Digital Commons Network^™

Tumor-Derived Arachidonic Acid Reprograms Neutrophils To Promote Immune Suppression And Therapy Resistance In Triple-Negative Breast Cancer, Liqun Yu, Keziah Liebenberg, Yichao Shen, Fengshuo Liu, Zhan Xu, Xiaoxin Hao, Ling Wu, Weijie Zhang, Hilda L Chan, Bo Wei, Philip L Lorenzi, Yang Gao, Igor Bado, Luis Becerra-Dominguez, Charlotte Helena Rivas, Sergio Aguirre, Bradley C Pingel, Yi-Hsuan Wu, Yunfeng Ding, Jun Liu, David G Edwards, Livia S Eberlin, Xiang H-F Zhang

Faculty, Staff and Students Publications

The combination of immune checkpoint blockade and chemotherapies is the standard of care for triple-negative breast cancer (TNBC). However, initially, responsive tumors can still develop recurrences, suggesting acquired resistance mechanisms that remain poorly understood. Herein, we discover that TNBC cells surviving anti-programmed cell death protein-1 (anti-PD-1) and chemotherapy treatment accumulate neutral lipids. Disrupting lipid droplet formation in cancer cells reverses resistance and mitigates the immunosuppressive microenvironment. Single-cell RNA sequencing reveals a subset of neutrophils exhibiting a lipid-laden phenotype similar to adjacent tumor cells. Mechanistically, tumor-derived extracellular vesicles carrying lipids, including arachidonic acid (AA), mediate neutrophil reprogramming. Blocking dietary intake of …

Challenges In Transitioning From Methadone To Buprenorphine-Naloxone For Chronic Pain Management: Two Cases, Jamal Hasoon, Anvinh Nguyen, Omar Viswanath, Alaa Abd-Elsayed

Faculty, Staff and Students Publications

Background: Methadone is frequently used for chronic pain management due to its long half-life and NMDA receptor activity, making it an effective option for opioid-tolerant patients. Buprenorphine-naloxone is increasingly explored as an alternative for chronic pain and opioid use disorder, offering partial opioid agonism with a ceiling effect on respiratory depression. The transition from methadone to buprenorphine-naloxone remains clinically challenging, requiring careful management to prevent withdrawal and ensure adequate pain control.

Case descriptions: Two patients with chronic pain were transitioned from methadone to buprenorphine-naloxone. The first patient, a mid-40s female, was abruptly switched from methadone 10 mg twice daily dosing …

Pediatric And Congenital Cardiac Services: An Innovative And Empowering Approach To Global Training And Equitable Care, Wyman W. Lai, Dominique Vervoort, David Bradley, Antonio G. Cabrera, Casey Culbertson, Alejandro Floh, Saurabh K. Gupta, Babar S. Hasan, Adrian Holloway, Jeffrey P. Jacobs, Kathy J. Jenkins, R. K. Kumar, L.A. Larrazabal, Colin J. Mcmahon, Daniel J. Penny, Alistair Phillips, Emilio Quezada, Craig A. Sable, Shubhika Srivastava, Sandra L. Staveski, Patcharapong Suntharos, David F. Teitel, Betsy Tirado, Brian C. Tran, Bistra Zheleva, Liesl Zuhkle, Anthony C. Chang

Division of Cardiology Faculty Papers

Congenital heart disease is a leading cause of preventable death in children, with a disproportionate impact on low- and middle-income countries. Despite progress in treating congenital heart disease globally, significant challenges remain in accessing specialized cardiovascular care, particularly cardiac surgery, in low- and middle-income countries. This review examines current models of assistance and proposes a novel global training program to address these inequities. Key challenges identified include building program infrastructure, training health care providers, ensuring financial sustainability, and promoting local engagement. The proposed program, structured under a new international organization, will leverage emerging technologies to deliver accessible and rigorously assessed …

Structural Updates To The Implant And Refill Needle Of The Port Delivery Platform, Dante J. Pieramici, Peter A. Campochiaro, Margaret Chang, Ian Pearce, Carl D. Regillo, Shamika Gune, Nancy Holekamp, Carlos Quezada-Ruiz, Shrirang V. Ranade, Natasha Singh, Geoffrey Wise, Joshua Horvath

Wills Eye Hospital Papers

PURPOSE: The purpose of this study was to report the impact of component-level changes and manufacturing process improvements on septum durability in the ocular implant of the Port Delivery Platform (PD-P), more commonly known as the Port Delivery System with ranibizumab (PDS) with its current formulation.

