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The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the Clinical Validity of 111 Gene-Disease Relationships.
Get PDFPURPOSE: The Clinical Genome Resource (ClinGen) Gene Curation Expert Panels (GCEPs) have historically focused on specific organ systems or phenotypes; thus, the ClinGen Syndromic Disorders GCEP (SD-GCEP) was formed to address an unmet need.
METHODS: The SD-GCEP applied ClinGen\u27s framework to evaluate the clinical validity of genes associated with rare syndromic disorders. 111 Gene-Disease Relationships (GDRs) associated with 100 genes spanning the clinical spectrum of syndromic disorders were curated.
RESULTS: From April 2020 through March 2024, 38 precurations were performed on genes with multiple disease relationships and were reviewed to determine if the disorders were part of a spectrum or distinct entities. 14 genes were lumped into a single disease entity and 24 were split into separate entities, of which 11 were curated by the SD-GCEP. A full review of 111 GDRs for 100 genes followed, with 78 classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited highlighting where further data are needed. All diseases involved two or more organ systems, while the majority (88/111 GDRs, 79.2%) had five or more organ systems affected.
CONCLUSION: The SD-GCEP addresses a critical gap in gene curation efforts, enabling inclusion of genes for syndromic disorders in clinical testing and contributing to keeping pace with the rapid discovery of new genetic syndromes
Testing SIPA1L2 as a modifier of CMT1A using mouse models.
No full textCharcot-Marie-Tooth disease type 1A (CMT1A) is a demyelinating peripheral neuropathy caused by the duplication of peripheral myelin protein 22 (PMP22), leading to muscle weakness and loss of sensation in the hands and feet. A recent case-only genome-wide association study of CMT1A patients conducted by the Inherited Neuropathy Consortium identified a strong association between strength of foot dorsiflexion and variants in signal induced proliferation associated 1 like 2 (SIPA1L2), indicating that it may be a genetic modifier of disease. To validate SIPA1L2 as a candidate modifier and to assess its potential as a therapeutic target, we engineered mice with deletion of exon 1 (including the start codon) of the Sipa1l2 gene and crossed them to the C3-PMP22 mouse model of CMT1A. Neuromuscular phenotyping showed that Sipa1l2 deletion in C3-PMP22 mice preserved muscular endurance assayed by inverted wire hang duration and changed femoral nerve axon morphometrics such as myelin thickness. Gene expression changes suggest involvement of Sipa1l2 in cholesterol biosynthesis, a pathway that is also implicated in C3-PMP22 mice. Although Sipa1l2 deletion did impact CMT1A-associated phenotypes, thereby validating a genetic interaction, the overall effect on neuropathy was mild
Histone Modifications and Their Contributions to Hypertension.
No full textEssential hypertension, a multifaceted disorder, is a worldwide health problem. A complex network of genetic, epigenetic, physiological, and environmental components regulates blood pressure (BP), and any dysregulation of this network may result in hypertension. Growing evidence suggests a role for epigenetic factors in BP regulation. Any alterations in the expression or functions of these epigenetic regulators may dysregulate various determinants of BP, thereby promoting the development of hypertension. Histone posttranslational modifications are critical epigenetic regulators that have been implicated in hypertension. Several studies have demonstrated a clear association between the increased expression of some histone-modifying enzymes, especially HDACs (histone deacetylases), and hypertension. In addition, treatment with HDAC inhibitors lowers BP in hypertensive animal models, providing an excellent opportunity to design new drugs to treat hypertension. In this review, we discuss the potential contribution of different histone modifications to the regulation of BP
Diverging Phenotypes and Regional Accumulation of Human Microglia in Engrafted hCSF1 - and hll-34-expressing Mice
