaboration. A researcher who shares code receives recognition as a leader in reproducible, trustworthy research consistent with NIH’s GSS principles.

Abstract Background Celiac disease (CeD) is a chronic autoimmune disorder triggered by the ingestion of gluten in persons with the genetic risk factors human leukocyte antigens (HLA)-DQ2 and DQ8. Diagnostic evaluation of patients with suspected CeD often includes serology tests for tissue transglutaminase (tTG) antibodies. While the presence of HLA-DQ2 or DQ8 is required for the initiation and development of CeD, the genetic risk associated with the various alleles is not equivalent. Previous studies in patients with normal total IgA demonstrated the risk gradients of various HLA-DQ2 and DQ8 heterodimers in CeD. However, the impact of both gene variants in IgA deficient patients has not been investigated. In this study, HLA-DQ2 and HLA-DQ8 as risk factors for tTG-IgG positivity in IgA deficient patients were evaluated. Methods Retrospective data was collected from a cohort of individuals (n=3,515) with IgA concentrations below the age-dependent reference interval with suspicion for CeD who were tested for HLA-DQ genotyping and tTG-IgG (reference interval < 6 U/mL) at Mayo Clinic Laboratories. Total IgA was measured using quantitative nephelometry (Siemens BN™ II System); HLA typing was performed using the reverse SSO DNA typing assay (LABType SSO kits). tTG-IgG was determined by enzyme-linked immunosorbent assay (QUANTA Lite R h-tTG, Werfen Diagnostics) on the Dynex Agility System. The prevalence and frequency distribution of HLA-DQ2 and DQ8 haplotypes were determined and the odds ratio (OR) was calculated to evaluate the risk gradient for tTG-IgG positivity based on different HLA-DQ variants. Results Among IgA deficient patients, 58% (n=2,041) expressed HLA-DQ2 or DQ8 haplotypes. Relative to patients without permissive alleles, patients homozygous for HLA-DQ2.5 exhibited a significantly increased risk for tTG-IgG positivity (OR = 10.98, 95% CI: 6.56-18.18, p < 0.001) while those homozygous for HLA-DQ2.2 and DQ8 did not (DQ2.2/DQ2.2_OR = 0.72, 95% CI: 0.04-3.44, p = 0.75; DQ8/DQ8_OR = 0.96, 95% CI: 0.05-4.64, p = 0.97). Patients heterozygous for HLA-DQ2.5 (DQ2.5/x) displayed a lower odds ratio relative to homozygous patients (OR = 3.31, 95% CI: 2.29-4.82, p < 0.001); however, the risk for tTG-IgG positivity increased in the presence of HLA-DQ2.2 (DQ2.5/DQ2.2_OR = 7.59, 95% CI: 4.48-12.65, p < 0.001) or HLA-DQ8 (DQ2.5/DQ8_OR = 6.26, 95% CI: 3.55-10.73, p < 0.001) alleles. Conversely, in the absence of HLA-DQ2.5, HLA-DQ2.2 heterozygotes (DQ2.2/x_OR = 2.80, 95% CI: 1.77-4.39, p < 0.001) and HLA-DQ8 heterozygotes (DQ8/x_OR = 0.99, 95% CI: 0.52-1.77, p = 0.99) displayed lower correlations with tTG-IgG positivity, suggesting a potential risk elevation for tTG-IgG positivity is associated with the combination of DQ2.5 and DQ2.2 or DQ8. Conclusions Our study indicates the risk gradient of HLA-DQ genes in IgA deficient patients. Overall, compared to patients without HLA-DQ2 or DQ8 haplotypes, the homozygous HLA-DQ2.5 genotype had the highest correlation with tTG-IgG positivity, followed by HLA-DQ2.5/DQ2.2 and HLA-DQ2.5/DQ8 heterodimers. The results suggest that HLA-DQ2.2 or HLA-DQ8 alone does not confer risk, but when in the presence of HLA-DQ2.5 these alleles may increase the risk for tTG-IgG positivity. Results from this study shed light on the risk of CeD in patients with IgA deficiency.