METHODS: Laboratory tests were conducted to determine (1) the bond strength of the septum to the overmold, (2) the amount of force utilized for the refill needle to puncture the septum, and (3) septum durability over 50 years. To simulate multiple refill-exchanges over long-term clinical use, implants were aged at elevated temperature in saline …

Association Of Age, Sex And Education With Access To The Intravenous Thrombolysis For Acute Ischemic Stroke, Yoona Ko, Beom Joon Kim, Youngran Kim, Jong-Moo Park, Kyusik Kang, Jae Guk Kim, Jae-Kwan Cha, Tai Hwan Park, Kyungbok Lee, Jun Lee, Keun-Sik Hong, Byung-Chul Lee, Kyung-Ho Yu, Dong-Eog Kim, Joon-Tae Kim, Jay Chol Choi, Jee Hyun Kwon, Wook-Joo Kim, Kyu Sun Yum, Sung-Il Sohn, Hyungjong Park, Sang-Hwa Lee, Kwang-Yeol Park, Chi Kyung Kim, Sung Hyuk Heo, Moon-Ku Han, Anjail Z Sharrief, Sunil A Sheth, Hee-Joon Bae

Faculty, Staff and Student Publications

Background: Barriers to treatment with intravenous thrombolysis (IVT) for patients with acute ischemic stroke (AIS) in South Korea remain incompletely characterized. We analyze a nationwide prospective cohort to determine patient-level features associated with delayed presentation and non-treatment of potential IVT-eligible patients.

Methods: We identified consecutive patients with AIS from 01/2011 to 08/2023 from a multicenter and prospective acute stroke registry in Korea. Patients were defined as IVT candidates if they presented within 4.5 hours from the last known well, had no lab evidence of coagulopathy, and had National Institute of Health Stroke Scale (NIHSS) ≥ 4. Multivariable generalized linear mixed …

Adaptations Of An Online Cognitive-Behavioral Therapy Intervention For Binge Type Eating Disorders In Publicly-Insured And Uninsured Adults: A Pilot Study, Siena S Vendlinski, Agatha A Laboe, Peyton Crest, Claire G Mcginnis, Molly F Steinhoff, Denise E Wilfley, C Barr Taylor, Ellen E Fitzsimmons-Craft, Erin C Accurso

2020-Current year OA Pubs

BACKGROUND: Publicly-insured and uninsured individuals-many of whom are marginalized because of race/ethnicity, ability status, and/or other social identities-experience barriers to accessing evidence-based interventions (EBIs) for eating disorders (EDs). Additionally, EBIs have not been developed with or for diverse populations, exacerbating poor treatment uptake. Mobile technology is well-positioned to bridge this gap and increase access to low-cost, culturally-sensitive EBIs.

METHODS: This study leverages a user-centered design approach to adapt an existing coached cognitive-behavioral therapy-based digital program and evaluate its usability in a sample of 11 participants with (sub)clinical binge type EDs who are publicly-insured (n = 10) or uninsured (n = …

Mechanistic Insights Into The Structure-Based Design Of A Cspz-Targeting Lyme Disease Vaccine, Kalvis Brangulis, Jill Malfetano, Ashley L Marcinkiewicz, Alan Wang, Yi-Lin Chen, Jungsoon Lee, Zhuyun Liu, Xiuli Yang, Ulrich Strych, Dagnija Tupina, Inara Akopjana, Maria-Elena Bottazzi, Utpal Pal, Ching-Lin Hsieh, Wen-Hsiang Chen, Yi-Pin Lin