No full textMicroglia are the resident macrophages of the central nervous system (CNS) and perform diverse functions during embryonic and adult development of the brain.1 Activation of microglia surrounding beta-amyloid (Aβ) plaques is a hallmark of Alzheimer’s Disease (AD).2 Human colony stimulating factor 1 (CSF1) and interluekin- 34 (IL-34) are cytokines that stimulate CSF1 receptor (CSF1R), a tyrosine kinase receptor important for the growth and proliferation of microglia.3 While transgenic human CSF1 (h-CSF1) expression has been used to support human microglia (hMG) engraftment by stimulating cell surface CSF1R, human IL-34 (h-IL34) has been underutilized despite its significant role in microglia survival in the hippocampus and cortex.4 This study examines the differences of hMG engraftment in h-CSF1Tg and h- IL34KI mice. Through fluorescent imaging, engrafted hMG were found to largely localize to the cortex region in h-IL34KI expressing mice. In contrast, hMG in h-CSF1Tg mice largely accumulated within the fimbria. Flow cytometry analysis of brain and spinal cord tissue revealed a greater proportion of human cells in h-IL34KI expressing mice in both tissues. The human cells in each strain could be grouped into high, low, and negative expressors of P2RY12 and CX3CR1. The P2RY12hiCX3CR1hi cells were most similar to mouse microglia in regards to expression of classical microglia markers, while P2RY12- CX3CR1- cells more closely resembled the phenotype seen in peripheral myeloid cells. The P2RY12lowCX3CR1low cells were most different between h-CSF1Tg and h-IL34KI mice. HLA-DR expression in this group was higher in h-IL34KI as compared to h-CSF1Tg expressing mice. However, the low CD44 expression observed in this population in h- CSF1Tg hMG more closely resembled CD44 profiles of mouse microglia. In conclusion while h-IL34KI mice support a larger population of human microglia, expression profiles suggest that there may be differences between phenotype of human microglia supported by h-IL34 and homeostatic microgli
Multi-Omics Analyses to Detect Changes in the Mouse Hippocampus with Differences in Age, Diet and Strain
No full textRecent advances have drastically improved the capabilities of mass spectrometry analysis, allowing for the generation of large datasets quantifying protein, lipid, and metabolite levels within biological tissues. We have leveraged these capabilities towards seeking new insights into how various modifiable and disease-related factors (diet, age, mutation status, learning) induce changes in the mouse brain, specifically the hippocampus, with whole-brain to single-cell resolution. These analyses are aimed at discovering novel therapeutic targets that RNA sequencing-based gene expression alone may not capture, such as faults in the proteostasis network that accumulate during aging and are hallmarks of neurodegenerative diseases like Alzheimer’s disease. We compared across age, strain, transgenic genotype, and behavioral conditioning to identify how these factors influence changes in the brain metabolome and proteome. We performed bulk proteomic and metabolomic analyses of the mouse hippocampus and hypothalamus and found strain-dependent and independent metabolite, protein, and pathway dysregulation between high- and low-fat diets. In parallel, we optimized a hippocampus cell dissociation protocol to generate cell samples suitable for single-cell proteomic analysis. This will aid in determining protein-function associations within the hippocampus and, when combined with mass spectrometry imaging, be used to create a single-cell proteomic atlas of the mouse hippocampus
Microglia differentiation from human induced pluripotent stem cells
No full textMicroglia, constituting about 10% of brain cells, play crucial roles in CNS development and regulation. They constantly monitor for damage, prune synapses, mediate neuronal plasticity, and phagocytose dead cells and debris. Microglia exhibit significant heterogeneity and plasticity, giving them various morphologies. Over the last decade, many microglial transcripts have been identified, including disease-associated microglia (DAMs) observed in conditions like Alzheimer\u27s (AD) and Parkinson\u27s (PD) diseases. DAM’s effects can be both harmful .and beneficial, depending on the disease stage and age. The study of human microglia in vivo and in vitro has proven to be challenging, whereas research relying on rodent models, immortalized cell lines, and postmortem human brain tissues, often fails to replicate the progression of these complex human diseases. Human microglia, derived from yolk sac progenitor cells, can now be studied more accurately by utilizing the differentiation potential of human induced pluripotent stem cells (hiPSCs). These cells can be reprogrammed and differentiated into microglia though signaling cascades mimicking in vivo development and their identities validated through flow cytometry (FC) and immunocytochemistry (ICC). The Jackson Laboratory’s development of human microglia from hiPSCs will enable more precise studies of neurodegenerative diseases, neuronglia interactions, and potentially novel therapeutic strategies
Identifying Markers to Determine Optimal Stage of Differentiation of Retinal Pigmented Epithelial Cells into Photoreceptors
