Digital Commons Network^™

Organ Of Corti Macrophages: A Distinct Group Of Cochlear Macrophages With Potential Roles In Supporting Cell Degeneration And Survival, Mengxiao Ye, Celia Zhang, Dalian Ding, Guang-Di Chen, Henry J Adler, Rania Sharaf, Bo Hua Hu

Faculty, Staff and Student Publications

Macrophages are the primary immune cells in the cochlea, essential for maintaining cochlear homeostasis and orchestrating inflammatory responses to pathological events. Although these cells have been found in various parts of the cochlea, their presence in the organ of Corti, a critical structure for acoustic sensing, remains poorly understood. The present study was designed to examine macrophage responses to ototoxic drug-induced cochlear damage and age-related cochlear degeneration, with a particular focus on the pathological conditions that trigger macrophage recruitment into the organ of Corti. We used a model of ototoxicity induced by cyclodextrin, a cyclic oligosaccharide known for its ability …

Integrating Multi-Omics Data To Uncover Prostate Tissue Dna Methylation Biomarkers And Target Genes For Prostate Cancer Risk, Shuai Liu, Jingjing Zhu, Dylan Green, Hua Zhong, Quan Long, Chong Wu, Liang Wang, Youping Deng, Lang Wu

Faculty, Staff and Student Publications

Previous studies have indicated that specific CpG sites may be linked to the risk of prostate cancer (PCa) by regulating the expression of PCa target genes. However, most existing studies aim to identify DNA methylation (DNAm) biomarkers through blood tissue genetic instruments, which impedes the identification of relevant biomarkers in prostate tissue. To identify PCa risk-associated CpG sites in prostate tissue, we established genetic prediction models of DNAm levels using data from normal prostate samples in the GTEx (N = 108) and assessed associations between genetically predicted DNAm in prostate and PCa risk by studying 122,188 cases and 604,640 controls. …

Three-Dimensional Deep Learning Normal Tissue Complication Probability Model To Predict Late Xerostomia In Patients With Head And Neck Cancer, Hung Chu, Suzanne P M De Vette, Hendrike Neh, Nanna M Sijtsema, Roel J H M Steenbakkers, Amy Moreno, Johannes A Langendijk, Peter M A Van Ooijen, Clifton D Fuller, Lisanne V Van Dijk

Faculty, Staff and Student Publications

Purpose: Conventional normal tissue complication probability (NTCP) models for patients with head and neck cancer are typically based on single-value variables, which, for radiation-induced xerostomia, are baseline xerostomia and mean salivary gland doses. This study aimed to improve the prediction of late xerostomia by using 3-dimensional information from radiation dose distributions, computed tomography imaging, organ-at-risk segmentations, and clinical variables with deep learning (DL).

Methods and materials: An international cohort of 1208 patients with head and neck cancer from 2 institutes was used to train and twice validate DL models (deep convolutional neural network, EfficientNet-v2, and ResNet) with 3-dimensional dose distribution, …

Deep Dive Into Targeted Therapies: Understanding Idh1-Mutant Aml Treatments [Podcast], Amer M Zeidan, Courtney Dinardo

Faculty, Staff and Student Publications

This podcast episode reviews recent advances in the treatment of IDH1-mutant acute myeloid leukemia (AML), focusing on the mechanisms, efficacy, and safety profiles of approved IDH1 inhibitors. The purpose is to present expert insights and clinical data from key trials that underscore the clinical benefits of these targeted therapies. Through discussion of key findings from pivotal clinical trial studies, including data supporting the use of these agents in both newly diagnosed and relapsed or refractory (R/R) settings, the episode highlights significant outcomes such as increased overall response and prolonged duration of remission in patients treated with IDH1 inhibitors. The analysis …

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 …

Quality Of Life Is Impaired In Shrimp Allergic Adults And Caregivers, Melissa L Hearrell, Sara Anvari, Sharon Chinthrajah, Sana Hasan, David P Huston, Evan Li, Chen-Hsing Lin, Edwin Kim, Andreas L Lopata, Sarbjit Singh Saini, Sayantani Sindher, Panida Sriaroon, Bin Su, Julie Wang, Carla M Davis

Faculty, Staff and Students Publications

Rationale: Shrimp (Litopenaeus vannamei) allergies (SA) can result in allergic reactions ranging from life threatening severe anaphylaxis to oral allergy syndrome. SA may pose lifestyle restrictions on daily life and interfere with social relationships and school performance, but this has not been thoroughly investigated. We examined the QoL in SA adults and caregivers.

