76555 research outputs found
Sort by
Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response.
Get PDFIdentifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy is experimentally challenging. Our approach, utilizing the Collaborative Cross mouse genetic resource, fixes the tumor genomic configuration while varying host genetics. We find that response to anti-PD-1 (aPD1) immunotherapy is significantly heritable in four distinct murine tumor models (H2: 0.18–0.40). For the MC38 colorectal carcinoma system, we map four significant ICI response quantitative trait loci (QTLs) with significant epistatic interactions. The differentially expressed genes within these QTLs that define responder genetics are highly enriched for processes involving antigen processing and presentation, allograft rejection, and graft vs. host disease (all p \u3c 1 × 10−10). Functional blockade of two top candidate immune targets, GM-CSF and IL-2RB, completely abrogates the MC38 transcriptional response to aPD1 therapy. Thus, our in vivo experimental platform is a powerful approach for discovery of host genetic factors that establish the tumor immune microenvironment propitious for ICI response
A feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric central nervous system tumor patients for molecular classification.
Get PDFBACKGROUND: Array-based DNA methylation profiling is the gold standard for central nervous system (CNS) tumor molecular classification, but requires over 100 ng input DNA from surgical tissue. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) offers an alternative for diagnosis and disease monitoring. This study aimed to test the utilization of enzymatic DNA methylation sequencing (EM-seq) methods to overcome input DNA limitations.
METHODS: We used the NEBNext EM-seq v2 kit on various amounts of cfDNA, as low as 0.1 ng, extracted from archival CSF samples of 10 patients with CNS tumors. Tumor classification was performed via MNP-Flex using CpG sites overlapping those on the MethylationEPIC array.
RESULTS: EM-seq provided sufficient genomic coverage for 10 and 1 ng input DNA samples to generate global DNA methylation profiles. Samples with 0.1 ng input showed lower coverage due to read duplication. Methylation levels for CpG sites with at least 5× coverage were highly correlated across various input DNA amounts, indicating that lower input cfDNA can still be used for tumor classification. The MNP-Flex classifier, trained on tissue DNA methylation data, successfully predicted CNS tumor types for 7 out of 10 CSF samples using EM-seq methylation data with only 1 ng of input cfDNA, consistent with diagnoses based on tissue MethylationEPIC classification and/or histopathology. Additionally, we detected focal and arm-level copy number alterations previously identified via clinical cytogenetics of tumor tissue.
CONCLUSIONS: This study demonstrated the feasibility of CNS tumor molecular classification based on CSF using the EM-seq approach, and establishes potential sample quality limitations for future studies
Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells.
Get PDFGenetic variation leads to phenotypic variability in pluripotent stem cells that presents challenges for regenerative medicine. Although recent studies have investigated the impact of genetic variation on pluripotency maintenance and differentiation capacity, less is known about how genetic variants affecting the pluripotent state influence gene regulation later in development. Here, we characterized expression of 12,000 genes in a large panel of donor-matched Diversity Outbred mouse embryonic stem cell and mouse neural progenitor cell lines. QTL mapping identified 4,060 expression QTLs in mouse neural progenitor cells, including 2,998 local and 1,062 distant expression QTLs. In a comparison of mouse neural progenitor cell and mouse embryonic stem cell expression QTLs, we found that local expression QTLs were more likely than distant expression QTL to be detected in both cell types. Distant expression QTLs were largely unique to 1 cell type, and we mapped 3 mouse neural progenitor cell-specific expression QTL hotspots on chromosomes 1, 10, and 11. Mediation analysis of the chromosome 1 hotspot identified Rnf152 as the best candidate mediator expressed in mouse neural progenitor cells, while cross-cell-type mediation using mouse embryonic stem cell gene expression along with partial correlation analysis strongly implicated genetic variant(s) affecting Pign expression in the mouse embryonic stem cell state as regulating the mouse neural progenitor cell chromosome 1 hotspot. These findings highlight that local mouse neural progenitor cell expression QTLs are more likely than distant expression QTLs to be shared with mouse embryonic stem cells; distant mouse neural progenitor cell expression QTLs are numerous but largely unique to that cell type, with many colocalizing to mouse neural progenitor cell-specific hotspots; and mediation analysis across cell types suggests that expression of Pign in mouse embryonic stem cells shapes the transcriptome of the more specialized mouse neural progenitor cell state
Gridded Visualization of Statistical Trees for High‐Dimensional Multipartite Data in Systems Genetics
No full textIn systems genetics and other multi-omics research, exploring high-dimensional relationships among molecular and physiological variables across individuals poses significant challenges. We present the Gridded Trees interface, a novel interactive visualization tool designed to facilitate the exploration of conditional inference trees, which are hierarchical models of relationships in these complex datasets. Traditional static tools struggle to reveal patterns in tree-structured data, but the Gridded Trees interface provides interactive, coordinated views, allowing users to navigate between overview and detail, filter data dynamically, and compare molecular-physiological relationships across subgroups. By combining filtering techniques, strip plots, Sankey diagrams, and small multiples, the Gridded Trees interface enhances exploratory data analysis and supports hypothesis generation. In our systems genetics research use case, this tool has revealed significant associations among microbial populations and addiction-related behavioral traits in genetically diverse mice. The Gridded Trees interface suggests broad potential for visualizing hierarchical and multipartite data across domains. A preprint of this paper as well as Supplemental Materials are available on OSF at https://osf.io/9emn5/
Artificial intelligence-based digital pathology using H&E-stained whole slide images in immuno-oncology: from immune biomarker detection to immunotherapy response prediction.