Faculty, Staff and Students Publications

Borrelia burgdorferi (Bb) causes Lyme disease (LD), one of the most common vector-borne diseases in the Northern Hemisphere. Here, we solve the crystal structure of a mutated Bb vaccine antigen, CspZ-YA that lacks the ability to bind to host complement factor H (FH). We generate point mutants of CspZ-YA and identify CspZ-YAI183Y and CspZ-YAC187S to trigger more robust bactericidal responses. Compared to CspZ-YA, these CspZ-YA mutants require a lower immunization frequency to protect mice from LD-associated inflammation and bacterial colonization. Antigenicity of wild-type and mutant CspZ-YA proteins are similar, as measured using sera from infected people or immunized …

Benchmarking Large Language Models For Biomedical Natural Language Processing Applications And Recommendations, Qingyu Chen, Yan Hu, Xueqing Peng, Qianqian Xie, Qiao Jin, Aidan Gilson, Maxwell B Singer, Xuguang Ai, Po-Ting Lai, Zhizheng Wang, Vipina K Keloth, Kalpana Raja, Jimin Huang, Huan He, Fongci Lin, Jingcheng Du, Rui Zhang, W Jim Zheng, Ron A Adelman, Zhiyong Lu, Hua Xu

Faculty, Staff and Student Publications

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs-GPT and LLaMA representatives-on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with the traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here, we show that traditional fine-tuning outperforms zero- or …

Life On The Dry Side: A Roadmap To Understanding Desiccation Tolerance And Accelerating Translational Applications, R A Marks, J T B Ekwealor, M A S Artur, L Bondi, T C Boothby, O M S Carmo, D C Centeno, K K Coe, H J W Dace, S Field, A Hutt, S Porembski, A Thalhammer, L Van Der Pas, A J Wood, P Alpert, D Bartels, S Boeynaems, M N Datar, T Giese, W I Seidou, S M Kirchner, J Köhler, U G V S S Kumara, J Kyung, R Lyall, B D Mishler, J B V T Ndongmo, M S Otegui, V Reddy, J Rexroth, S M Tebele, R Vanburen, J Verdier, U C Vothknecht, M F Wittenberg, E Zokov, M J Oliver, S Y Rhee

Duncan NRI Faculty and Staff Publications

To thrive in extreme conditions, organisms have evolved a diverse arsenal of adaptations that confer resilience. These species, their traits, and the mechanisms underlying them comprise a valuable resource that can be mined for numerous conceptual insights and applied objectives. One of the most dramatic adaptations to water limitation is desiccation tolerance. Understanding the mechanisms underlying desiccation tolerance has important potential implications for medicine, biotechnology, agriculture, and conservation. However, progress has been hindered by a lack of standardization across sub-disciplines, complicating the integration of data and slowing the translation of basic discoveries into practical applications. Here, we synthesize current knowledge …

Comparing Analgesic Regimen Effectiveness And Safety After Surgery (Cares): Protocol For A Pragmatic, International Multicentre Randomised Trial, Mark C Bicket, Karim Shiraz Ladha, Simon Haroutounian, Kellie Mcfarlin, Mary Neff, Rachel L Mcduffie, Jennifer F Waljee, Duminda Nalaka Wijeysundera, Chad Brummet, Yi Li, Cares Investigators

2020-Current year OA Pubs

INTRODUCTION: Acute pain is commonly experienced by millions of patients who undergo outpatient surgical procedures. Moreover, an increasing number of procedures are performed on an outpatient basis, requiring greater postoperative planning to ensure effective pain management. Analgesic approaches commonly involve prescription opioids and non-steroidal anti-inflammatory drugs (NSAIDs), but an optimal regimen that balances pain and adverse effects has not been identified. In addition, critical gaps in evidence exist regarding how opioids and NSAIDs compare as analgesic regimens after surgery.

