Digital Commons Network^™

Computational Analysis Of Dna Methylation From Long-Read Sequencing, Yilei Fu, Winston Timp, Fritz J Sedlazeck

Faculty, Staff and Students Publications

DNA methylation is a critical epigenetic mechanism in numerous biological processes, including gene regulation, development, ageing and the onset of various diseases such as cancer. Studies of methylation are increasingly using single-molecule long-read sequencing technologies to simultaneously measure epigenetic states such as DNA methylation with genomic variation. These long-read data sets have spurred the continuous development of advanced computational methods to gain insights into the roles of methylation in regulating chromatin structure and gene regulation. In this Review, we discuss the computational methods for calling methylation signals, contrasting methylation between samples, analysing cell-type diversity and gaining additional genomic insights, and …

Cmr Findings In The Long-Term Outcomes After Multisystem Inflammatory Syndrome In Children (Music) Study, Sean M Lang, Dongngan T Truong, Andrew J Powell, Valiantsina Kazlova, Jane W Newburger, Jordan D Awerbach, Edem Binka, Tamara T Bradford, Mark Cartoski, Andrew Cheng, Michael P Dilorenzo, Audrey Dionne, Adam L Dorfman, Matthew D Elias, Olukayode Garuba, Jennifer F Gerardin, Keren Hasbani, Pei-Ni Jone, Christopher Z Lam, Nilanjana Misra, Lerraughn M Morgan, Arni Nutting, Jyoti K Patel, Joshua D Robinson, Eleanor L Schuchardt, Kristen Sexson Tejtel, Gautam K Singh, Timothy C Slesnick, Felicia Trachtenberg, Michael D Taylor, Music Study Investigators

Faculty, Staff and Students Publications

Background: Multisystem Inflammatory Syndrome in Children is characterized by high rates of acute cardiovascular involvement with rapid recovery of organ dysfunction. However, information regarding long-term sequelae is lacking. We sought to characterize the systolic function and myocardial tissue properties using cardiac magnetic resonance (CMR) imaging in a multicenter observational cohort of patients with Multisystem Inflammatory Syndrome in Children.

Methods: In this observational cohort study, comprising 32 centers in North America, CMR studies were analyzed by a core laboratory to assess ventricular volumetric data, tissue characterization, and coronary involvement.

Results: A total of 263 CMRs from 255 patients with Multisystem Inflammatory …

Eugenics And Polygenic Embryo Screening: Public, Clinician, And Patient Perceptions Of Conditions Versus Traits, Dorit Barlevy, Rémy A Furrer, Asha Kalapatapu, Abigail Martinez, Todd Lencz, Shai Carmi, Gabriel Lázaro-Muñoz, Stacey Pereira

Center for Medical Ethics and Health Policy Staff Publications

Purpose: Polygenic embryo screening (PES) estimates an embryo's genetic chances of developing complex conditions (eg, cancer) and traits (eg, height). Stakeholders have raised concerns that PES promotes eugenic practices and ideology.

Methods: We surveyed a nationally representative sample of the US public on approval of screening embryos for 12 conditions and 12 traits and examined the association between disapproval and concern about eugenics. We also conducted semistructured interviews with US-based reproductive endocrinology and infertility specialists and patients undergoing in vitro fertilization on their perspectives toward PES.

Results: Among the US public (n = 1423), disapproval of screening embryos for traits …

Coenzyme Q Headgroup Intermediates Can Ameliorate A Mitochondrial Encephalopathy, Guangbin Shi, Claire Miller, Sota Kuno, Alejandro G Rey Hipolito, Salsabiel El Nagar, Giulietta M Riboldi, Megan Korn, Wyatt C Tran, Zixuan Wang, Lia Ficaro, Tao Lin, Quentin Spillier, Begoña Gamallo-Lana, Drew R Jones, Matija Snuderl, Soomin C Song, Adam C Mar, Alexandra L Joyner, Roy V Sillitoe, Robert S Banh, Michael E Pacold