Get PDFImmuno-oncology and the advent of immunotherapies, in particular immune checkpoint inhibitors (ICIs), have fundamentally altered the way we treat cancer. Yet only a small subset of patients actually responds to ICIs, and many face significant adverse effects, making the accurate selection of patients for ICIs essential to the work of immuno-oncology. Immune biomarkers, such as programmed death-ligand 1, microsatellite instability/defective mismatch repair, and tumor mutational burden have been developed for patient selection and stratification for ICIs, though their predictive abilities remain limited. This is due to several challenges: lack of adequate tissue sampling, the time-consuming and subjective nature of manual visual-based quantification techniques, and the growing recognition of the complexity of the tumor microenvironment, for which these tests cannot fully capture on their own. Meanwhile, emerging technologies in the field of artificial intelligence (AI), such as the performance of deep learning techniques in digital pathology, have garnered significant attention for their potential to be used in this space. Many have now turned their attention towards the immuno-oncology-related applications for digital pathology, particularly in analyzing whole-slide images of widely available H&E-stained slides to aid in immune biomarker detection and ICI response prediction. In this review, we discuss the current landscape of AI-based digital pathology in immuno-oncology, including its applications for identifying and measuring immune biomarkers and, importantly, its potential for predicting ICI response and survival outcomes. We will end by discussing the challenges and future directions of adopting AI technologies for clinical deployment
In vivo prime editing rescues alternating hemiplegia of childhood in mice.
Get PDFAlternating hemiplegia of childhood (AHC) is a neurodevelopmental disorder with no disease-modifying treatment. Mutations in ATP1A3, encoding an Na+/K+ ATPase subunit, cause 70% of AHC cases. Here, we present prime editing (PE) and base editing (BE) strategies to correct ATP1A3 and Atp1a3 mutations in human cells and in two AHC mouse models. We used PE and BE to correct five prevalent ATP1A3 mutations with 43%–90% efficiency. AAV9-mediated in vivo PE corrects Atp1a3 D801N and E815K in the CNS of two AHC mouse models, yielding up to 48% DNA correction and 73% mRNA correction in bulk brain cortex. In vivo PE rescued clinically relevant phenotypes, including restoration of ATPase activity; amelioration of paroxysmal spells, motor defects, and cognition deficits; and dramatic extension of animal lifespan. This work suggests a potential one-time PE treatment for AHC and establishes the ability of PE to rescue a neurological disease in animals
SARM1 Inhibition in Three Mouse Models of Charcot-Marie-Tooth Disease.
No full textBACKGROUND: Charcot-Marie-Tooth (CMT) disease can be caused by mutations in over 100 different genes, most of which lead to demyelination (type 1) or degeneration (type 2) of peripheral motor and sensory axons. SARM1 is a protein involved in the active process of Wallerian degeneration after axonal injury. Inhibition of SARM1 protects against axon degeneration following injury or in cases such as chemotherapy-induced peripheral neuropathy. However, the effects of SARM1 inhibition on axon degeneration in genetic diseases such as CMT are less clear.
AIMS: Here we tested whether SARM1 inhibition may be of benefit in three different mouse models of axonal CMT: Gars
METHODS: For these proof-of-concept studies, mice were treated as neonates with an AAV9 to deliver a dominant negative SARM1 construct (dnSARM1) to the nervous system by intracerebroventricular injection. At ages appropriate for each mouse model, animals were then evaluated with a combination of behavioral, neurophysiological, and histological outcomes.
RESULTS: We reproduced the protective effects of the dnSARM1 construct in positive control experiments following sciatic nerve crush. However, we did not see a change in the phenotypes of any of the CMT mouse models examined. The neuropathy-related phenotypes neither worsened nor improved. Wild-type littermate controls treated with the AAV9 dnSARM1 had minor reductions in body weight and variable changes in motor performance compared to untreated controls, but no deficits by neurophysiology or histology.