METHODS AND ANALYSIS: The Comparing Analgesic Regimen Effectiveness and Safety after Surgery (CARES) trial is a pragmatic, international, multicentre randomised trial …

Tobacco Smoke Exposure Is A Driver Of Altered Oxidative Stress Response And Immunity In Head And Neck Cancer, Yang Li, Pedram Yadollahi, Fonma N Essien, Vasanta Putluri, Chandra Shekar R Ambati, Karthik Reddy Kami Reddy, Abu Hena Mostafa Kamal, Nagireddy Putluri, Lama M Abdurrahman, Maria E Ruiz Echartea, Keenan J Ernste, Akshar J Trivedi, Jonathan Vazquez-Perez, William H Hudson, William K Decker, Rutulkumar Patel, Abdullah A Osman, Farrah Kheradmand, Stephen Y Lai, Jeffrey N Myers, Heath D Skinner, Cristian Coarfa, Kwangwon Lee, Antrix Jain, Anna Malovannaya, Mitchell J Frederick, Vlad C Sandulache

Faculty, Staff and Student Publications

Background: Exposomes are critical drivers of carcinogenesis. However, how they modulate tumor behavior remains unclear. Extensive clinical data show cigarette smoke to be a key exposome that promotes aggressive tumors, higher rates of metastasis, reduced response to chemoradiotherapy, and suppressed anti-tumor immunity. We sought to determine whether smoke itself can modulate aggressive tumor behavior in head and neck squamous cell carcinoma (HNSCC) through reprogramming of the cellular reductive state.

Methods: Using established human and murine HNSCC cell lines and syngeneic mouse models, we utilized conventional western blotting, steady state and flux metabolomics, RNA sequencing, quantitative proteomics and flow cytometry to …

Protocol For A Multisite, Observational Clinical Study Of The Association Between Skin Colour And Pulse Oximeter Accuracy In Children Undergoing Cardiac Catheterisation (Pach Study), Halley Ruppel, Liming Huang, Christopher J Petit, Athar M Qureshi, Christopher P Bonafide, Elizabeth E Foglia, Jeffery Feldman, Meghan B Lane-Fall, Jennifer M Lynch, Anna Chien, Michelle Dunn, Michael L O'Byrne

Faculty, Staff and Students Publications

Introduction: Prospective, real-world clinical studies of the association between skin color and pulse oximeter (SpO2) accuracy in children are needed to address the limitations of previous research. Such studies are essential for generating evidence for clinicians, regulators and industry. This is the protocol for a multisite study funded by the National Heart, Lung, and Blood Institute (R01HL171313; 1 January 2024-31 December 2028).

Methods and analysis: In this pragmatic, observational study conducted in three large paediatric cardiac catheterisation centres in the USA, children undergoing cardiac catheterisation with directly measured arterial oxygen saturation will be prospectively enrolled. The outcome variable (SpO2 bias) …

Parasite Contamination Of Soil In Different Peruvian Locations And Outside Built Environments, Carlos Pineda, Maritza Dalí Camones Rivera, Eddyson Montalva Sabino, Lucia Estela Mejia, Katherine Elizabeth Keegan, Lizbet Pilar Patricio Alvarez, Javier Jorge Mora, Fernanda Espinoza Vega, Emilio Rey Mejia, Patrick Olivas Herrera, Elisa Palomino Pando, Zhen Zeng, Athos Silva De Oliveira, Maria Jose Villar Mondragon, Barton Slatko, Eric J Wetzel, Rojelio Mejia

Faculty, Staff and Students Publications

Background: Soil is a reservoir for many parasites that can affect human and animal health, especially in tropical regions where soil-transmitted helminths and protozoa thrive. Understanding how environmental factors influence parasite distribution will provide a basis for relating how climate changes may intensify their impacts, altering parasite habitats and increasing transmission risks. We surveyed soil parasite prevalence, burden, and diversity in several different Peruvian environmental ecologies to catalog current parasite presence and provide a baseline for future surveys.

Methods: A total of 198 soil samples from 43 locations across three Peruvian regions-Tingo María (TM) (Amazon rainforest), Andabamba/Marabamba (A/M) (Andean highlands), …

Alpha-Synuclein Seed Amplification Assays: Data Sharing, Standardization Needed For Clinical Use, Hilal A Lashuel, D James Surmeier, Tanya Simuni, Kalpana Merchant, Byron Caughey, Claudio Soto, Mohamed-Bilal Fares, Roland G Heym, Ronald Melki

Faculty, Staff and Student Publications

Alpha-synuclein seed amplification assays can improve neurodegenerative disease diagnosis and care, but widespread use depends on a framework that standardizes protocols and encourages data sharing.