Duncan NRI Faculty and Staff Publications

Decreased brain levels of coenzyme Q10 (CoQ10), an endogenously synthesized lipophilic antioxidant1,2, underpin encephalopathy in primary CoQ10 deficiencies3,4 and are associated with common neurodegenerative diseases and the ageing process5,6. CoQ10 supplementation does not increase CoQ10 pools in the brain or in other tissues. The recent discovery of the mammalian CoQ10 headgroup synthesis pathway, in which 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL) makes 4-hydroxymandelate (4-HMA) to synthesize the CoQ10 headgroup precursor 4-hydroxybenzoate (4-HB)7, offers an opportunity to pharmacologically restore CoQ10 synthesis and mechanistically treat CoQ10 deficiencies. To test whether 4-HMA …

Heightened Risk: Childhood Trauma And Anticipatory Grief Exacerbate The Impact Of Loneliness On Depressive Symptoms And Lps-Stimulated Cytokines In Dementia Caregivers, Kelly N Brice, Jensine Paoletti-Hatcher, E Lydia Wu-Chung, Vincent D Lai, Daniel L Argueta, Michelle A Chen, Itee Mahant, Bryan T Denny, Charles Green, Luis D Medina, Paul Schulz, Jennifer Stinson, Samantha K Henry, Cobi Heijnen, Christopher P Fagundes

Faculty, Staff and Student Publications

Dementia spousal caregivers are at a disproportionate risk for adverse mental and physical health outcomes. Loneliness is associated with depressive symptoms and proinflammatory cytokine production among caregivers. Additionally, childhood trauma, anticipatory grief, and poor sleep quality are all associated with enhanced stress reactivity. This study used a cross-sectional design to investigate whether loneliness is associated with proinflammatory cytokine production and depressive symptoms in caregivers, and whether these relationships are strongest among caregivers who report high levels of childhood trauma, high amounts of anticipatory grief, or poor sleep quality. A sample of 111 dementia spousal caregivers provided blood samples and completed …

Acad10 And Acad11 Enable Mammalian 4-Hydroxy Acid Lipid Catabolism, Edrees H Rashan, Abigail K Bartlett, Jingying Zhang, Andrew J Smith, Zakery N Baker, Patrick Forny, Peng Yuan, David J Pagliarini, Et Al.

2020-Current year OA Pubs

Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation machinery before being modified. Here we reveal that two atypical acyl-CoA dehydrogenases, ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains that phosphorylate the 4-hydroxy position as a requisite step in converting 4-hydroxyacyl-CoAs into conventional 2-enoyl-CoAs. Through cryo-electron microscopy and molecular modeling, we identified an atypical dehydrogenase binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain …

Association Between Chd And Cerebral Abscess: Insights From A National Database., Keats Ewing, Rohit Seath Loomba, Saul Flores, Enrique G. Villarreal, Juan S. Farias, Matthew Taylor Coghill

Manuscripts, Articles, Book Chapters and Other Papers

CHD has been historically associated with the development of cerebral abscess. This retrospective cohort study examines the association of CHD with the occurrence of cerebral abscess in an inpatient paediatric population. We analysed data from the Pediatric Health Information System database, an administrative database that captures data from participating children's hospitals in the United States. We included all patients admitted to participating paediatric ICUs between 2016 and 2021 for a total of 426,029 admissions. Including all admissions, 1,387 (0.3%) patients experienced a cerebral abscess, and of 80,927 (19%) patients with CHD, only 88 (0.1%) experienced a cerebral abscess (odds ratio …

