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Wu Q, Ma L, Joesch-Cohen L, Schmidt M, Uzun EDG, Morrow EM. Targeting NHE6 gene expression identifies lysosome and neurodevelopmental mechanisms in a haploid in vitro cell model. Biol Open 2023; 12:bio059778. [PMID: 37747131 PMCID: PMC10695175 DOI: 10.1242/bio.059778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Christianson syndrome (CS) is an X-linked disorder resulting from loss-of-function (LoF) mutations in SLC9A6 encoding the endosomal Na+/H+ exchanger 6 (NHE6). CS presents with developmental delay, seizures, intellectual disability, nonverbal status, postnatal microcephaly, and ataxia. To define transcriptome signatures of NHE6 LoF, we conducted in-depth RNA-sequencing (RNA-seq) analysis on a haploid NHE6 null cell model. CRIPSR/Cas9 genome editing introduced multiple LoF mutations into SLC9A6 in the near haploid human cell line Hap1. Isogenic, paired parental controls were also studied. NHE6 mutant cell lines were confirmed to have intra-endosomal over-acidification as was seen in other NHE6 null cells. RNA-seq analysis was performed by two widely used pipelines: HISAT2-StringTie-DEseq2 and STAR-HTseq-DEseq2. We identified 1056 differentially expressed genes in mutant NHE6 lines, including genes associated with neurodevelopment, synapse function, voltage-dependent calcium channels, and neuronal signaling. Weighted gene co-expression network analysis was then applied and identified a critical module enriched for genes governing lysosome function. By identifying significantly changed gene expression that is associated with lysosomal mechanisms in NHE6-null cells, our analyses suggest that loss of NHE6 function may converge on mechanisms implicated in lysosome-related neurologic disease. Further, this haploid cell model will serve as an important tool for translational science in CS.
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Affiliation(s)
- Qing Wu
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Center for Computational Molecular Biology, Brown University, Center for Computational Molecular Biology, Providence, RI 02912, USA
| | - Li Ma
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Lena Joesch-Cohen
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Center for Computational Molecular Biology, Brown University, Center for Computational Molecular Biology, Providence, RI 02912, USA
| | - Michael Schmidt
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ece D. Gamsiz Uzun
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Center for Computational Molecular Biology, Brown University, Center for Computational Molecular Biology, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown University, Providence, RI 02912, USA
| | - Eric M. Morrow
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
- Center for Computational Molecular Biology, Brown University, Center for Computational Molecular Biology, Providence, RI 02912, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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Baykara Y, Gamsiz Uzun ED, Jackson C, Kurt H. Exon 19 Deletion in EGFR in a Patient with a High-Grade Glioma: A Case Report. Ann Clin Lab Sci 2023; 53:789-791. [PMID: 37945023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Yigit Baykara
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Ece D Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Cynthia Jackson
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Habibe Kurt
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and The Warren Alpert Medical School of Brown University, Providence, RI, USA
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Leung CS, Rosenzweig SJ, Yoon B, Marinelli NA, Hollingsworth EW, Maguire AM, Cowen MH, Schmidt M, Imitola J, Gamsiz Uzun ED, Lizarraga SB. Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder. Hum Mol Genet 2023; 32:1634-1646. [PMID: 36621967 PMCID: PMC10162432 DOI: 10.1093/hmg/ddad002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Autism spectrum disorder (ASD) affects 1 in 44 children. Chromatin regulatory proteins are overrepresented among genes that contain high risk variants in ASD. Disruption of the chromatin environment leads to widespread dysregulation of gene expression, which is traditionally thought of as a mechanism of disease pathogenesis associated with ASD. Alternatively, alterations in chromatin dynamics could also lead to dysregulation of alternative splicing, which is understudied as a mechanism of ASD pathogenesis. The anticonvulsant valproic acid (VPA) is a well-known environmental risk factor for ASD that acts as a class I histone deacetylase inhibitor. However, the precise molecular mechanisms underlying defects in human neuronal development associated with exposure to VPA are understudied. To dissect how VPA exposure and subsequent chromatin hyperacetylation influence molecular signatures involved in ASD pathogenesis, we conducted RNA sequencing (RNA-seq) in human cortical neurons that were treated with VPA. We observed that differentially expressed genes (DEGs) were enriched for mRNA splicing, mRNA processing, histone modification and metabolism related gene sets. Furthermore, we observed widespread increases in the number and the type of alternative splicing events. Analysis of differential transcript usage (DTU) showed that exposure to VPA induces extensive alterations in transcript isoform usage across neurodevelopmentally important genes. Finally, we find that DEGs and genes that display DTU overlap with known ASD-risk genes. Altogether, these findings suggest that, in addition to differential gene expression, changes in alternative splicing correlated with alterations in the chromatin environment could act as an additional mechanism of disease in ASD.