Introduction: Hypoplastic left heart syndrome (HLHS) is a severe form of single ventricle congenital heart disease characterized by the underdeveloped left ventricle. Early serial postmortem examinations revealed a high rate of coronary artery abnormalities in HLHS fetal hearts (e.g., thickened wall and kinking arteries). However, the intrinsic defect in HLHS coronary vessels and its genetic basis remain unclear. Methods: We profiled human fetal heart with an underdeveloped left ventricle (ULV) and induced pluripotent stem cells derived endothelial cells (iPSC-ECs) from HLHS patients at single-cell resolution. CD144 + / NPR3 - vascular ECs were selected and classified as venous, arterial, and late arterial populations. To study the arterial EC phenotypes, we generated iPSC-arterial ECs (AECs, CDH5 + CXCR4 + NT5E -/low ) derived from 3 HLHS patients and 3 age-matched controls, and evaluated their functionalities including cell cycle regulation, angiogenesis, and inflammatory response. Results: Revealed by single cell RNA-seq and subsequent gene ontology analysis, ULV late arterial EC population showed significant defects in EC development, proliferation, angiogenesis, and Notch signaling compared to the control. Consistently, HLHS iPSCs exhibited impaired AEC differentiation judged by the reduced CXCR4 + NT5E -/low AEC progenitors. Mature HLHS iPSC-AECs showed reduced angiogenesis and enhanced G0/G1 cell cycle arrest with downregulated cell cycle-related genes (e.g., Ki67, CCND1/2 ). Healthy human aortic smooth muscle cells exhibited abnormal proliferation and synthetic phenotypes when co-cultured with HLHS iPSC-AECs. Additionally, NOTCH pathway genes (e.g., DLL4, HEY1, GJA5 ) were suppressed in both ULV AECs and HLHS iPSC-AECs. HLHS de novo variant KMT2D directly regulated the transcription of NOTCH targeted genes involved in arterial development and proliferation via H3K4me2. Intriguingly, the treatment of NOTCH ligands (Jag1, Dll1) significantly improved the proliferation of HLHS AECs. Conclusions: Our study revealed that HLHS coronary AECs were dysfunctional in angiogenesis, proliferation, and EC-SMC interaction. KMT2D-NOTCH signaling may contribute to the impaired development and proliferation of HLHS AECs.

Background: The study of hypertrophic cardiomyopathy (HCM) can yield insight into the mechanisms underlying the complex trait of cardiac hypertrophy. To date, most genetic variants associated with HCM have been found in sarcomeric genes. Here, we describe a novel HCM-associated variant in the noncanonical Wnt signaling interactor WTIP (Wilms tumor interacting protein) and provide evidence of a role for WTIP in complex disease. Methods: In a family affected by HCM, we used exome sequencing and identity-by-descent analysis to identify a novel variant in WTIP (p.Y233F). We knocked down WTIP in isolated neonatal rat ventricular myocytes with lentivirally delivered short hairpin ribonucleic acids and in Danio rerio via morpholino injection. We performed weighted gene coexpression network analysis for WTIP in human cardiac tissue, as well as association analysis for WTIP variation and left ventricular hypertrophy. Finally, we generated induced pluripotent stem cell–derived cardiomyocytes from patient tissue, characterized size and calcium cycling, and determined the effect of verapamil treatment on calcium dynamics. Results: WTIP knockdown caused hypertrophy in neonatal rat ventricular myocytes and increased cardiac hypertrophy, peak calcium, and resting calcium in D rerio . Network analysis of human cardiac tissue indicated WTIP as a central coordinator of prohypertrophic networks, while common variation at the WTIP locus was associated with human left ventricular hypertrophy. Patient-derived WTIP p.Y233F-induced pluripotent stem cell–derived cardiomyocytes recapitulated cellular hypertrophy and increased resting calcium, which was ameliorated by verapamil. Conclusions: We demonstrate that a novel genetic variant found in a family with HCM disrupts binding to a known Wnt signaling protein, misregulating cardiomyocyte calcium dynamics. Further, in orthogonal model systems, we show that expression of the gene WTIP is important in complex cardiac hypertrophy phenotypes. These findings, derived from the observation of a rare Mendelian disease variant, uncover a novel disease mechanism with implications across diverse forms of cardiac hypertrophy.