Phenotypic Divergence Of Jag1- And Notch2-Associated Alagille Syndrome & Disease-Specific Notch2 Variant Classification Guidelines., Shannon M. Vandriel, Li-Ting Li, Huiyu She, Jian-She Wang, Kathleen M. Loomes, David A. Piccoli, Irena Jankowska, Piotr Czubkowski, Dorota Gliwicz-Miedzińska, Lorenzo D'Antiga, Emanuele Nicastro, Florence Lacaille, Dominique Debray, Étienne M. Sokal, Tanguy Demaret, Rima L. Fawaz, Silvia Nastasio, Kyung Mo Kim, Seak Hee Oh, Björn Fischler, Henrik Arnell, Catherine Larson-Nath, Winita Hardikar, Sahana Shankar, Shikha S. Sundaram, Alexander Chaidez, Pinar Bulut, Pier Luigi Calvo, Mureo Kasahara, Niviann Blondet, Eberhard Lurz, Anna-Maria Kavallar, Emmanuel M. Gonzales, Emmanuel Jacquemin, Jérôme Bouligand, Noelle H. Ebel, Jeffrey A. Feinstein, Susan M. Siew, Michael O. Stormon, Saul J. Karpen, Rene Romero, M Kyle Jensen, Catalina Jaramillo, James E. Squires, Sarah M. Bedoyan, Deirdre A. Kelly, Jane Hartley, Henkjan J. Verkade, Way Seah Lee, Chatmanee Lertudomphonwanit, Ryan T. Fischer, Henry C. Lin, Nathalie Rock, Yael Mozer-Glassberg, Amin J. Roberts, Helen M. Evans, Wikrom Karnsakul, Gabriella Nebbia, Victorien M. Wolters, Pamela L. Valentino, Jesus Quintero Bernabeu, Amal A. Aqul, Cigdem Arikan, María Legarda Tamara, Cristina Molera Busoms, Thomas Damgaard Sandahl, Giuseppe Indolfi, Andréanne N. Zizzo, Aglaia Zellos, Ruben E. Quiros-Tejeira, Ermelinda Santos-Silva, Kathleen B. Schwarz, Jernej Brecelj, Maria Camila Sanchez, Maria Lorena Cavalieri, Christos Tzivinikos, Sabina Wiecek, John Eshun, Nanda Kerkar, Quais Mujawar, Zerrin Önal, Cristina Gonçalves, Jennifer Garcia, Seema Alam, Carolina Jimenez-Rivera, Luis Bujanda, Richard J. Thompson, Bettina E. Hansen, Nancy B. Spinner, Melissa A. Gilbert, Binita M. Kamath, Global Alagille Alliance (Gala) Study Group

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND & AIMS: Alagille syndrome (ALGS) is a rare, autosomal dominant disorder with high phenotypic heterogeneity. Disease-causing variants are primarily identified in Jagged1 (JAG1), with fewer reported in NOTCH2. JAG1 variants cause disease through a mechanism of haploinsufficiency, but the mechanism for NOTCH2 variants is not completely understood, making classification of variants more challenging. Using a large, international patient cohort acquired through the Global ALagille Alliance (GALA) study, we sought to improve classification of NOTCH2 variants and study phenotypic differences between NOTCH2- and JAG1-related disease.

METHODS: Clinical and molecular data from 952 individuals with ALGS in GALA were analysed and …

Eular/Acr Classification Criteria For Paediatric Chronic Nonbacterial Osteomyelitis (Cno)., Yongdong Zhao, Melissa S. Oliver, Anja Schnabel, Eveline Y. Wu, Zhaoyi Wang, Achille Marino, Cassyanne L. Aguiar, Jonathan D. Akikusa, Ummusen Kaya Akca, Beverley Almeida, Simone Appenzeller, Erin Balay-Dustrude, Ozge Basaran, Matthew L. Basiaga, Yelda Bilginer, David A. Cabral, Martina Capponi, Nathan Donaldson, Bugra Han Egeli, Emily Fox, Antonella Insalaco, Ramesh S. Iyer, Annette F. Jansson, Inna Kostik, Mikhail Kostik, Leonard K. Kovalick, Katia Tomie Kozu, Sivia K. Lapidus, Tzielan C. Lee, Aleksander Lenert, Kamran Mahmood, Edoardo Marrani, Doaa Mosad Mosa, Ian Muse, Alexander Mushkin, Katherine D. Nowicki, Farzana Nuruzzaman, Karen Onel, Manuela Pardeo, Trang Sophia Pham, Lauren Potts, Athimalaipet V. Ramanan, Angelo Ravelli, Nathan D. Rogers, Andrew W. Grim, Micol Romano, Natalie Rosenwasser, Takashi Shawn Sato, Gabriele Simonini, Jennifer B. Soep, Sara M. Stern, Timmy Strauss, Angela Taneja Kohli, Alexander C. Theos, Lori B. Tucker, Leslie F. Vogel, Shima Yasin, Stephen C. Wong, Katerina Bouchalova, Alison M. Hendry, Kevin C. Cain, Hermann J. Girschick, Fatma Dedeoglu, Christian M. Hedrich, Ronald M. Laxer, Polly J. Ferguson, Raymond Naden, Seza Ozen

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVES: To develop and validate classification criteria for paediatric chronic nonbacterial osteomyelitis (CNO) jointly supported by the European Alliance of Associations for Rheumatology (EULAR) and the American College of Rheumatology (ACR).