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Affiliation(s)
- Calvin S Leung
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Shoshana J Rosenzweig
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Brian Yoon
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Nicholas A Marinelli
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Ethan W Hollingsworth
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Abbie M Maguire
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Mara H Cowen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Jaime Imitola
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
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Hacking SM, Karam J, Singh K, Gamsiz Uzun ED, Brickman A, Yakirevich E, Taliano R, Wang Y. Whole slide image features predict pathologic complete response and poor clinical outcomes in triple-negative breast cancer. Pathol Res Pract 2023; 246:154476. [PMID: 37146413 DOI: 10.1016/j.prp.2023.154476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023]
Abstract
INTRODUCTION Breast cancers are complex ecosystem like networks of malignant cells and their associated microenvironment. Applications for machine intelligence and the tumoral microenvironment are expanding frontiers in pathology. Previously, computational approaches have been developed to quantify and spatially analyze immune cells, proportionate stroma, and detect tumor budding. Little work has been done to analyze different types of tumor-associated stromata both quantitatively and computationally in relation to clinical endpoints. METHODS We aimed to quantify stromal features from whole slide images (WSI) including stromata (myxoid, collagenous, immune) and tumoral components and combined them with traditional clinical and pathologic parameters in 120 triple-negative breast cancer (TNBC) patients treated with neoadjuvant chemotherapy (NAC) to predict pathologic complete response (pCR) and poor clinical outcomes. RESULTS High collagenous stroma on WSI was best associated with lower rates of pCR, while combined high proportionated stroma (myxoid, collagenous, and immune) most optimally predicted worse clinical survival outcomes. When combining clinical, pathologic, and WSI features, Receiver Operator Characteristics (ROC) curves for LASSO features was up to 0.67 for pCR and 0.77 for poor outcomes. CONCLUSION The techniques demonstrated in the present study can be performed with appropriate quality assurance. Future trials are needed to demonstrate whether coupling applications for machine intelligence, inclusive of the tumor mesenchyme, can improve outcomes prediction for patients with breast cancer.
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Affiliation(s)
- Sean M Hacking
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Julie Karam
- Center for Computational Molecular Biology, Brown University, Providence, RI, United States
| | - Kamaljeet Singh
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Women and Infants Hospital, Providence, RI, United States
| | - Ece D Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States; Center for Computational Molecular Biology, Brown University, Providence, RI, United States
| | - Arlen Brickman
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Evgeny Yakirevich
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Ross Taliano
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States.
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De Souza AL, Mega AE, Douglass J, Olszewski AJ, Gamsiz Uzun ED, Uzun A, Chou C, Duan F, Wang J, Ali A, Golijanin DJ, Holder SL, Lagos GG, Safran H, El-Deiry WS, Carneiro BA. Clinical features of patients with MTAP-deleted bladder cancer. Am J Cancer Res 2023; 13:326-339. [PMID: 36777505 PMCID: PMC9906077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/03/2023] [Indexed: 02/14/2023] Open
Abstract
Advanced urothelial carcinoma continues to have a dismal prognosis despite several new therapies in the last 5 years. FGFR2 and FGFR3 mutations and fusions, PD-L1 expression, tumor mutational burden, and microsatellite instability are established predictive biomarkers in advanced urothelial carcinoma. Novel biomarkers can optimize the sequencing of available treatments and improve outcomes. We describe herein the clinical and pathologic features of patients with an emerging subtype of bladder cancer characterized by deletion of the gene MTAP encoding the enzyme S-Methyl-5'-thioadenosine phosphatase, a potential biomarker of response to pemetrexed. We performed a retrospective analysis of 61 patients with advanced urothelial carcinoma for whom demographics, pathologic specimens, next generation sequencing, and clinical outcomes were available. We compared the frequency of histology variants, upper tract location, pathogenic gene variants, tumor response, progression free survival (PFS) and overall survival (OS) between patients with tumors harboring MTAP deletion (MTAP-del) and wild type tumors (MTAP-WT). A propensity score matching of 5 covariates (age, gender, presence of variant histology, prior surgery, and prior non-muscle invasive bladder cancer) was calculated to compensate for disparity when comparing survival in these subgroups. Non-supervised clustering analysis of differentially expressed genes between MTAP-del