Methods: A QoL online questionnaire adapted from the validated Food Allergy Quality of Life Questionnaire (FAQLQ) was administered between September 30, 2023-July 15, 2024 to adults and caregivers of at least one SA child. Descriptive statistics, Wilcoxon rank sum test, and Fisher exact test were …

Mutations In Retinal Cyclic Nucleotide-Gated Channels Identified In Familial Cases Of Inherited Retinal Dystrophies From Pakistan, Zainab Akhtar, Kiran Afshan, Yumei Li, Sumaira Altaf, Aleesha Asghar, Ume Sughra, Wajid Ali Khan, Haiba Kaul, Rui Chen, Sabika Firasat

Faculty, Staff and Students Publications

Purpose: Cyclic nucleotide-gated (CNG) channels are ligand-gated ion channels that transduce light signals into electrical signals in the retinal photoreceptors. Pathogenic variants in CNG channel genes are reported to cause inherited retinal dystrophies (IRDs). The current study used targeted panel sequencing to describe the mutational spectrum of CNG channel genes in familial cases of IRDs from eight consanguineous Pakistani families.

Methods: The current study included consanguineous Pakistani families with at least two affected members. DNA was extracted from whole blood samples by the phenol-chloroform method. Two affected members from each family were initially analyzed using targeted panel sequencing of 344 …

Folate Receptor Β Performs An Immune Checkpoint Function In Activated Macrophages, Fenghua Zhang, Md Yusuf Al-Amin, Sagar Utturkar, Rina Jiang, Gregory Cresswell, Rami Alfar, Ian Ophaug-Johansen, Gabriel Bachman, Madduri Srinivasarao, Richard Finnell, Amaya Puig-Kröger, Timothy Ratliff, Philip S Low

Faculty, Staff and Students Publications

Monocytes and macrophages are sentinels of the immune system that distinguish themselves from other cells by expressing the beta isoform of the folate receptor (FRβ). Because FRβ does not bind folate until the monocyte/macrophage is exposed to immunosuppressive cytokines, the question naturally arose whether FRβ might also perform an immune-related function. To examine this matter, we compared the properties of wild type (WT) and FRβ knockout mice. We observe that FRβ knockout (KO) mice display autoimmune symptoms that can include alopecia, enlarged spleens, and dermatitis, despite having normal cellular folate levels. We further demonstrate that syngeneic tumors (TRAMP C2, MC38) …

Id-Gba: Subgraph Extension With Information Distance Guilt By Association In Complex Networks, Predrag Obradovic, Vladimir Kovacevic, Aleksandar Milosavljevic, Varduhi Petrosyan

Faculty, Staff and Students Publications

Here, we introduce the ID-GBA (Information Distance Guilt By Association) method to expand highly connected sets of nodes by deploying a novel algorithm for subgraph extension based on the guilt-by-association principle and information distance. In this study, ID-GBA was utilized to expand disease clusters, and identify novel disease genes. We first validate its ability to expand related disease sets from disease/disease graphs built using Open Targets' gene association scores. We then analyze disease/control gene expression networks and show that ID-GBA recaptures known disease genes in nine disease/control graphs. Compared to existing methods such as Random Walk with Restarts and Personalized …

Bayesian Covariate-Dependent Circadian Modeling Of Rest-Activity Rhythms, Beniamino Hadj-Amar, Vaishnav Krishnan, Marina Vannucci

Faculty, Staff and Students Publications

We propose a Bayesian covariate-dependent anti-logistic circadian model for analyzing activity data collected via wrist-worn wearable devices. The proposed approach integrates covariates into the modeling of the amplitude and phase parameters, facilitating cohort-level analysis with enhanced flexibility and interpretability. To promote model sparsity, we employ an l1-ball projection prior, enabling precise control over complexity while identifying significant predictors. We assess performances on simulated data and then apply the method to real-world actigraphy data from people with epilepsy. Our results demonstrate the model’s effectiveness in uncovering complex relationships among demographic, psychological, and medical factors influencing rest-activity rhythms, offering insights for …