METHODS: This international initiative had 4 phases: (1) candidate items were proposed in a survey of paediatric rheumatologists, (2) criteria definition and reduction by Delphi and nominal group technique exercises, (3) criteria weighting using multicriteria decision analysis, and (4) refinement of weights and threshold score in a development cohort of 441 patients and validation in another cohort of 514 patients.

RESULTS: The new EULAR/ACR classification criteria for CNO require …

Contemporary Characteristics And Outcomes Of Pediatric Oncology Patients Participating In Early Phase Clinical Trials., Avina Rami, Kira Bona, Suzanne Shusterman, Karen Wright, Andrew E. Place, Puja J. Umaretiya, Ketki Bhushan, Steven G. Dubois, Kevin Campbell

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Phase 1 or phase 1/2 trials are a first step in pediatric cancer drug development. Currently, there is a paucity of information regarding contemporary outcomes for pediatric patients enrolled in these trials. We describe characteristics and outcomes of patients enrolled in pediatric phase 1 clinical trials over a 9-year period at a single institution.

METHODS: We queried our clinical trials management system to generate a list of patients enrolled and treated on pediatric phase 1 or phase 1/2 trials from 2011 to 2019. We collected baseline demographics, clinical data, efficacy, and safety endpoints post-enrollment including: time to death, objective …

Changes In Child Placement After Child Abuse Pediatrics Consultation For Suspected Physical Abuse., Kristine A. Campbell, Antoinette L. Laskey, Daniel M. Lindberg, M Katherine Henry, Porcia Vaughn, James Anderst, Megan M. Letson, Angela N. Bachim, Nancy S. Harper, Carmen M. Coombs, Lori D. Frasier, Joanne N. Wood

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: The association between child abuse pediatric (CAP) assessments and child welfare outcomes is unknown.

OBJECTIVE: To determine the association between a CAP determination of the likelihood of physical abuse and change in child placement. We hypothesized that child race would be associated with CAP determination of abuse likelihood and child welfare outcomes.

PARTICIPANTS AND SETTING: Children under age ten years with in-person CAP consultation and referral to child protective services for suspected physical abuse at a U.S. pediatric referral center participating in CAPNET, a CAP research network, from 02/2021 to 01/2023.

METHODS: We created a series of generalized estimating …

"My Child Needs A Chance And A Choice To Talk About Their Pain": Parents' Experiences And Perspectives Of Pain Communication In Paediatric Rheumatology., Rebecca R. Lee, Jade Edwards, Danielle C. Mountain, Janet E. Mcdonagh, Mark Connelly, Tonya Palermo, Sarah Peters

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVE: To investigate parents' experiences and perspectives about pain communication with healthcare professionals in paediatric rheumatology.

METHODS: Data were collected using semi-structured telephone interviews with parents of children/adolescents recruited from three UK tertiary paediatric rheumatology centres. A framework analysis was used to characterise parents' experiences and perspectives.

RESULTS: Eighteen parents participated. Their children had a median age of 13 years (SD= 3.16 years, Range= 6-16 years, 55 % male), with diagnoses of chronic primary pain (e.g. Ehlers Danlos syndrome/Hypermobility) and chronic secondary pain (e.g. Juvenile Idiopathic Arthritis). Data were organised into four themes: 1) Parents' active role in pain communication, …

Expression Graph Network Framework For Biomarker Discovery, Yang Liu, Jason Huse, Kasthuri Kannan

Faculty, Staff and Student Publications

Biomarker discovery for complex diseases, such as cancer, hinges on uncovering molecular signatures that capture intricate, interconnected relationships within biological data-a challenge that traditional statistical and machine learning methods often fail to meet due to the complexity of high-dimensional gene expression profiles. To overcome this, we introduce the expression graph network framework (EGNF). This cutting-edge graph-based approach integrates graph neural networks with network-based feature engineering to enhance the predictive identification of biomarkers. EGNF constructs biologically informed networks by combining gene expression data and clinical attributes within a graph database, utilizing hierarchical clustering to generate dynamic, patient-specific representations of molecular interactions. …

Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long

Faculty, Staff and Student Publications

In silico perturbation models, computational methods that can predict cellular responses to perturbations, present an opportunity to reduce the need for costly and time-intensive in vitro experiments. Many recently proposed models predict high-dimensional cellular responses, such as gene or protein expression to perturbations such as gene knockout or drugs. However, evaluating in silico performance has largely relied on metrics such as $R^{2}$, which assess overall prediction accuracy but fail to capture biologically significant outcomes like the identification of differentially expressed (DE) genes. In this study, we present a novel evaluation framework that introduces the AUPRC metric to assess the precision …

Braingenebot: A Framework For Variant Prioritization And Generative Pretrained Transformer-Informed Interpretation Across Polygenic Risk Score Studies, Gang Qu, Nitesh Enduru, Xinyi Liu, Xiaoqian Jiang, Zhongming Zhao

Faculty, Staff and Student Publications

Polygenic risk scores (PRS) are widely used to assess genetic susceptibility in Alzheimer's disease (AD) research. However, the rapid expansion of PRS studies has led to dataset-specific biases-stemming from factors like population makeup, genotyping methods, and analysis pipelines-that result in inconsistent variant prioritization and limit generalizability and reproducibility. To address these challenges, we propose a transductive learning framework that integrates multiple PRS datasets for more robust risk variant prioritization, incorporating genome-wide association study (GWAS) priority scores as biologically informed priors. Additionally, we introduce BrainGeneBot, an AI-driven tool leveraging generative pretrained transformers with retrieval-augmented generation technology to streamline genomic analyses in …

Assessing Stages Of Objective Memory Impairment And Neuroimaging As Risk Factors Of Incident Cognitive Impairment, Kellen K Petersen, Ali Ezzati, Bhargav T Nallapu, Richard B Lipton, Reisa A Sperling, Kathryn V Papp, Dorene M Rentz, Keith A Johnson, Ellen Grober

2020-Current year OA Pubs

OBJECTIVE: The Stages of Objective Memory Impairment (SOMI) system, based on the Free and Cued Selective Reminding Test (FCSRT), is a potential marker of subtle cognitive impairment in cognitively normal persons defined by a Clinical Dementia Rating (CDR) = 0. We investigated SOMI's ability to predict incident cognitive impairment (CDR >0) in combination with demographic features and neuroimaging biomarkers.

METHODS: Cognitively unimpaired participants (CDR = 0) from the Harvard Aging Brain Study had baseline FCSRT scores, MRI, FDG-PET, and PiB-PET as well as follow-up CDRs for 5 years. Cox proportional hazards models with correction for multiple testing assessed the predictive …

Drug-Drug Interaction Between Dolutegravir And Artemether-Lumefantrine In Hiv And Malaria Mono- And Co-Infections: A Pharmacogenetic Analysis From Ghana, Nicholas Ekow Thomford, Tracy Kellermann, Joel Adu Twum, John Anyimadu, Charné Dixon, Dennis Sappor, Dee Blackhurst, Prince Amoah Barnie, Oksana Ryabinina, Samuel Badu Nyarko, Robert Peter Biney, Martins Ekor, George B Kyei

2020-Current year OA Pubs

BACKGROUND: Human Immunodeficiency Virus and malaria are significant public health challenges in sub-Saharan Africa, contributing substantially to morbidity and mortality in the region. The trajectory of HIV and malaria mono- and coinfections may be different with presentations of drug-drug and disease-disease interactions. Current medications of artemether-lumefantrine and dolutegravir (DTG) -based anti-retroviral therapy which are the preferred drugs are metabolised by CYP2B6, CYP3A4/5 and UGTs which are polymorphic and may contribute to drug disposition and clinical outcomes. This study investigated the pharmacogenetic effects of co-administration of arthemeter-lumfantrine and DTG in HIV-malaria mono and coinfection.

