Browsing by Subject "Genetic mutations"

Now showing 1 - 7 of 7
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    Current Status of Genetics and Polygenic Risk Scores in Metabolic Dysfunction-Associated Steatohepatitis
    (Millennium Medical, 2024) Chalasani, Naga; Medicine, School of Medicine
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    Inherited Human XY Sex Reversal and Gonadal Neoplasia Due to Enhanced Formation of Non-Specific Enhanceosomes by an Architectural Transcription Factor
    (Endocrine Society, 2021-05-03) Chen, Yen-Shan; Racca, Joseph D.; Belgorosky, Alicia; Weiss, Michael Aaron; Biochemistry and Molecular Biology, School of Medicine
    The development of organisms is regulated by a fine-tuned gene-regulatory network, which is driven by transcription factors (TFs). In the embryogenesis, these TFs control diverse cell fates and final body plan. This is precisely regulated by a specific DNA-binding process and enhanceosome formation. A model is provided by testis determination in mammals, which is initiated by a Y-encoded architectural transcription factor, SRY. Mutations in SRY cause gonadal dysgenesis leading to various developmental defects. Such mutations cluster in SRY’s high mobility group (HMG) box, a sequence-specific DNA-binding domain shared by a conserved family of TFs. Here, we have characterized several mutations at the same position in HMG box, which are compatible with either male or female phenotypes as observed in an XY father and XY daughter, respectively. These mutations, at a function-unknown motif in the SRY HMG box, markedly disturb the specific DNA affinity. On transient transfection of human and rodent cell lines, the SRY variants exhibit decreased specific DNA-binding activity (relative to wild type) are associated with mis-formed enhanceosomes. The variants’ gene regulatory activities were reduced by 2-fold relative to wild-type SRY at similar levels of mRNA expression. When engineered mutations that functions to increase the DNA-binding specificity were deployed to SRY variants, the transcriptional activity was in association with restored occupancy of sex-specific enhancer elements in principal downstream gene Sox9. Our findings define a novel mechanism of impaired organogenesis, disturbed specific DNA-binding activity of a master transcription factor, leading to a developmental decision poised at the edge of ambiguity.
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    Reduced Efficacy of Glucagon-Like Peptide-1 Receptor Agonists Therapy in People With Type 1 Diabetes and Genetic Forms of Obesity
    (Sage, 2024-04-17) Klein, Matthew P.; Akturk, Halis Kaan; Snell-Bergeon, Janet K.; Shah, Viral N.; Medicine, School of Medicine
    Background: Once weekly Glucagon-Like Peptide-1 Receptor Agonists (GLP-1 RA) have been shown to improve glycemic outcomes and cause significant weight loss. However, 9% to 27% of individuals have little or no response to these drugs. In this article, we investigated the efficacy of GLP-1 RA therapy among adults with type 1 diabetes and obesity likely related to genetic mutations compared with obesity likely unrelated to genetic mutations. Methods: In this retrospective study, we compared body weight and glycated hemoglobin (HbA1c) change with the use of GLP-1 RA therapy (including a dual agonist, Tirzepatide) over six months among adults with type 1 diabetes and obesity likely (n = 11, median age 39.5 years with a median BMI of 43.0 kg/m2) versus unlikely related to genetic mutation(s) (n = 15, median age 45.8 years with a median BMI of 38.7 kg/m2). Results: Six months of GLP-1 RA treatment resulted in a numerically lower reduction of weight (-5.75 ± 9.46 kg vs -8.65 ± 9.36 kg, P = .44) and HbA1c (-0.28 ± 0.96% vs -0.43 ± 0.57%, P = .64) among individuals with obesity likely versus unlikely related to a genetic mutation(s), respectively. Fewer individuals with genetic obesity met goal weight loss ≥5% or HbA1c decrease ≥0.4% than did individuals with obesity unlikely related to a genetic cause (36.4% vs 80.0%, P = .04). Conclusions: The weight loss and glycemic lowering effects of GLP-1 RA therapy may be decreased in people with type 1 diabetes and obesity likely related to genetic causes. Further research is needed to understand GLP-1 RA mechanisms via energy regulating genes.
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    Single-Cell Profiling Reveals the Impact of Genetic Alterations on the Differentiation of Inflammation-Induced Murine Colon Tumors
    (MDPI, 2024-05-28) Ghobashi, Ahmed H.; Lanzloth, Rosie; Ladaika, Christopher A.; Masood, Ashiq; O’Hagan, Heather M.; Medicine, School of Medicine
    Genetic mutations and chronic inflammation of the colon contribute to the development of colorectal cancer (CRC). Using a murine model of inflammation-induced colon tumorigenesis, we determined how genetic mutations alter colon tumor cell differentiation. Inflammation induced by enterotoxigenic Bacteroides fragilis (ETBF) colonization of multiple intestinal neoplasia (MinApcΔ716/+) mice triggers loss of heterozygosity of Apc causing colon tumor formation. Here, we report that the addition of BRAFV600E mutation (BRAFF-V600ELgr5tm1(Cre/ERT2)CleMinApcΔ716/+, BLM) or knocking out Msh2 (Msh2LoxP/LoxPVil1-creMinApcΔ716/+, MSH2KO) in the Min model altered colon tumor differentiation. Using single-cell RNA sequencing, we uncovered the differences between BLM, Min, and MSH2KO tumors at a single-cell resolution. BLM tumors showed an increase in differentiated tumor epithelial cell lineages and a reduction in the tumor stem cell population. Interestingly, the tumor stem cell population of BLM tumors had revival colon stem cell characteristics with low WNT signaling and an increase in RevCSC marker gene expression. In contrast, MSH2KO tumors were characterized by an increased tumor stem cell population that had higher WNT signaling activity compared to Min tumors. Furthermore, overall BLM tumors had higher expression of transcription factors that drive differentiation, such as Cdx2, than Min tumors. Using RNA velocity, we identified additional potential regulators of BLM tumor differentiation such as NDRG1. The role of CDX2 and NDRG1 as putative regulators for BLM tumor cell differentiation was verified using organoids derived from BLM tumors. Our results demonstrate the critical connections between genetic mutations and cell differentiation in inflammation-induced colon tumorigenesis. Understanding such roles will deepen our understanding of inflammation-associated colon cancer.