INTERPRETATION: Inhibiting SARM1 using a virally delivered dominant negative construct was not efficacious in any of the three mouse models of CMT we tested. These mouse models were chosen for their relevance to the human disease and their prominent axon degeneration, and not for metabolic changes that would suggest SARM1 as a therapeutic target. SARM1 inhibition may remain an option for some forms of CMT, but a method for prescreening CMT subtypes to predict efficacy is needed
Genetic Deletion of Sarm1 in Mouse Models of Three Neurological Diseases.
No full textBACKGROUND: Degeneration of peripheral motor and sensory axons is a key aspect of the pathophysiology of Charcot-Marie-Tooth disease and related inherited neurodegenerative conditions.
AIMS: Given that mutations in many (\u3e 100) genes can cause these disorders, it is unclear if a generalized therapeutic strategy can be identified that will apply across these disease subtypes; however, strategies to prevent or slow axon degeneration are attractive candidates. Wallerian axon degeneration is an active process following insults such as nerve injury, and SARM1 is a central mediator of this process. When SARM1 is inhibited, axons distal to the site of injury persist for weeks rather than degenerating. In addition, SARM1 inhibition or genetic deletion has been shown to provide benefit in acquired neuropathies such as diabetic/metabolic neuropathy and chemotherapy-induced neuropathy in animal models. Here we examined the effects of genetically deleting Sarm1 in mouse models of CMT.
METHODS: We bred knockout mice lacking Sarm1 to three different mouse models of CMT or related disorders. These include mice lacking Gjb1, modeling CMT1X, mice with mutations in Kif1a, modeling hereditary sensory neuropathy IIC and spastic paraplegia type 30, and mice lacking Fig4, modeling CMT4J and Yunis-Varon syndrome. Clinically relevant outcomes measures including survival (Kif1a and Fig4), grip strength and motor behavior, peripheral neurophysiology, molecular biomarkers, and nerve histopathology were assessed for each model with and without Sarm1 expression.
RESULTS: No improvement in the mutant phenotype was found for any model, although elevated levels of circulating neurofilament light chain levels were delayed in the Fig4 mice. Kif1a mice showed deficits slightly earlier in the absence of Sarm1.
INTERPRETATION: While we found no benefit from deleting Sarm1 in these mouse models, they were chosen for their human disease relevance and not for biochemical indicators that SARM1 may be a good target. Thus, SARM1 inhibition may still be effective in other forms of inherited neuropathy, but additional research will be required to identify those candidate subtypes
Using Deep Learning Approaches to Quantify Behavioral Changes in Normal Aging and Alzheimer\u27s Disease Mouse Models
No full textThis study aims to characterize early changes in spontaneous behavior in normal aging mice and the Alzheimer’s Disease (AD) mouse model (App-SAA). By quantifying these changes, we will be able to identify early signs of spontaneous behavior that predict late-stage cognitive decline. Using the open field test (OFT), I quantified the amount of time spent and distance travelled by the mice in predefined regions (e.g., center vs periphery) in an open field arena. These measurements provided insight into the emergence of anxiety-related behavior during normal aging and in AD pathology
Intracranial germ cell tumors: advancement in genomic diagnostics and the need for novel therapeutics.
Get PDFINTRODUCTION: The outcomes for patients with intracranial germ cell tumors (GCT) has improved over the past few decades. However, there remains a lack of a consensus on a standard diagnostic and treatment approach of these tumors. The diagnostic work-up of intracranial GCT remains variable, and the treatment for patients with recurrent disease remains challenging.
METHODS: We review the current approach in the diagnosis and treatment of intracranial GCT. Given the heterogeneity of these tumors, we highlight the challenges and controversy with these conventional approaches.
RESULTS: We discuss the advancements in the understanding of the underlying genetic changes in intracranial GCT and the utility of novel molecular techniques in the diagnosis and classification of intracranial germ cell tumors as well as development of potential novel therapeutics.
DISCUSSION: Development of liquid biopsy platforms for diagnosis and management of malignancies is a rapidly growing field. Current approach utilizing traditional tumor markers have significant limitations. In this review, we will discuss profiling of intracranial GCTs for genetic and epigenetic signatures, which are emerging as promising biomarkers to assist in the diagnosis and management of intracranial GCTs. Various studies have shown that activating mutations in MAPK pathway are common alterations in intracranial GCTs, with KIT expression seen in most germinomas. Development of targeted therapeutics against KIT has led to the prospect of targeted therapy in germinoma. Other treatment modalities being considered for clinical development include immunotherapy and the use of immune checkpoint inhibitors, especially in NGGCT. In this review, we will discuss the potential novel therapeutics and the clinical trials that are currently under development