Neurosciences Commons^™

Resort Enhances Reference-Based Cell Type Deconvolution For Spatial Transcriptomics Through Regional Information Integration, Linhua Wang, Ling Wu, Guantong Qi, Chaozhong Liu, Wanli Wang, Xiang H-F Zhang, Zhandong Liu

Duncan NRI Faculty and Staff Publications

Motivation: Spatial transcriptomics (ST) captures positional gene expression within tissues but lacks single-cell resolution. Reference-based cell type deconvolution methods were developed to understand cell type distributions for ST. However, batch/platform discrepancies between references and ST impact their accuracy.

Results: We present Region-based Cell Sorting (ReSort), which utilizes ST's region-level data to lessen reliance on reference data and alleviate these technical issues. In simulation studies, ReSort enhances reference-based deconvolution methods. Applying ReSort to a mouse breast cancer model highlights macrophages M0 and M2 enrichment in the epithelial clone, revealing insights into epithelial-mesenchymal transition and immune infiltration.

Availability and implementation: Source codes …

Recurrent Carotid Paragangliomas In A Syndromic Patient With A Heterozygous Missense Variant In Dna Methyltransferase 3 Alpha, Ryan J German, Blake Vuocolo, Liesbeth Vossaert, Lisa Saba, Robin Fletcher, Matthew L Tedder, Bekim Sadikovic, Jennifer Kerkhof, Michael Wangler, Carlos A Bacino

Duncan NRI Faculty and Staff Publications

We report a 40-year-old African American female with a novel variant in exon 8 of DNA methyltransferase 3 alpha (DNMT3A), (NM_022552.4: c.905G>C, p.G302A) who presented with a history of recurrent carotid paragangliomas, mediastinal mass, intellectual disability, dysarthria, cholelithiasis, diabetes mellitus, hypertension, and dysmorphic features. We interpret this novel variant as likely pathogenic and causative for the patient's syndromic features of Heyn-Sproul-Jackson syndrome. Heyn-Sproul-Jackson syndrome is a condition caused by gain-of-function genetic changes in DNMT3A. Paragangliomas have also been observed in non-syndromic patients with genetic alterations in DNMT3A. We describe a patient with clinical features of Heyn-Sproul-Jackson syndrome such as …

Survey And Improvement Strategies For Gene Prioritization With Large Language Models, Matthew B Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu

Duncan NRI Faculty and Staff Publications

Motivation: Rare diseases remain difficult to diagnose due to limited patient data and genetic diversity, with many cases remaining undiagnosed despite advances in variant prioritization tools. While large language models have shown promise in medical applications, their optimal application for trustworthy and accurate gene prioritization downstream of modern prioritization tools has not been systematically evaluated.

Results: We benchmarked various language models for gene prioritization using multi-agent and Human Phenotype Ontology classification approaches to categorize patient cases by phenotype-based solvability levels. To address language model limitations in ranking large gene sets, we implemented a divide-and-conquer strategy with mini-batching and token limiting …

Drosophila Models Uncover Substrate Channeling Effects On Phospholipids And Sphingolipids In Peroxisomal Biogenesis Disorders, Michael F Wangler, Yu-Hsin Chao, Mary Roth, Ruth Welti, James A Mcnew

Duncan NRI Faculty and Staff Publications

Peroxisomal Biogenesis Disorders Zellweger Spectrum (PBD-ZSD) disorders are a group of autosomal recessive defects in peroxisome formation that produce a multi-systemic disease presenting at birth or in childhood. Well documented clinical biomarkers such as elevated very long chain fatty acids (VLCFA) are key biochemical diagnostic findings in these conditions. Additional, secondary biochemical alterations such as elevated very long chain lysophosphatidylcholines are allowing newborn screening for peroxisomal disease. In addition, a more widespread impact on metabolism and lipids is increasingly being documented by metabolomic and lipidomic studies. Here we utilize Drosophila models of pex2 and pex16 as well as human plasma …