and MTAP-WT urothelial carcinomas was performed. MTAP-del occurred in 19 patients (31%). Tumors with MTAP-del were characterized by higher prevalence of squamous differentiation (47.4 vs 11.9%), bone metastases (52.6 vs 23.5%) and lower frequency of upper urinary tract location (5.2% vs 26.1%). Pathway gene set enrichment analysis showed that among the genes upregulated in the MTAP-del cohort, at least 5 were linked to keratinization (FOXN1, KRT33A/B, KRT84, RPTN) possibly contributing to the higher prevalence of squamous differentiation. Alterations in the PIK3 and MAPK pathways were more frequent when MTAP was deleted. There was a trend to inferior response to chemotherapy among MTAP-del tumors, but no difference in the response to immune checkpoint inhibitors or enfortumab. Median progression free survival after first line therapy (PFS1) was 5.5 months for patients with MTAP-WT and 4.5 months for patients with MTAP-del (HR = 1.30; 95% CI, 0.64-2.63; P = 0.471). There was no difference in the time from metastatic diagnosis to death (P = 0.6346). Median OS from diagnosis of localized or de novo metastatic disease was 16 months (range 1.5-60, IQR 8-26) for patients with MTAP-del and 24.5 months (range 3-156, IQR 16-48) for patients with MTAP-WT (P = 0.0218), suggesting that time to progression to metastatic disease is shorter in MTAP-del patients. Covariates did not impact significantly overall survival on propensity score matching. In conclusion, MTAP -del occurs in approximately 30% of patients with advanced urothelial carcinoma and defines a subgroup of patients with aggressive features, such as squamous differentiation, frequent bone metastases, poor response to chemotherapy, and shorter time to progression to metastatic disease.
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Affiliation(s)
- Andre L De Souza
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - Anthony E Mega
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - John Douglass
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - Adam J Olszewski
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - Ece D Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical CenterProvidence, RI, United States
| | - Alper Uzun
- Center for Computational Molecular Biology, Brown UniversityProvidence RI, United States,Department of Pediatrics, The Warren Alpert Medical School, Brown UniversityProvidence, RI, United States
| | - Charissa Chou
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical CenterProvidence, RI, United States
| | - Fenghai Duan
- Department of Biostatistics and Center for Statistical Sciences, Brown University School of Public HealthProvidence, RI, United States
| | - Jinyu Wang
- Data Science Initiative, Brown UniversityProvidence, RI, United States
| | - Amin Ali
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical CenterProvidence, RI, United States
| | - Dragan J Golijanin
- Urology Department, Minimally Invasive Urology Institute, The Miriam Hospital, The Warren Alpert Medical School of Brown UniversityProvidence, RI, United States
| | - Sheldon L Holder
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States,Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical CenterProvidence, RI, United States
| | - Galina G Lagos
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - Howard Safran
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
| | - Wafik S El-Deiry
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States,Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical CenterProvidence, RI, United States
| | - Benedito A Carneiro
- Division of Hematology Oncology, Legorreta Cancer Center at Brown University, Lifespan Cancer InstituteProvidence RI, United States
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Lai J, Yang J, Gamsiz Uzun ED, Rubenstein BM, Sarkar IN. LYRUS: a machine learning model for predicting the pathogenicity of missense variants. Bioinform Adv 2021; 2:vbab045. [PMID: 35036922 PMCID: PMC8754197 DOI: 10.1093/bioadv/vbab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/08/2021] [Accepted: 12/21/2021] [Indexed: 01/27/2023]
Abstract
SUMMARY Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information. This study presents 〈Lai Yang Rubenstein Uzun Sarkar〉 (LYRUS), a machine learning method that uses an XGBoost classifier to predict the pathogenicity of SAVs. LYRUS incorporates five sequence-based, six structure-based and four dynamics-based features. Uniquely, LYRUS includes a newly proposed sequence co-evolution feature called the variation number. LYRUS was trained using a dataset that contains 4363 protein structures corresponding to 22 639 SAVs from the ClinVar database, and tested using the VariBench testing dataset. Performance analysis showed that LYRUS achieved comparable performance to current variant effect predictors. LYRUS's performance was also benchmarked against six Deep Mutational Scanning datasets for PTEN and TP53. AVAILABILITY AND IMPLEMENTATION LYRUS is freely available and the source code can be found at https://github.com/jiaying2508/LYRUS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Jiaying Lai
- Center for Biomedical Informatics, Brown University, Providence, RI 02903, USA,Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Jordan Yang