No full textAccording to the CDC, approximately 12 million people in the United States over the age of 40 suffer from vision impairment.7 Stem cell therapies have grown widely in popularity as treatment options for conditions of vision impairment.11 These therapies include differentiating stem cells into retinal pigmented epithelium (RPE) cells which are then transplanted into the epithelial layer that lines the back of the eye, the retina. Although there have been clinical trials using stem cell therapies to treat vision loss, various issues, such as the presence of off target cell types during the differentiation process, exist which require the refinement of these therapeutic techniques. Through this work, the goal was to determine various markers that were expressed at different stages of RPE differentiation from induced pluripotent stem cells (iPSCs). Using immunocytochemistry, markers that were expressed at specific timepoints of RPE differentiation from iPSCs were determined. By knowing what markers are expressed by RPEs during their development, the issues of mixed cultures can be avoided. Additionally, the most adequate seeding density to conduct the differentiation process based on the protocol that was used was determined, resulting in improved yields of RPE
Studying the Effect of Cancer-Associated-Fibroblasts on Colorectal Cancer Organoid Growth and Phenotype
No full textAlthough human intestine in vitro models have shown significant progress in the field of biomedical engineering, they still lack the physiological components needed to study complex gut diseases such as colorectal cancer (CRC). Recent studies have attempted to mimic the CRC tumor microenvironment (TME) on a chip, discovering that cancer-associated fibroblasts (CAFs) increase the growth of patient derived tumor organoids (PDTOs), potentially influencing tumor response to therapy. This project aimed to further investigate the growth and advancement of CRC organoids in co-culture with CAFs and determine whether co-culturing with healthy adjacent fibroblasts can lead to the reversal of cancer or vice versa. To accomplish this, healthy and CRC organoid models were cultured alone and with healthy adjacent fibroblasts/CAFs. After 6 days of co-culture, the domes were fixed and processed _for immunofluorescence staining. Additionally, brightfield images of each dome were taken to assess differences in organoid morphology, size, and number. The results of these analyses indicate that CAFs may have a decreased ability to support healthy colon organoid growth when compared to CRC organoids. In the future, this experiment could be repeated to confirm these findings and better understand the mechanisms behind the observed growth differences
An emerging multi-omic understanding of the genetics of opioid addiction.
Get PDFOpioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction-associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease
Clinically relevant mouse models of severe spinal muscular atrophy with respiratory distress type 1.
Get PDFSpinal Muscular Atrophy with Respiratory Distress (SMARD1) is a lethal infantile disease, characterized by the loss of motor neurons leading to muscular atrophy, diaphragmatic paralysis, and weakness in the trunk and limbs. Mutations in IGHMBP2, a ubiquitously expressed DNA/RNA helicase, have been shown to cause a wide spectrum of motor neuron disease. Though mutations in IGHMBP2 are mostly associated with SMARD1, milder alleles cause the axonal neuropathy, Charcot-Marie-Tooth disease type 2S (CMT2S), and some null alleles are potentially a risk factor for sudden infant death syndrome (SIDS). Variant heterogeneity studied using an allelic series can be informative in order to create a broad spectrum of models that better exhibit the human variation. We previously identified the nmd2J mouse model of SMARD1, as well as two milder CMT2S mouse models. Here, we used CRISPR-Cas9 genome editing to create three new, more severe Ighmbp2 mouse models of SMARD1, including a null allele, a deletion of C495 (C495del) and a deletion of L362 (L362del). Phenotypic characterization of the IGHMBP2L362del homozygous mutants and IGHMBP2C495del homozygous mutants respectively show a more severe disease presentation than the previous nmd2J model. The IGHMBP2L362del mutants lack a clear denervation in the diaphragm while the IGHMBP2C495del mutants display a neurogenic diaphragmatic phenotype as observed in SMARD1 patients. Characterization of the Ighmbp2-null model indicated neo-natal lethality (median lifespan = 0.5 days). These novel strains expand the spectrum of SMARD1 models to better reflect the clinical continuum observed in the human patients with various IGHMBP2 recessive mutations