METHODS: Malaria and HIV mono- and coinfected …

Predictors Of Perceived Hiv Stigma Among People Who Inject Drugs In The United States, Itunu Sokale, Paige Wermuth, Johnny Wilkerson, Folefac Atem, Salma Khuwaja, Catherine Troisi

Faculty, Staff and Student Publications

Background: HIV stigma is a huge impediment to ending the HIV epidemic. To develop effective HIV interventions, we must determine factors associated with HIV stigma, particularly among high-risk groups like people who inject drugs (PWID). We aimed to identify predictors of perceived HIV stigma (PHS) among a sample of PWID from 23 U.S. cities.

Methods: We analyzed the 2018 National HIV Behavioral Surveillance data on PWID aged ≥ 18 years. PHS was assessed using a validated survey that measured four PHS constructs: perceived unfriendliness, perceived discrimination, perceived punishment, and perceived support. We created a composite PHS index score by summing …

Zika In Infants And Pregnancy (Zip) Study: Results From A Prospective International Cohort Study Of Prenatal Zika Virus Infection And Adverse Fetal And Infant Outcomes, Jill Farnell Lebov, Martha Nason, Kristen B Stolka, Ricardo Ximenes, Marisa M Mussi-Pinhata, Jack Moye, Carmen D Zorrilla, Carmen M Velez Vega, José F Cordero, Deolinda M F Scalabrin, Albert I Ko, Maria Elisabeth Lopes Moreira, Luiz Augusto Galvão, William Britt, Ernesto T A Marques, Angel Balmaseda, Eva Harris, Juan F Arias, Stacey Schultz-Cherry, Ana Lucía Garces, Nancy F Krebs, Theresa J Ochoa, César Augusto Ugarte-Gil, Elizabeth Fogleman, Erin Gabriel, Michael Welton, Carmen M Irizarry, Silvia Biason De Moura Negrini, Conrado Milani Coutinho, Demócrito De Barros Miranda-Filho, Ulisses Ramos Montarroyos, Marli Tenorio Cordeiro, Anna Gajewski, Jorge E Osorio, Lester Figueroa

Faculty, Staff and Student Publications

Background: Before Zika virus (ZIKV) infections were observed in the Americas, an association between ZIKV and microcephaly or other congenital malformations was not well documented. Initial reports suggested strong associations between ZIKV and congenital malformations, but plausible estimates of causal effects from prospective studies with adequate sample size and covariate data were few.

Methods: From 2016-2018, the Zika in Infants and Pregnancy (ZIP) study enrolled pregnant people before 18 weeks gestation or with confirmed symptomatic ZIKV in a prospective cohort across 10 sites in South and Central America, and in Puerto Rico. Pregnancies were followed monthly through delivery and 6 …

Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott

Faculty, Staff and Student Publications

In studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole-genome sequencing (∼27X) of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study). We increased power by incorporating 14,812 jointly called psychiatrically unscreened ancestry-matched controls from the Trans-Omics for Precision Medicine (TOPMed) Program for a total of …

Deciphering Transcriptomic Changes In Chemobrain: A Comprehensive Review, Tusar Kanta Acharya, Yuan Pan, Peter M Grace, Cobi J Heijnen, Rajasekaran Mahalingam

Faculty, Staff and Student Publications

Chemotherapy-induced cognitive impairments (CICI), colloquially known as "chemobrain," represents a profound and debilitating side effect experienced by a significant number of cancer survivors, impacting their memory, multitasking, and quality of life. This review critically evaluates the molecular mechanisms underlying CICI, with a particular focus on the insights gained from transcriptomic analyses. As cancer incidence rises globally, understanding the complex interplay between chemotherapy agents and their cognitive repercussions becomes increasingly vital. Key mechanisms implicated in CICI include blood-brain barrier disruption, neuroinflammation, and oxidative stress as a result of various chemotherapy treatments, such as doxorubicin, cisplatin, and paclitaxel. We delve into advanced …