Zic1 Is A Context-Dependent Medulloblastoma Driver In The Rhombic Lip, John J Y Lee, Ran Tao, Zhen You, Parthiv Haldipur, Anders W Erickson, Hamza Farooq, Liam D Hendriske, Namal Abeysundara, Cory M Richman, Evan Y Wang, Neha Das Gupta, Jennifer Hadley, Melissa Batts, Christopher W Mount, Xiaochong Wu, Alex Rasnitsyn, Swneke Bailey, Florence M G Cavalli, Sorana Morrissy, Livia Garzia, Kulandaimanuvel Antony Michealraj, Abhi Visvanathan, Vernon Fong, Jonelle Palotta, Raul Suarez, Bryn G Livingston, Miao Liu, Betty Luu, Craig Daniels, James Loukides, Anne Bendel, Pim J French, Johan M Kros, Andrey Korshunov, Marcel Kool, Fernando Chico Ponce De León, Mario Perezpeña-Diazconti, Boleslaw Lach, Sheila K Singh, Sarah E S Leary, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Ji-Yeoun Lee, Teiji Tominaga, William A Weiss, Joanna J Phillips, Shizhong Dai, Gelareh Zadeh, Ali G Saad, László Bognár, Almos Klekner, Ian F Pollack, Ronald L Hamilton, Young-Shin Ra, Wieslawa A Grajkowska, Marta Perek-Polnik, Reid C Thompson, Anna M Kenney, Michael K Cooper, Stephen C Mack, Nada Jabado, Mathieu Lupien, Marco Gallo, Vijay Ramaswamy, Mario L Suva, Hiromichi Suzuki, Kathleen J Millen, L Frank Huang, Paul A Northcott, Michael D Taylor

Faculty, Staff and Students Publications

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma …

Pattern Integration And Differentiation: Dual Process Model Of Episodic Memory, Hallvard Røe Evensmoen, Lars M. Rimol, Henning Stople Rise, Tor Ivar Hansen, Hamed Nili, Anderson M. Winkler, Asta K. Håberg

Human Genetics Publications

The role of precise timing in episodic memory remains obscure. We showed 139 participants episodes consisting of objects, and tested subsequent memory for the precise timing and order of the objects and episodes. Temporal compression of the episode enhanced memory for relative but not absolute timing of the objects’ presentation and their order. Conversely, temporal expansion between neighboring episodes was associated with successful memory for episode order. fMRI in 36 participants revealed that temporal compression of the episode was associated with more similar activation patterns within episodes in several brain regions including the posterior hippocampus. However, the activation pattern in …

Blood Biomarker Profiles In Young-Onset Neurocognitive Disorders: A Cohort Study, Oneil G. Bhalala, Jessica Beamish, Dhamidhu Eratne, Patrick Summerell, Tenielle Porter, Simon M. Laws, Matthew J.Y. Kang, Aamira J. Huq, Wei Hsuan Chiu, Claire Cadwallader, Mark Walterfang, Sarah Farrand, Andrew H. Evans, Wendy Kelso, Leonid Churilov, Rosie Watson, Nawaf Yassi, Dennis Velakoulis, Samantha M. Loi

Research outputs 2022 to 2026

Introduction: Young-onset neurocognitive symptoms result from a heterogeneous group of neurological and psychiatric disorders which present a diagnostic challenge. To identify such factors, we analysed the Biomarkers in Younger-Onset Neurocognitive Disorders cohort, a study of individuals < 65 years old presenting with neurocognitive symptoms for a diagnosis and who have undergone cognitive and biomarker analyses. Methods: Sixty-five participants (median age at assessment of 56 years, 45% female) were recruited during their index presentation to the Royal Melbourne Hospital Neuropsychiatry Centre, a tertiary specialist service in Melbourne, Australia, and categorized as either early-onset Alzheimer’s disease (n = 18), non-Alzheimer’s disease neurodegeneration (n = 23) or primary psychiatric disorders (n = 24). Levels of neurofilament light chain, glial fibrillary acidic protein …

Developing, Implementing, And Evaluating The First National Memory And Cognition Clinic Guidelines In Australia, Inga Mehrani, Matthew Paradise, Lee Fay Low, Sue Kurrle, Valerie Arsenova, Gemma Jahn, Katrina Fyfe, Johannes C. Michaelian, Katharine Salmon, Jane Alty, Sharon L. Naismith, Perminder S. Sachdev

Research outputs 2022 to 2026

Introduction: A lack of national consensus on the roles and responsibilities of Australian memory and cognition clinics contributes to the large variability seen across services. The introduction of guidelines and a quality assessment framework could facilitate greater harmonization and quality improvements.