Epilepsy Clinic Analytics: Leveraging Emr Reporting Tools To Characterize Center Volume And Complexity, Vanuli Arya, Arindam Ghosh Mazumder, Muna Nnamani, Mark A Abboud, Samuel C Lee, Michael S Guzman, Vaishnav Krishnan

Faculty, Staff and Students Publications

Introduction: Epilepsy centers connect patients to multidisciplinary provider groups that can coordinate surgical interventions and/or investigational treatments. Automated techniques to cross-sectionally review patient volume and complexity may reveal objective metrics to assign appropriate personnel and resources. Here, we leveraged an electronic medical record (EMR) reporting tool to examine how patient and visit volumes, antiseizure medication (ASM) prescriptions and neuromodulation use evolved over an 11-year epoch at a single level 4 adult epilepsy center in Texas, USA.

Methods: Using Epic Workbench Reporting, we acquired the dates of (i) all clinic visits (office or telemedicine), (ii) CPT codes for neuromodulation interrogation/programming, and …

Cadherin 1 Germline Mutation Co-Occurs With Medullary Thyroid Cancer And Choroid Plexus Papilloma: A Case Report And Review Of Literature, Vijay Nitturi, Sricharan Gopakumar, Hsiang-Chih Lu, Akash J Patel

Faculty, Staff and Students Publications

Background: We describe the case of a 23-year-old woman with a history of medullary thyroid cancer (MTC) who presented with a choroid plexus papilloma (CPP) and review the literature regarding the co-occurrence of these two pathologies.

Case description: A 23-year-old woman with a history of MTC treated with thyroidectomy 3 months prior was referred to neurosurgery with an incidental fourth ventricular mass found on prior imaging of her neck. She presented to the clinic with intermittent headaches and underwent MRI which demonstrated a hyperintense, heterogeneously enhancing lobular mass at the obex of the fourth ventricle. She underwent suboccipital craniotomy and …

Leveraging Human Microbiomes For Disease Prediction And Treatment, Henok Ayalew Tegegne, Tor C Savidge

Faculty, Staff and Students Publications

The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision …

A New Interpolated Pseudodifferential Preconditioner For The Helmholtz Equation In Heterogeneous Media, Sebastian Acosta, Tahsin Khajah, Benjamin Palacios

Faculty, Staff and Students Publications

This paper introduces a new pseudodifferential preconditioner for the Helmholtz equation in variable media with absorption. The pseudodifferential operator is associated with the multiplicative inverse to the symbol of the Helmholtz operator. This approach is well suited for the intermediate and high-frequency regimes. The main novel idea for the fast evaluation of the preconditioner is to interpolate its symbol, not as a function of the (high-dimensional) phase-space variables, but as a function of the wave speed itself. Since the wave speed is a real-valued function, this approach allows us to interpolate in a univariate setting even when the original problem …

Atherogenic Lipoproteins Associate With Loss Of Glycemic Control In Youth-Onset Type 2 Diabetes: Results From The Today Study, Lorraine E Levitt Katz, Samuel S Gidding, James D Otvos, Kimberly L Drews, Fida Bacha, Steven Willi, Santica Marcovina, Siripoom Mckay, Ruth S Weinstock, Today Study Group

Faculty, Staff and Students Publications

Background: Type 2 diabetes (T2D) in adolescents is associated with an unfavorable lipid profile, but lipoprotein particle subspecies and branched-chain amino acid (BCAA) data are scarce.

Objective: To evaluate lipoprotein particle distributions, lipoprotein insulin resistance index (LP-IR), and BCAA levels longitudinally and their relationships with sex, race/ethnicity, treatment, and loss of glycemic control in adolescents with youth-onset T2D.

Methods: Participants from the TODAY study (n = 348) had samples analyzed yearly for glycated hemoglobin and nuclear magnetic resonance lipoprotein and BCAA assessments.