Longitudinal Meta-Cohort Study Protocol Using Systems Biology To Identify Vaccine Safety Biomarkers, Joann Diray-Arce, Ana C Chang, Sara Moradipoor, Donato Amodio, Bruce Carleton, Wan-Chun Chang, Nigel W Crawford, Meagan Karoly, Annmarie Hoch, Kerry Mcenaney, Tahir S Kafil, Mahitha Donthireddy, Sarah K Steltz, Simon D Van Haren, Asimenia Angelidou, Kinga K Smolen, Hanno Steen, Jessica Lasky-Su, Huyen Tran, Peter Liu, C Buddy Creech, Clare L Cutland, Helen Petousis-Harris, Ishac Nazy, Rae S M Yeung, Sonali Kochhar, Steve Black, Nicholas Wood, Dale Nordenberg, Paolo Palma, Inna G Ovsyannikova, Richard B Kennedy, Gregory A Poland, Al Ozonoff, Robert T Chen, Ofer Levy, Karina A Top, International Network Of Special Immunization Services (Insis) Members

Faculty, Staff and Students Publications

The International Network of Special Immunization Services (INSIS) was established to investigate the causes and risk factors of rare adverse events following immunizations (AEFIs) and develop immunization strategies for mitigating or preventing risk for individuals with prior AEFIs or at risk of AEFIs. INSIS integrates clinical data with multi-omic technologies (e.g., transcriptomics, proteomics, metabolomics) through a global consortium of clinical networks, leading immunology, pharmacogenomics teams to uncover the molecular mechanisms behind AEFIs. The network ensures accurate and standardized data collection and analysis through rigorous data management and quality assurance processes. INSIS also implements harmonized case definitions and protocols for collecting …

Excitotoxic Neuronal Death Requires Superoxide Entry Into Neurons Through Volume-Regulated Anion Channels, Kate Harris, Seok Joon Won, Gokhan Uruk, Nguyen Mai, Devran Ogut, Yonghui Zhao, Litao Xie, Paul Baxter, Katharina Everaerts, Rajan Sah, Raymond A Swanson

2020-Current year OA Pubs

Neuronal death in stroke and other conditions stems in part from stimulation of

Prefoldin Complex Promotes Interferon-Stimulated Gene Expression And Is Inhibited By Rotavirus Vp3, Yinxing Zhu, Yanhua Song, Dilip Kumar, Peter K Jackson, B V Venkataram Prasad, Siyuan Ding

2020-Current year OA Pubs

Timely induction of interferons and interferon-stimulated genes (ISGs) is critical for successful host defense against viral infections. VP3 encoded by rotavirus is implicated in interferon antagonism. However, the precise mechanisms remain incompletely understood. By conducting tandem-affinity purification coupled with high-resolution mass spectrometry, we identify the prefoldin complex as the top cellular binding partner of VP3. Rotavirus infection is significantly enhanced in prefoldin subunit knockout cells. Using proteome-wide label-free quantification, we find that prefoldin assists in folding ubiquitin-like-modifier-activating-enzyme-3 (UBA3), both of which positively regulate ISG expression. Through direct and competitive binding, VP3 interferes with the chaperone activity of prefoldin, leading to …

Adapt-3d: Accelerated Deep Adaptable Processing Of Tissue For 3-Dimensional Fluorescence Tissue Imaging For Research And Clinical Settings, Daniel D Lee, Kevin A Telfer, Deanna L Davis, Leon C D Smyth, Rahul Ravindran, Rafael S Czepielewski, Christopher G Huckstep, Siling Du, Kento Kurashima, Ajay K Jain, Jonathan Kipnis, Bernd H Zinselmeyer, Gwendalyn J Randolph

2020-Current year OA Pubs

Light sheet microscopy and preparative clearing methods that improve light penetration in 3D tissues have revolutionized imaging in biomedical research. Here we present ADAPT-3D, a streamlined 3-step approach to turn tissues optically transparent while preserving tissue architecture with the versatility to handle diverse tissue sizes and types across species. Unlike extensive lipid removal utilized by existing protocols, ADAPT-3D only partially removes lipids to preserve cell membranes, yet the non-toxic aqueous refractive indexing solution still rapidly turns tissues transparent while preserving the fluorescence of endogenous and antibody conjugated fluorophores. ADAPT-3D prepares whole mouse brains for light sheet microscopy in a 4-hour …

Whf Roadmap On Single Pill Combination Therapies, Enrico G Ferro, Mark Huffman, Orly Vardeny, Et Al.