A Phase Ii Trial Of Sitravatinib + Nivolumab After Progression On Immune Checkpoint Inhibitor In Patients With Metastatic Clear Cell Rcc, Andrew W Hahn, Nabil Adra, Ulka Vaishampayan, Lianchun Xiao, Nazli Dizman, Ying Yuan, Sagar S Mukhida, Matthew T Campbell, Jianjun Gao, Amado J Zurita, Eric Jonasch, Nizar M Tannir, Amishi Y Shah, Pavlos Msaouel

Faculty, Staff and Student Publications

Background: Sitravatinib, an oral multi-kinase inhibitor targeting VEGFR, TAM, and MET, has been shown to resensitize the tumor microenvironment to immune checkpoint inhibitors (ICI) by reducing immune-suppressive myeloid cells in metastatic clear cell RCC (ccRCC). ICI is the standard first-line (1L) treatment of metastatic ccRCC, and there is unmet need for improved treatment outcomes after progression on ICI. We hypothesized that sitravatinib plus nivolumab would revert an immunosuppressive tumor microenvironment (TME) to improve clinical outcomes.

Methods: In this investigator-initiated, phase II, multicenter trial (NCT04904302), patients with progressive metastatic ccRCC after 1-2 lines of treatment were enrolled into 3 …

Year 1 Of Medicare's Accountable Care Organization Realizing Equity, Access, And Community Health Model, Gmerice Hammond, Sunny Lin, Sukruth A Shashikumar, R J Waken, Fengxian Wang, Khavya Avula, Vi-Anh Hoang, Kenton J Johnston, Karen Joynt Maddox

2020-Current year OA Pubs

IMPORTANCE: The US Centers for Medicare & Medicaid Services launched the Accountable Care Organization (ACO) Realizing Equity, Access, and Community Health (REACH) payment model in January 2023. In contrast to prior ACO initiatives, such as the Medicare Shared Savings Program (MSSP), ACO REACH includes equity-focused measures and payment adjustments, including an equity plan and financial risk adjustment for ACOs with higher proportions of underserved beneficiaries. However, it is unknown whether these changes have incented participation from organizations that serve beneficiaries from marginalized communities.

OBJECTIVE: To compare characteristics between participants in ACO REACH with those in MSSP and the broader pool …

Findings From A Qualitative Analysis: Social Media Influencers Of Color As Trusted Messengers Of Hpv Vaccination Messages, Amelia Burke-Garcia, Erin Cutroneo, Dasha Afanaseva, Kayla Madden, Angela Sustaita-Ruiz, Preethi Selvan, Estefany Rivera Sanchez, Amy Leader

Department of Medical Oncology Faculty Papers

BACKGROUND: Despite HPV vaccination reducing the prevalence of cervical cancer by 90%, vaccination rates remain lower among communities of color due to vaccine hesitancy and mistrust in traditional public health messengers. The emergence of social media influencers, a newer kind of messenger, presents a unique opportunity to share immunization messages in new ways with a variety of communities. This paper reviews the qualitative findings from a study aimed at assessing influencers' perceptions of and approaches to sharing messaging about the HPV vaccine.

METHODS: Guided by several theories (Theory of Planned Behavior, Narrative Theory, and Opinion Leader Theory), the study team …

Bright And Photostable Yellow Fluorescent Proteins For Extended Imaging, Jihwan Lee, Shujuan Lai, Shuyuan Yang, Shiqun Zhao, Francisco A Blanco, Anne C Lyons, Raquel Merino-Urteaga, John F Ahrens, Nathan A Nguyen, Haixin Liu, Zhuohe Liu, Gerard G Lambert, Nathan C Shaner, Liangyi Chen, Kimberley F Tolias, Jin Zhang, Taekjip Ha, François St-Pierre