Methods: We used a modified Delphi process to develop the guidelines. Pilot clinics completed a self-assessment, case-note audit, and review meeting to evaluate their service against the guidelines.

Results: The final guidelines included 160 standards on 14 different topics. Standards around maximum waiting times for an assessment and minimum post-diagnostic care responsibilities were particularly controversial. Seven clinics participated in …

Exploring Non-Invasive Brain Stimulation Effects On Physical Outcomes In People With Parkinson’S Disease: An Umbrella Evidence Mapping Review With Meta-Analyses, Dale M. Harris, Christopher Latella, Nicholas Tripodi, Steven J. O’Bryan

Research outputs 2022 to 2026

Background: Non-invasive brain stimulation (NIBS) is sometimes used alongside medication to alleviate motor symptoms in people with Parkinson’s disease (PD). However, the evidence supporting NIBS’s effectiveness for improving motor function in PD patients is uncertain.

Objective: This umbrella review aims to synthesize recent systematic reviews and meta-analyses that have evaluated the effectiveness of NIBS in improving motor function in people with PD, with a key focus being to examine the quality of the evidence presented. Methods: The review protocol was registered in PROSPERO (CRD42022380544) and conducted per Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The search strategy was …

Exploring The Relationship Between Melanopsin Gene Variants, Sleep, And Markers Of Brain Health, Ayeisha Milligan Armstrong, Eleanor O'Brien, Tenielle Porter, Vincent Dore, Pierrick Bourgeat, Paul Maruff, Christopher C. Rowe, Victor L. Villemagne, Stephanie R. Rainey-Smith, Simon M. Laws

Research outputs 2022 to 2026

INTRODUCTION: Melanopsin is a photopigment with roles in mediating sleep and circadian-related processes, which are often disrupted in Alzheimer's disease (AD). Melanopsin also impacts cognition and synaptogenesis. This study investigated the associations between melanopsin genetic variants, sleep, and markers of brain health. METHODS: Linear regression analyses examined the relationship of single-nucleotide polymorphisms (SNPs) within the melanopsin gene (OPN4), with cortical amyloid beta (Aβ), cognition, brain volumes, and self-reported sleep traits in cognitively unimpaired older adults. Further analyses assessed whether sleep traits x OPN4 SNP interactions were associated with markers of brain health. RESULTS: OPN4 SNPs rs2355009 and rs3740334 were associated …

Motor Cortex Inhibition And Facilitation Changes Within Two Weeks Of Anterior Cruciate Ligament Reconstruction (Aclr): A Case Series, Colin Sylvester, Ann Maree Vallence, Casey Whife, Peter D'Alessandro, Christopher Latella, Ebonie Rio, Myles C. Murphy

Research outputs 2022 to 2026

Purpose: Anterior cruciate ligament reconstruction (ACLR) can cause arthrogenic muscle inhibition (AMI) or persistent muscle weakness that impairs physical function and return to sport. Deficits in voluntary activation (one method to measure AMI) are thought to contribute to AMI, however, the specific neurophysiological underpinnings remain inconclusive. The primary objective of this study was to explore changes in intracortical excitability (inhibition and facilitation) of the quadriceps representation in the primary motor cortex pre- and post-ALCR. Our secondary objective was to explore changes in hamstrings intracortical excitability pre- and post-ALCR. Methods: Prospective case-series pre-post-ACLR. Single- and paired-pulse transcranial magnetic stimulation (TMS) was …

Sex Differences In Inter-Temporal Decision Making And Cortical Thickness Of The Orbitofrontal And Insula In Young Adult Cannabis Users: Evidence From 1111 Subjects, Alan N. Francis, Joan A. Camprodon, Francesca Filbey