- Department of Chemistry, Brown University, Providence, RI 02906, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA,Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA,Department of Pathology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Brenda M Rubenstein
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA,Department of Chemistry, Brown University, Providence, RI 02906, USA,To whom correspondence should be addressed. and
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence, RI 02903, USA,Rhode Island Quality Institute, Providence, RI 02908, USA,To whom correspondence should be addressed. and
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Lizarraga SB, Ma L, Maguire AM, van Dyck LI, Wu Q, Ouyang Q, Kavanaugh BC, Nagda D, Livi LL, Pescosolido MF, Schmidt M, Alabi S, Cowen MH, Brito-Vargas P, Hoffman-Kim D, Gamsiz Uzun ED, Schlessinger A, Jones RN, Morrow EM. Human neurons from Christianson syndrome iPSCs reveal mutation-specific responses to rescue strategies. Sci Transl Med 2021; 13:13/580/eaaw0682. [PMID: 33568516 DOI: 10.1126/scitranslmed.aaw0682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Christianson syndrome (CS), an X-linked neurological disorder characterized by postnatal attenuation of brain growth (postnatal microcephaly), is caused by mutations in SLC9A6, the gene encoding endosomal Na+/H+ exchanger 6 (NHE6). To hasten treatment development, we established induced pluripotent stem cell (iPSC) lines from patients with CS representing a mutational spectrum, as well as biologically related and isogenic control lines. We demonstrated that pathogenic mutations lead to loss of protein function by a variety of mechanisms: The majority of mutations caused loss of mRNA due to nonsense-mediated mRNA decay; however, a recurrent, missense mutation (the G383D mutation) had both loss-of-function and dominant-negative activities. Regardless of mutation, all patient-derived neurons demonstrated reduced neurite growth and arborization, likely underlying diminished postnatal brain growth in patients. Phenotype rescue strategies showed mutation-specific responses: A gene transfer strategy was effective in nonsense mutations, but not in the G383D mutation, wherein residual protein appeared to interfere with rescue. In contrast, application of exogenous trophic factors (BDNF or IGF-1) rescued arborization phenotypes across all mutations. These results may guide treatment development in CS, including gene therapy strategies wherein our data suggest that response to treatment may be dictated by the class of mutation.
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Affiliation(s)
- Sofia B Lizarraga
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Li Ma
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Abbie M Maguire
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA
| | - Laura I van Dyck
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Qing Wu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Qing Ouyang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Brian C Kavanaugh
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Dipal Nagda
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Liane L Livi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Matthew F Pescosolido
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Shanique Alabi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mara H Cowen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Paul Brito-Vargas
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Diane Hoffman-Kim
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA.,Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA.,Center for Biomedical Engineering, Brown University, Providence, RI 02912, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard N Jones
- Quantitative Sciences Program, Department of Psychiatry and Human Behavior and Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA. .,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
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Howard M, Kane B, Lepry M, Stey P, Ragavendran A, Gamsiz Uzun ED. VarStack: a web tool for data retrieval to interpret somatic variants in cancer. Database (Oxford) 2020; 2020:6008711. [PMID: 33247936 PMCID: PMC7698661 DOI: 10.1093/database/baaa092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/15/2020] [Accepted: 10/14/2020] [Indexed: 11/24/2022]
Abstract
Advances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer, gnomAD, cBioPortal, ClinVar, OncoKB, CiViC and UCSC Genome Browser. It retrieves the data from these databases and returns them back to the user in a fraction of the time it would take to manually navigate each site independently. Users submit a variant with a gene symbol, peptide change and coding sequence change. They may select a variety of tumor-specific studies in cBioPortal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as an Excel file. VarStack also has the batch search feature in which the user can submit a list of variants and download an Excel file with the data from the databases. With the batch search and data download options, users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing somatic variant information to the user from multiple databases in an easy-to-export and interpretable format. VarStack is freely available under https://varstack.brown.edu.