Faculty, Staff and Students Publications

Fluorescent proteins are indispensable molecular tools for visualizing biological structures and processes, but their limited photostability restricts the duration of dynamic imaging experiments. Yellow fluorescent proteins (YFPs), in particular, photobleach rapidly. Here, we introduce mGold2s and mGold2t, YFPs with up to 25-fold greater photostability than mVenus and mCitrine, two commonly used YFPs, while maintaining comparable brightness. These variants were identified using a high-throughput pooled single-cell platform, simultaneously screening for high brightness and photostability. Compared with our previous benchmark, mGold, the mGold2 variants display a ~4-fold increase in photostability without sacrificing brightness. mGold2s and mGold2t extend imaging durations across diverse modalities, …

K-Mer Analysis Of Long-Read Alignment Pileups For Structural Variant Genotyping, Adam C English, Fabio Cunial, Ginger A Metcalf, Richard A Gibbs, Fritz J Sedlazeck

Faculty, Staff and Students Publications

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. Benchmarking against the latest SV datasets shows kanpig achieves a single-sample genotyping concordance of 82.1%, significantly outperforming existing tools, which average 66.3%. We explore kanpig's use for multi-sample projects by testing on 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), and produces higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample's 20x …

A Mapping Review And Critique Of The Literature On Translation, Dissemination, And Implementation Capacity Building Initiatives For Different Audiences, Ana A Baumann, Danielle R Adams, Laura-Mae Baldwin, Rachel G Tabak, Sara Malone, Maura M Kepper, Anita D Misra-Hebert, Kathleen R Stevens, Maria E Fernandez, Sunil Kripalani

Faculty, Staff and Student Publications

Background: Capacity building is critical for research and practice as the fields of dissemination, implementation and translation science continue to grow. Some scholars state that capacity building should be grounded in competencies. However, the fields are unclear in determining which competencies are relevant for whom, including the content and appropriate level of information and skills for different roles. The goal of this study was to catalogue competencies across current D&I capacity building initiatives.

Methods: We conducted a mapping review to examine to what extent are theories or frameworks used to guide capacity building, who is being trained, to what extent …

Polygenic Score Analysis Identifies Distinct Genetic Risk Profiles In Alzheimer’S Disease Comorbidities, Carlos F Hernández, Camilo Villaman, Costin Leu, Dennis Lal, Ignacio Mata, Andrés D Klein, Eduardo Pérez-Palma

Faculty, Staff and Student Publications

Alzheimer’s disease (AD) is usually accompanied by comorbidities such as type 2 diabetes (T2D), epilepsy, major depressive disorder (MDD), and migraine headaches (MH) that can significantly affect patient management and progression. As AD, these comorbidities have their own cumulative common genetic risk component that can be explored in a single individual through polygenic scores. Utilizing data from the UK Biobank, we investigated the correlation between polygenic scores (PGS) for these comorbidities and their actual presentation in AD patients. We show that individuals with higher PGS values showed an elevated risk of developing T2D (OR 2.1, p = 1.07 × 10−11) …

Hif Regulates Multiple Translated Endogenous Retroviruses: Implications For Cancer Immunotherapy, Qinqin Jiang, David A Braun, Karl R Clauser, Vijyendra Ramesh, Nitin H Shirole, Joseph E Duke-Cohan, Nancy Nabilsi, Nicholas J Kramer, Cleo Forman, Isabelle E Lippincott, Susan Klaeger, Kshiti M Phulphagar, Vipheaviny Chea, Nawoo Kim, Allison P Vanasse, Eddy Saad, Teagan Parsons, Melissa Carr-Reynolds, Isabel Carulli, Katarina Pinjusic, Yijia Jiang, Rong Li, Sudeepa Syamala, Suzanna Rachimi, Eva K Verzani, Jonathan D Stevens, William J Lane, Sabrina Y Camp, Kevin Meli, Melissa B Pappalardi, Zachary T Herbert, Xintao Qiu, Paloma Cejas, Henry W Long, Sachet A Shukla, Eliezer M Van Allen, Toni K Choueiri, L Stirling Churchman, Jennifer G Abelin, Cagan Gurer, Gavin Macbeath, Richard W Childs, Steven A Carr, Derin B Keskin, Catherine J Wu, William G Kaelin

Faculty, Staff and Student Publications

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERV), ERVE-4. We report that ERVE-4 is one of many ERVs that are induced by HIF, translated …

Open Access Dataset And Common Data Model For Pulse Oximeter Performance Data, Nicholas Fong, Leonid Shmuylovich, Et Al.