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    The radiogenomic and spatiogenomic landscapes of glioblastoma and their relationship to oncogenic drivers
    (Springer Nature, 2025-03-01) Fathi Kazerooni, Anahita; Akbari, Hamed; Hu, Xiaoju; Bommineni, Vikas; Grigoriadis, Dimitris; Toorens, Erik; Sako, Chiharu; Mamourian, Elizabeth; Ballinger, Dominique; Sussman, Robyn; Singh, Ashish; Verginadis, Ioannis I.; Dahmane, Nadia; Koumenis, Constantinos; Binder, Zev A.; Bagley, Stephen J.; Mohan, Suyash; Hatzigeorgiou, Artemis; O'Rourke, Donald M.; Ganguly, Tapan; De, Subhajyoti; Bakas, Spyridon; Nasrallah, MacLean P.; Davatzikos, Christos; Pathology and Laboratory Medicine, School of Medicine
    Background: Glioblastoma is a highly heterogeneous brain tumor, posing challenges for precision therapies and patient stratification in clinical trials. Understanding how genetic mutations influence tumor imaging may improve patient management and treatment outcomes. This study investigates the relationship between imaging features, spatial patterns of tumor location, and genetic alterations in IDH-wildtype glioblastoma, as well as the likely sequence of mutational events. Methods: We conducted a retrospective analysis of 357 IDH-wildtype glioblastomas with pre-operative multiparametric MRI and targeted genetic sequencing data. Radiogenomic signatures and spatial distribution maps were generated for key mutations in genes such as EGFR, PTEN, TP53, and NF1 and their corresponding pathways. Machine and deep learning models were used to identify imaging biomarkers and stratify tumors based on their genetic profiles and molecular heterogeneity. Results: Here, we show that glioblastoma mutations produce distinctive imaging signatures, which are more pronounced in tumors with less molecular heterogeneity. These signatures provide insights into how mutations affect tumor characteristics such as neovascularization, cell density, invasion, and vascular leakage. We also found that tumor location and spatial distribution correlate with genetic profiles, revealing associations between tumor regions and specific oncogenic drivers. Additionally, imaging features reflect the cross-sectionally inferred evolutionary trajectories of glioblastomas. Conclusions: This study establishes clinically accessible imaging biomarkers that capture the molecular composition and oncogenic drivers of glioblastoma. These findings have potential implications for noninvasive tumor profiling, personalized therapies, and improved patient stratification in clinical trials.
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    The Role of the Surgeon in the Germline Testing of the Newly Diagnosed Breast Cancer Patient
    (MDPI, 2023-05-01) Schick, Stephanie; Manghelli, Joshua; Ludwig, Kandice K.; Surgery, School of Medicine
    For patients with newly diagnosed breast cancer, information regarding hereditary predisposition can influence treatment decisions. From a surgical standpoint, patients with known germline mutations may alter decisions of local therapy to reduce the risk of second breast primaries. This information may also be considered in the choice of adjuvant therapies or eligibility for clinical trials. In recent years, the criteria for the consideration of germline testing in patients with breast cancer has expanded. Additionally, studies have shown a similar prevalence of pathogenic mutations in those patients outside of these traditional criteria, prompting calls for genetic testing for all patients with a history of breast cancer. While data confirms the benefit of counseling by certified genetics professionals, the capacity of genetic counselors may no longer meet the needs of these growing numbers of patients. National societies assert that counseling and testing can be performed by providers with training and experience in genetics. Breast surgeons are well positioned to offer this service, as they receive formal genetics training during their fellowship, manage these patients daily in their practices, and are often the first providers to see patients after their cancer diagnosis.
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    Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease
    (The American Society for Cell Biology, 2016-11-07) Belmonte, Julio M.; Clendenon, Sherry G.; Oliveira, Guilherme M.; Swat, Maciej H.; Greene, Evan V.; Jeyaraman, Srividhya; Glazier, James A.; Bacallao, Robert L.; Department of Medicine, IU School of Medicine
    In autosomal dominant polycystic kidney disease (ADPKD), cysts accumulate and progressively impair renal function. Mutations in PKD1 and PKD2 genes are causally linked to ADPKD, but how these mutations drive cell behaviors that underlie ADPKD pathogenesis is unknown. Human ADPKD cysts frequently express cadherin-8 (cad8), and expression of cad8 ectopically in vitro suffices to initiate cystogenesis. To explore cell behavioral mechanisms of cad8-driven cyst initiation, we developed a virtual-tissue computer model. Our simulations predicted that either reduced cell-cell adhesion or reduced contact inhibition of proliferation triggers cyst induction. To reproduce the full range of cyst morphologies observed in vivo, changes in both cell adhesion and proliferation are required. However, only loss-of-adhesion simulations produced morphologies matching in vitro cad8-induced cysts. Conversely, the saccular cysts described by others arise predominantly by decreased contact inhibition, that is, increased proliferation. In vitro experiments confirmed that cell-cell adhesion was reduced and proliferation was increased by ectopic cad8 expression. We conclude that adhesion loss due to cadherin type switching in ADPKD suffices to drive cystogenesis. Thus, control of cadherin type switching provides a new target for therapeutic intervention.