School of Medicine Publications

To test for sex differences in the impact of cannabis use on decision-making and brain correlates, we employed cortical thickness (CT) analysis of brain regions involved in intertemporal decision-making namely bilateral orbitofrontal cortex(OFC) and insula in young adult nondependent cannabis-users(CU) and non-users(NU) and their scores on delay discounting task. Neuroimaging analyzes of previously collected data were performed on 608CU and 503NU. CT analysis was performed on MRI images. OFC and insula thickness, scores on the delay discounting test were compared between groups and correlated. Controlling alcohol-use and intra-cranial-volume, CU exhibited sex differences in CT. The bilateral insula was significantly thinner …

Comparing Guillain-Barré Syndrome Outcomes Between Rural And Urban Hospitals In The United States: A Retrospective Cohort Study, Anudeep Surendranath, Rahul Damani, Anushareddy Muddasani, Anupam Kumar Gupta

Faculty, Staff and Students Publications

Background and purpose: Rural-urban disparities in neurological care have been well documented, but limited data exist regarding Guillain-Barré Syndrome (GBS). This study examines differences in patient demographics, hospital characteristics, and outcomes among GBS admissions to rural versus urban hospitals in the United States.

Methods: Using the 2021 National Inpatient Sample, we conducted a retrospective cohort study of adult hospitalizations with a principal diagnosis of GBS. Hospitals were classified as rural or urban based on U.S. census designations. Multivariate logistic and linear regression models were used to assess associations between hospital location and outcomes, adjusting for demographic, clinical, and hospital-level factors. …

Validation Of The Polish Version Of The Movement Disorder Society Non-Motor Rating Scale (Mds-Nms), Joanna Siuda, Mateusz Toś, Tomasz Chmiela, Andrzej Bogucki, Barbara Borodziuk, Sławomir Budrewicz, Marek Dąbrowski, Marceli Gacan, Agata Gajos, Justyna Gawryluk, Piotr Janik, Justyna Kaczyńska, Ewa Koziorowska-Gawron, Jakub Malkiewicz, Ewa Papuć, Paulina Kaczmarska, Monika Rudzińska-Bar, Jarosław Sławek, Magdalena Wójcik-Pędziwiatr, Luowen Yu, Sheng Luo, Christopher Goetz, Glenn Stebbins, Pablo Martinez-Martin, Tiago Mestre, Alvaro Sanchez-Ferro, Monika Kurtis, Michelle Hyczy De Siqueira Tosin, Roberta Balestrino, Chi-Ying Roy Lin, Carmen Gasca-Salas

Faculty, Staff and Students Publications

Aim of the study: We aimed to translate and validate the Polish version of the MDS-NMS and compare it with the original English version.

Clinical rationale for the study: Non-motor symptoms (NMS) affect a significant portion of the Parkinson's disease (PD) patient population and may negatively impact their quality of life. Non-motor symptoms may contribute to an increased sense of illness among patients and to a greater burden upon their caregivers. It is therefore advisable to develop a Polish validation of a reference scale for diagnosing and assessing the severity of NMS.

Material and methods: The MDS-NMS was translated into …

Early Cerebrospinal Fluid Elevations Of Ptau-217 In Severe Traumatic Brain Injury Subjects, Hamad Yadikar, Firas H Kobeissy, Claudia Robertson, Spyridoula Tsetsou, John B Williamson, Damon G Lamb, Amy K Wagner, Todd Kibaugh, Shih-Han Kao, Zhifeng Kou, Robert D Welch, Jose-Miguel Yamal, Luis Leon-Novelo, Richard Rubenstein, Kevin K W Wang

Faculty, Staff and Students Publications

Introduction: Tauopathies, including Alzheimer's disease (AD), feature abnormal accumulations of hyperphosphorylated Tau protein; however, their biomarker potential in traumatic brain injury (TBI) is not well-defined. This study investigated whether cerebrospinal fluid (CSF) phosphorylated Tau at threonine-217 (pTau-217) could serve as an early biomarker for severe TBI (sTBI).

Methods: CSF samples from 26 sTBI patients, collected between 6 and 240 h post-injury, and 19 healthy controls were analyzed using an optimized direct enzyme-linked immunosorbent assay (ELISA; sensitivity < 4.7 pg/mL) for pTau-217 detection, complemented by Western blot validation. Temporal analysis, ROC curves, and trajectory clustering were used for interpretation.