Abstract Therapeutic monoclonal immunoglobulins (mAbs) are used to treat patients with a wide range of disorders including autoimmune diseases. As pharmaceutical companies bring more fully humanized therapeutic mAb drugs to the healthcare market analytical platforms that perform therapeutic drug monitoring (TDM) without relying on mAb specific reagents will be needed. In this study we demonstrate that liquid-chromatography?mass spectrometry (LC?MS) can be used to perform TDM of mAbs in the same manner as smaller nonbiologic drugs. The assay uses commercially available reagents combined with heavy and light chain disulfide bond reduction followed by light chain analysis by microflow-LC?electrospray ionization-quadrupole-time-of-flight mass spectrometry (ESI-Q-TOF MS). Quantification is performed using the peak areas from multiply charged mAb light chain ions using an in-house developed software package developed for TDM of mAbs. The data presented here demonstrate the ability of an LC?MS assay to quantify a therapeutic mAb in a large cohort of patients in a clinical trial. The ability to quantify any mAb in serum via the reduced light chain without the need for reagents specific for each mAb demonstrates the unique capabilities of LC?MS. This fact, coupled with the ability to phenotype a patient?s polyclonal repertoire in the same analysis further shows the potential of this approach to mAb analysis.

Abstract Next-generation sequencing is now commonly applied to measure genomic modifications, providing the opportunity for a more accurate view of cancer progression. That being said, several challenges including tumor purity, heterogeneity and the broad set of cancer associated cellular functions, increase the difficulty of interpreting cancer genomes and make analyzing them distinct from analysis of germline diseases. The ability to detect low allelic mutations in the broad set of cancer-associated genes is critically important. To address these issues, we developed an extended cancer panel, a targeted enrichment sequencing platform that includes over 1,300 cancer genes and 200 miRNAs that improves coverage in traditionally difficult to sequence NGS regions. In this study, we apply an integrated RNA/DNA analysis approach as well as our extended cancer panel to explore mutations in metastatic renal cell carcinoma (RCC) tissue samples before and after treatment. Our goal with this study was to test the importance of integrating DNA and RNA analysis, which allows for detection of mutational events that cannot be observed by either method alone. With RNA analysis it is possible to detect gene fusion events, expression of small variants (SNVs/indels), and gene expression levels while DNA analysis allows for detection of loss of heterozygosity (LOH), copy number variants (CNVs), and small variants. By integrating both the RNA and DNA analysis, it is possible to identify unique variant classes, such as unexpressed variants, allele specific expression (ASE), effects of CNVs on gene expression levels, and how fusion gene integration sites affect CNVs. In our study, each variant class was interpreted pre- and post-treatment, allowing for optimal analysis of treatment effectiveness. By applying both our RNA/DNA integration approach and our extended cancer panel to investigate metastatic RCC samples, we were able to classify many genomic alterations that drive cancer progression. For example, we found that anywhere from 5% to 30% of small variant mutations in driver genes called in the DNA reside in genes that are unexpressed in the RNA. Likewise, we noted multiple cases of ASE, where high profile variants observed in DNA were entirely absent in the RNA despite high expression levels. Strong correlations between CNVs observed in DNA and gene expression changes found in RNA were also detected. We also observed that about half of the RCC samples we tested were biallelic for VHL mutations, suggesting inherited predisposition combined with second hit somatic mutations, facilitating cancer progression. This analysis demonstrates how combining an integrated RNA/DNA approach with a cancer focused augmented enrichment panel allows for detection of both low allelic representation variants and unique variant classes, both of which are critical for accurate interpretation of cancer samples. Citation Format: Sean M. Boyle, Michael J. Clark, Elena Helman, Alexander S. Parker, Thai Ho, Shujun Luo, Scott Kirk, Parin Sripakdeevong, Mirian Karbelashvili, Deanna M. Church, Michael Snyder, John West, Rich Chen. Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3899. doi:10.1158/1538-7445.AM2015-3899