Results: At baseline, participants with T2D were 13.7 years old with T2D, obesity, and from racial and ethnic …

Refinement Of A Published Gene-Physical Activity Interaction Impacting Hdl-Cholesterol: Role Of Sex And Lipoprotein Subfractions, Kenneth E Westerman, Tuomas O Kilpeläinen, Magdalena Sevilla-Gonzalez, Margery A Connelly, Alexis C Wood, Michael Y Tsai, Kent D Taylor, Stephen S Rich, Jerome I Rotter, James D Otvos, Amy R Bentley, Samia Mora, Hugues Aschard, D C Rao, Charles Gu, Daniel I Chasman, Alisa K Manning

Faculty, Staff and Students Publications

Large-scale gene-environment interaction (GxE) discovery efforts often involve analytical compromises for the sake of data harmonization and statistical power. Refinement of exposures, covariates, outcomes, and population subsets may be helpful to establish often-elusive replication and evaluate potential clinical utility. Here, we used additional datasets, an expanded set of statistical models, and interrogation of lipoprotein metabolism via nuclear magnetic resonance (NMR)-based lipoprotein subfractions to refine a previously discovered GxE modifying the relationship between physical activity (PA) and HDL-cholesterol (HDL-C). We explored this GxE in the Women’s Genome Health Study (WGHS; N=23,294; the strongest cohort-specific signal in the original meta-analysis), the UK …

The Treatment Naïve Microbiome Of Pediatric Ulcerative Colitis And Microbial Therapeutics: A Humbling Challenge, Richard Kellermayer

Faculty, Staff and Students Publications

No abstract provided.

Glutamatergic Lateral Habenula Neurons Modulate Consolidation Of Associative Memories, Snigdha Srivastava, I-Ching Wang, Mikhail Y Kochukov, Jessica L Swanson, Mauro Costa-Mattioli, Benjamin R Arenkiel

Duncan NRI Faculty and Staff Publications

INTRODUCTION: Despite the rise in psychiatric disorders worldwide, the underlying brain circuits responsible for these devastating conditions remain elusive. The lateral habenula (LHb) has emerged as a key brain structure in depression studies due to its hyperactive state in both patients and animal models. While this aligns with known roles in driving aversive states and regulating serotonin release, it is still unclear how acute and transient activity changes in the LHb can influence higher order cognitive processes such as learning, memory, and behavioral adaptation. Given the importance of these processes to psychiatric conditions, understanding how LHb activity impacts cognitive function …

Investigative Genetic Genealogy Practices Warranting Policy Attention: Results Of A Modified Policy Delphi, Christi J Guerrini, Louiza Kalokairinou, Jill O Robinson, Whitney Bash Brooks, Stephanie M Fullerton, Sara Huston, Jacklyn Dahlquist, Diana Madden, Norah Crossnohere, Nicola Campoamor, John F P Bridges, Amy L Mcguire

Center for Medical Ethics and Health Policy Staff Publications

A technique known as investigative genetic genealogy (IGG) was first introduced to criminal investigations in 2018, and it has since been used by U.S. law enforcement to help identify hundreds of criminal perpetrators and unidentified human remains. As expertise in IGG grows, policymakers have shown interest in regulating it. To help inform these efforts and to promote coherence in IGG governance as it expands, we recruited experts representing a spectrum of IGG-relevant professions and perspectives to identify and prioritize IGG practices for policy attention and to develop policy options for addressing them. In two rounds of a modified policy Delphi, …

When Families Bridge The Research-Clinical Divide: An Exploration Of Values Regarding Cascade Screening In Genomic Research, Katherine E Bonini, Lauren R Desrosiers-Battu, Ann Katherine M Foreman, Nuriye N Sahin-Hodoglugil, Mary A Majumder, Candice R Finnila, Stephanie A Kraft, Laura M Amendola, Eimear E Kenny, Stephanie M Fullerton, Sara L Ackerman, Benjamin S Wilfond, Amy L Mcguire, Hadley Stevens Smith

Center for Medical Ethics and Health Policy Staff Publications

Purpose: Genetic results are important for both patients and their biological relatives. However, cascade screening (CS) uptake is low, especially when testing occurs through research programs and not clinical care. Ethical guidance is needed for CS implementation when individuals receive clinical genetic results through research.

Methods: We conducted focus groups with 3 groups of individuals in the Clinical Sequencing Evidence-Generating Research Consortium: clinicians, patient representatives, and scholars of the ethical, legal, and social implications of genomics. We used inductive thematic and comparative analyses to analyze data within and across the groups.