Results: CSF pTau-217 levels were significantly elevated in sTBI patients at 6, 12, 18, 24, and 48 h post-injury compared to controls (p …

Optic Nerve Sheath Diameter: Which Axis Should Be Measured?, Jakob Pansell, Tina Thomsson, Emelie Eng, Andreas Wallin, Mohammad Hirzallah

Faculty, Staff and Students Publications

Background and purpose: Optic nerve sheath diameter (ONSD) measured by point-of-care ultrasound (POCUS) is a commonly used non-invasive estimate of intracranial pressure (ICP). However, methodological variations limit standardization of this promising technique. Different imaging axes are identified as one such source of ONSD POCUS methodological variation. This study aimed to evaluate the agreement and diagnostic accuracy for elevated ICP between transverse and sagittal ONSD measurements.

Methods: We conducted a post-hoc analysis of 213 intensive care patients from three prior studies. ONSD was measured in both transverse and sagittal planes, externally (ONSDext) and internally (ONSDint) of the dura mater. Agreement was …

Inferred Developmental Origins Of Brain Tumors From Single-Cell Rna-Sequencing Data, Su Wang, Rachel Naomi Curry, Malcolm F Mcdonald, Hyun Yong Koh, Anders W Erickson, Claudia L Kleinman, Michael D Taylor, Ganesh Rao, Benjamin Deneen, Arif O Harmanci, Akdes Serin Harmanci

Faculty, Staff and Students Publications

Background: The reactivation of neurodevelopmental programs in cancer highlights parallel biological processes that occur in both normal development and brain tumors. Achieving a deeper understanding of how dysregulated developmental factors play a role in the progression of brain tumors is therefore crucial for identifying potential targets for therapeutic interventions. Single-cell RNA-sequencing (scRNA-Seq) provides an opportunity to understand how developmental programs are dysregulated and reinitiated in brain tumors at single-cell resolution. The aim of this study is to identify the developmental origins of brain tumors using scRNA-Seq data.

Methods: Here, we introduce COORS (Cell Of ORigin like CellS), a computational tool …

Purely Cystic Intraosseous Meningioma Of The Skull: A Radiologic Conundrum And Histologic Challenge, Diego Rojas, Arman Kavoussi, Ashley Rose Ricciardelli, Alex Flores, Sricharan Gopakumar, Luis Carrete, Hsiang-Chih Lu, Alex W Brenner, Akash J Patel

Faculty, Staff and Students Publications

Background: Intraosseous meningiomas and cystic meningiomas are two rare subtypes of meningiomas. Meningiomas can develop with characteristics encompassing both cystic and intraosseous, termed intraosseous cystic meningiomas, that pose a diagnostic challenge.

Case description: We report the case of a 41-year-old woman with a history of hearing loss presented with a left frontal mass that had been present for 12 years. Her history of hearing loss was in the setting of ear infections bilaterally since she was a teenager and was being evaluated by ear, nose, and throat specialists at the time. Initial cranial computed tomography (CT) identified a skull lesion …

Learning-Associated Astrocyte Ensembles Regulate Memory Recall, Michael R Williamson, Wookbong Kwon, Junsung Woo, Yeunjung Ko, Ehson Maleki, Kwanha Yu, Sanjana Murali, Debosmita Sardar, Benjamin Deneen

Faculty, Staff and Students Publications

The physical manifestations of memory formation and recall are fundamental questions that remain unresolved1. At the cellular level, ensembles of neurons called engrams are activated by learning events and control memory recall1-5. Astrocytes are in close proximity to neurons and engage in a range of activities that support neurotransmission and circuit plasticity6-10. Moreover, astrocytes exhibit experience-dependent plasticity11-13; however whether specific ensembles of astrocytes participate in memory recall remains obscure. Here we show that learning events induce c-Fos expression in a subset of hippocampal astrocytes, which subsequently …

Opsoclonus In Alternating Hemiplegia Of Childhood Secondary To Atp1a3 Pgly803arg, Alyssa D Runco, Jesse M Levine, Cristina Trandafir, Rod Foroozan, Mered Parnes, Daniel G Calame

Faculty, Staff and Students Publications

No abstract provided.