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Affiliation(s)
- Morgan Howard
- Rhode Island Hospital Department of Pathology, Providence, RI 02903, USA
| | - Bruce Kane
- Computing and Information Services, Brown University, Providence, RI 02912, USA
| | - Mary Lepry
- Computing and Information Services, Brown University, Providence, RI 02912, USA
| | - Paul Stey
- Brown University, Providence, RI, 02906, USA
| | - Ashok Ragavendran
- Brown University, Providence, RI, 02906, USA.,Center for Computational Biology of Human Disease, Brown University, Providence, RI 02912, USA
| | - Ece D Gamsiz Uzun
- Rhode Island Hospital Department of Pathology, Providence, RI 02903, USA.,Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
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9
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McCormick CEB, Kavanaugh BC, Sipsock D, Righi G, Oberman LM, Moreno De Luca D, Gamsiz Uzun ED, Best CR, Jerskey BA, Quinn JG, Jewel SB, Wu PC, McLean RL, Levine TP, Tokadjian H, Perkins KA, Clarke EB, Dunn B, Gerber AH, Tenenbaum EJ, Anders TF, Sheinkopf SJ, Morrow EM. Autism Heterogeneity in a Densely Sampled U.S. Population: Results From the First 1,000 Participants in the RI-CART Study. Autism Res 2020; 13:474-488. [PMID: 31957984 DOI: 10.1002/aur.2261] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 01/25/2023]
Abstract
The objective of this study was to establish a large, densely sampled, U.S. population-based cohort of people with autism spectrum disorder (ASD). The Rhode Island Consortium for Autism Research and Treatment (RI-CART) represents a unique public-private-academic collaboration involving all major points of service for families in Rhode Island affected by ASD. Diagnosis was based on direct behavioral observation via the Autism Diagnostic Observation Schedule, Second Edition. For the first 1,000 participants, ages ranged from 21 months to 64 years. Using Geographic Information System and published prevalence rates, the overall cohort is estimated to represent between 20% and 49% of pediatric age persons in Rhode Island with ASD, with demographics representative of U.S. Census. We observed a high rate of co-occurring medical and psychiatric conditions in affected individuals. Among the most prominent findings of immediate clinical importance, we found that females received a first diagnosis of ASD at a later age than males, potentially due to more advanced language abilities in females with ASD. In summary, this is the first analysis of a large, population-based U.S. cohort with ASD. Given the depth of sampling, the RI-CART study reflects an important new resource for studying ASD in a representative U.S. population. Psychiatric and medical comorbidities in ASD constitute a substantial burden and warrant adequate attention as part of overall treatment. Our study also suggests that new strategies for earlier diagnosis of ASD in females may be warranted. Autism Res 2020, 13: 474-488. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: The Rhode Island Consortium for Autism Research and Treatment (RI-CART) represents a unique public-private-academic collaboration involving all major points of service for families in Rhode Island affected by autism spectrum disorder (ASD). In this article, we provide results from the first 1,000 participants, estimated to represent >20% of affected families in the state. Importantly, we find a later age at first diagnosis of ASD in females, which potentially calls attention to the need for improved early diagnosis in girls. Also, we report a high rate of co-occurring medical and psychiatric conditions in affected individuals.
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Affiliation(s)
- Carolyn E B McCormick
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Brian C Kavanaugh
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island
| | - Danielle Sipsock
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Giulia Righi
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island
| | - Lindsay M Oberman
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Daniel Moreno De Luca
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island
| | - Ece D Gamsiz Uzun
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown University, Providence, Rhode Island.,Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Carrie R Best
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island
| | - Beth A Jerskey
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | | | | | - Pei-Chi Wu
- Department of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island.,Rhode Island Hospital/Hasbro Children's Hospital, Providence, Rhode Island
| | - Rebecca L McLean
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Todd P Levine
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Brown Center for the Study of Children at Risk, Women & Infants Hospital, Providence, Rhode Island
| | - Hasmik Tokadjian
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Brown Center for the Study of Children at Risk, Women & Infants Hospital, Providence, Rhode Island
| | - Kayla A Perkins
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Elaine B Clarke
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island
| | - Brittany Dunn
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Alan H Gerber
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Elena J Tenenbaum
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Brown Center for the Study of Children at Risk, Women & Infants Hospital, Providence, Rhode Island
| | - Thomas F Anders
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island
| | | | - Stephen J Sheinkopf
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island.,Department of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island.,Brown Center for the Study of Children at Risk, Women & Infants Hospital, Providence, Rhode Island
| | - Eric M Morrow
- Emma Pendleton Bradley Hospital, East Providence, Rhode Island.,Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, Rhode Island.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, Rhode Island
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