Results: All participants (n = 27) agreed that …

Modeling Functional Connectivity With Learning And Memory In A Mouse Model Of Alzheimer’S Disease, Lindsay Fadel, Elizabeth Hipskind, Steen E Pedersen, Jonathan Romero, Caitlyn Ortiz, Eric Shin, Md Abul Hassan Samee, Robia G Pautler

Faculty, Staff and Students Publications

Introduction: Functional connectivity (FC) is a metric of how different brain regions interact with each other. Although there have been some studies correlating learning and memory with FC, there have not yet been, to date, studies that use machine learning (ML) to explain how FC changes can be used to explain behavior not only in healthy mice, but also in mouse models of Alzheimer's Disease (AD). Here, we investigated changes in FC and their relationship to learning and memory in a mouse model of AD across disease progression.

Methods: We assessed the APP/PS1 mouse model of AD and wild-type controls …

Deep Brain Stimulation For Childhood Treatment-Resistant Obsessive-Compulsive Disorder: Mental Health Clinician Views On Candidacy Factors, Ilona Cenolli, Tiffany A Campbell, Natalie Dorfman, Meghan Hurley, Jared N Smith, Kristin Kostick-Quenet, Eric A Storch, Jennifer Blumenthal-Barby, Gabriel Lázaro-Muñoz

Center for Medical Ethics and Health Policy Staff Publications

Introduction: Deep brain stimulation (DBS) is approved under a humanitarian device exemption to manage treatment-resistant obsessive-compulsive disorder (TR-OCD) in adults. It is possible that DBS may be trialed or used clinically off-label in children and adolescents with TR-OCD in the future. DBS is already used to manage treatment-resistant childhood dystonia. Evidence suggests it is a safe and effective intervention for certain types of dystonia. Important questions remain unanswered about the use of DBS in children and adolescents with TR-OCD, including whether mental health clinicians would refer pediatric patients for DBS, and who would be a good candidate for DBS.

Objectives: …

Advancing Medical Applications Of Cancer Nanotechnology: Highlighting Two Decades Of The Nci's Nanotechnology Characterization Laboratory Service To The Research Community, Rachael M Crist, Yechezkel Barenholz, Ahuva Cern, Kate N Clark, Pieter R Cullis, Cheryl Dean, Neil Desai, Mauro Ferrari, Matthieu Germain, Carmen A Giacomantonio, Emma Grabarnik, Piotr Grodzinski, Atara Hod, Barry E Kennedy, Ruvanthi N Kularatne, Glen S Kwon, Emmanuel Loeb, Erin B Noftall, Len Pagliaro, Morteza Rasoulianboroujeni, Alexander Roth, Darren Rowles, Kulbir Singh, Nicole F Steinmetz, Zhanna Yehtina, Yao Zhang, Daniel Zilbersheid, Jeffrey D Clogston, Stephan T Stern, Marina A Dobrovolskaia

Center for Medical Ethics and Health Policy Staff Publications

The Nanotechnology Characterization Laboratory (NCL) is a US federally funded resource providing characterization and expertise to the cancer nanomedicine research community. Founded as a formal partnership among the US National Cancer Institute (NCI), the US Food and Drug Administration (FDA), and the US National Institute of Standards and Technology (NIST), the NCL has spent two decades developing a one-of-a-kind service with broad multidisciplinary expertise to meet the needs of a rapidly evolving drug development field. To mark the 20th anniversary of the lab's founding, the NCL hosted a symposium to highlight the achievements of the cancer nanomedicine field, showcase novel, …

Flyphonedb2: A Computational Framework For Analyzing Cell-Cell Communication In Drosophila Scrna-Seq Data Integrating Alphafold-Multimer Predictions, Mujeeb Qadiri, Ying Liu, Ah-Ram Kim, Myeonghoon Han, Eric Zhou, Austin Veal, Tzu-Chiao Lu, Hongjie Li, Yanhui Hu, Norbert Perrimon

Center on Aging Staff Publications

Cell-cell communication (CCC) plays a critical role in the physiological regulation of organisms and has been implicated in numerous diseases. Previously, we introduced FlyPhoneDB, a tool designed to explore CCC in Drosophila single-cell RNA-sequencing datasets. The core algorithm of FlyPhoneDB infers tissue-specific signaling events between cell types by calculating cell-cell interaction scores based on curated ligand-receptor (L-R) expression across major signaling pathways. However, the utility of FlyPhoneDB was limited by the relatively small number of available L-R pairs.