2020-Current year OA Pubs

Cardiovascular diseases (CVDs) are the leading global cause of mortality, with treatment adherence posing a major barrier to effective prevention and control. Single pill combinations (SPCs), also known as fixed-dose combinations, simplify treatment by combining multiple agents into one pill, improving adherence and reducing cardiovascular risk. This World Heart Federation Roadmap synthesizes the latest clinical evidence and identifies key barriers to SPC implementation, including limited manufacturing, affordability, regulatory complexity, and inconsistent guideline inclusion. Drawing on global expert input and health systems analysis, the Roadmap outlines practical, context-specific solutions to improve access, scale-up, and integration of SPCs into national strategies, especially …

Risk Of Major Depression In Partners Of People With Alzheimer's Disease: A National Cohort Study, Casey Crump, Jingkai Wei, Barbara G Vickrey, Alexis C Edwards, Paul E Schulz, Weiva Sieh, Jan Sundquist, Kristina Sundquist

Faculty, Staff and Student Publications

Background: Alzheimer's disease (AD) may cause significant psychosocial distress not only in the patient but also their partner. However, long-term risks of major depression in partners of AD patients are largely unknown.

Methods: A national cohort study was conducted of all 145 289 partners of people diagnosed with all-cause dementia, including 57 113 partners of people diagnosed with AD, in Sweden during 1998-2017, and 1 300 561 population-based controls. Cox regression was used to compute hazard ratios (HRs) for subsequent risk of major depression identified from nationwide outpatient and inpatient diagnoses through 2018, adjusting for sociodemographic factors and prior mental …

Ras-Membrane Interaction And Oligomerization: There Is More Than Meets The Eye, Abraham C Sianoya, Vijay K Bhardwaj, Alemayehu A Gorfe

Faculty, Staff and Student Publications

Membrane association is fundamental to Rat sarcoma (RAS) function, driving both its physiologic signaling and oncogenic transformation. This review consolidates recent advances in the study of RAS-membrane interactions, emphasizing the molecular mechanisms underlying its membrane engagement and oligomerization. We first discuss the roles of RAS lipid modification and conformational diversity of its intrinsically disordered C-terminus in these processes, and we then examine the debate surrounding RAS dimerization and its potential role in the formation of higher-order oligomers. By integrating emerging insights into these issues, we offer our own perspectives on the driving forces of RAS oligomerization and propose potential new …

Hiv-1 Controllers Possess A Unique Cd8+ T Cell Activation Phenotype And Loss Of Control Is Associated With Increased Expression Of Exhaustion Markers, Amber D. Jones, Zachary Capriotti, Erin Santos, Angel Lin, Rachel Van Duyne, Stephen Smith, Zachary Klase

Kimmel Cancer Center Papers, Presentations, and Grand Rounds

BACKGROUND: HIV-1 controllers are a rare population of individuals that exhibit spontaneous control of HIV-1 infection without antiretroviral therapy. Understanding the mechanisms by which HIV-1 controllers maintain and eventually lose this ability would be highly valuable in HIV-1 cure or vaccine research. Previous work revealed the ability of CD8+ T cells isolated from HIV-1 controllers to suppress HIV-1 replication in matched CD4+ T cells and PBMCs ex vivo and suggested the loss of control may be tied to CD8+ T cell exhaustion.

RESULTS: We explored whether CD8+ T cell exhaustion plays a role in the maintenance and loss of control …

Adams Contribute To Triple Negative Breast Cancer Via Mtorc1 Pathway: Targeting Adam-Mtor Axis Improves Efficacy, Shuying Liu, Huiqin Chen, Mihai Gagea, Lorenzo Federico, Fan Zhang, Javier Gomez, Kim-Anh Do, William F Symmans, Gabriel N Hortobagyi, Gordon B Mills, Ana M Gonzalez-Angulo, Debasish Tripathy

Faculty, Staff and Student Publications

Breast cancer is the most frequently diagnosed cancer globally and the second leading cause of cancer-related deaths in American women. Triple-negative breast cancer (TNBC) lacks estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Thus, fewer targeting therapies are available for this most aggressive subtype. The A Disintegrin and Metalloproteinase (ADAM) family plays a vital role in cancer pathophysiology. Previous studies focused on single ADAM members. However, none of these have entered into the clinical arena as diagnostics or therapeutics for breast cancer. In this study, we demonstrate the upregulation of a panel of ADAM members in TNBC, …