Here, we present FlyPhoneDB2, a major upgrade featuring a significantly expanded knowledgebase that includes a greater number of L-R pairs, incorporating annotations …

Contributions Of Pathobiological And Translational Science To Understanding And Managing Ischemic Heart Disease: Progress, Impediments, And Future Directions, L Maximilian Buja

The Texas Heart Institute Journal

Key pathobiological components of ischemic heart disease have been identified as follows: (1) In 1970 to 1973, myocardial infarct size was found to be the primary determinant of prognosis after acute myocardial infarction (AMI); (2) in 1973 to 1989, vulnerable coronary artery plaques were found to predispose individuals to coronary plaque disruption and thrombosis, causing major AMI; (3) in 1972, timely coronary reperfusion was demonstrated to limit the size of evolving AMI but with risk of reperfusion injury; and (4) in 1986, myocardial conditioning was found to be a clinically significant modulator capable of delaying AMI progression. Promising cardioprotective strategies …

Digital Otoscopy With Computer-Aided Composite Image Generation: Impact On The Correct Diagnosis, Confidence, And Time, Seda Camalan, Carl D Langefeld, Amy Zinnia, Brigham Mckee, Matthew L Carlson, Nicholas L Deep, Michael S Harris, Taha A Jan, Vivian F Kaul, Nathan R Lindquist, Jameson K Mattingly, Jay Shah, Kevin Y Zhan, Metin N Gurcan, Aaron C Moberly

Faculty, Staff and Student Publications

Objective: This study investigated the comparative performance of ear, nose, and throat (ENT) physicians in correctly detecting ear abnormalities when reviewing digital otoscopy imaging using 3 different visualization methods, including computer-assisted composite images called "SelectStitch," single video frame "Still" images, and video clips. The study also explored clinicians' diagnostic confidence levels and the time to make a diagnosis.

Study design: Clinician diagnostic reader study.

Setting: Online diagnostic survey of ENT physicians.

Methods: Nine ENT physicians reviewed digital otoscopy examinations from 86 ears with various diagnoses (normal, perforation, retraction, middle ear effusion, tympanosclerosis). Otoscopy examinations used artificial-intelligence (AI)-based computer-aided composite image …

Small Molecule-Based Regulation Of Gene Expression In Human Astrocytes Switching On And Off The G-Quadruplex Control Systems, Vijay Kumar M J, Jérémie Mitteaux, Zi Wang, Ellery Wheeler, Nitin Tandon, Sung Yun Jung, Robert H E Hudson, David Monchaud, Andrey S Tsvetkov

Faculty, Staff and Student Publications

A great deal of attention is being paid to strategies seeking to uncover the biology of the four-stranded nucleic acid structure G-quadruplex (G4) via their stabilization in cells with G4-specific ligands. The conventional definition of chemical biology implies that a complete assessment of G4 biology can only be achieved by implementing a complementary approach involving the destabilization of cellular G4s by ad hoc molecular effectors. We report here on an unprecedented comparison of the cellular consequences of G4 chemical stabilization by pyridostatin (PDS) and destabilization by phenylpyrrolocytosine (PhpC) at both transcriptome- and proteome-wide scales in patient-derived primary human astrocytes. Our …

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 …

Talking About Suffering In The Intensive Care Unit, Brent M Kious, Judith B Vick, Peter A Ubel, Olivia Sutton, Jennifer Blumenthal-Barby, Christopher E Cox, Deepshikha Ashana

Center for Medical Ethics and Health Policy Staff Publications

Background: Some have hypothesized that talk about suffering can be used by clinicians to motivate difficult decisions, especially to argue for reducing treatment at the end of life. We examined how talk about suffering is related to decision-making for critically ill patients, by evaluating transcripts of conversations between clinicians and patients' families.

Methods: We conducted a secondary qualitative content analysis of audio-recorded family meetings from a multicenter trial conducted in the adult intensive care units of five hospitals from 2012-2017 to look at how the term "suffering" and its variants were used. A coding guide was developed by consensus-oriented discussion …