2020-Current year OA Pubs

The OpenOximetry Dataset stores clinical and lab pulse oximetry data. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.g., arterial blood pressure, end-tidal carbon dioxide), and arterial blood gas parameters (e.g., acid-base balance, hemoglobin concentration). All data, from desaturation studies to clinical trials, are collected prospectively to ensure accuracy. A common data model and standardized protocols for consistent archival and interpretation ensure consistent data archival and interpretation. The dataset aims to facilitate …

De Novo Variants In Cdkl1 And Cdkl2 Are Associated With Neurodevelopmental Symptoms, Ali H Bereshneh, Jonathan C Andrews, Daniel F Eberl, Guney Bademci, Nicholas A Borja, Stephanie Bivona, Wendy K Chung, Shinya Yamamoto, Michael F Wangler, Shane Mckee, Mustafa Tekin, Hugo J Bellen, Oguz Kanca

Duncan NRI Faculty and Staff Publications

The CDKL (cyclin-dependent kinase-like) family consists of five members in humans, CDKL1-5, that encode serine-threonine kinases. The only member that has been associated with a Mendelian disorder is CDKL5, and variants in CDKL5 cause developmental and epileptic encephalopathy type 2 (DEE2). Here, we study four de novo variants in CDKL2 identified in five individuals, including three unrelated probands and monozygotic twins. These individuals present with overlapping symptoms, including global developmental delay, intellectual disability, childhood-onset epilepsy, dyspraxia, and speech deficits. We also identified two individuals with de novo missense variants in CDKL1 in the published Deciphering Developmental Disorders (DDD) and GeneDx …

Biochemical Profiling And Structural Basis Of Adar1-Mediated Rna Editing, Xiangyu Deng, Lina Sun, Min Zhang, Rashmi Basavaraj, Jin Wang, Yi-Lan Weng, Yang Gao

Faculty, Staff and Students Publications

ADAR1 regulates RNA-induced immune responses by converting adenosine to inosine in double-stranded RNA. Mutations in ADAR1 are associated with human autoimmune disease, and targeting ADAR1 has been proposed for cancer immunotherapy. However, the molecular mechanisms underlying ADAR1-mediated editing remain unclear. Here, we provide detailed biochemical and structural characterizations of human ADAR1. Our biochemical profiling reveals that ADAR1 editing is both sequence and RNA-duplex-length dependent but can well tolerate mismatches near the editing site. High-resolution ADAR1-RNA complex structures, combined with mutagenesis, elucidate RNA binding, substrate selection, dimerization, and the essential role of RNA-binding domain 3. The ADAR1 structures also help explain …

Open Access Dataset And Common Data Model For Pulse Oximeter Performance Data, Nicholas Fong, Michael S Lipnick, Ella Behnke, Yu Chou, Seif Elmankabadi, Lily Ortiz, Christopher S Almond, Isabella Auchus, Garrett W Burnett, Ronald Bisegerwa, Desireé R Conrad, Carolyn M Hendrickson, Shubhada Hooli, Robert Kopotic, Gregory Leeb, Daniel Martin, Eric D Mccollum, Ellis P Monk, Kelvin L Moore, Leonid Shmuylovich, J Brady Scott, An-Kwok Ian Wong, Tianyue Zhou, Romain Pirracchio, Philip E Bickler, John Feiner, Tyler J Law

Faculty, Staff and Students Publications

The OpenOximetry Dataset stores clinical and lab pulse oximetry data. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.g., arterial blood pressure, end-tidal carbon dioxide), and arterial blood gas parameters (e.g., acid-base balance, hemoglobin concentration). All data, from desaturation studies to clinical trials, are collected prospectively to ensure accuracy. A common data model and standardized protocols for consistent archival and interpretation ensure consistent data archival and interpretation. The dataset aims to facilitate …

Clinical Validation Of Rna Sequencing For Mendelian Disorder Diagnostics, Sen Zhao, Kristina Macakova, Jefferson C Sinson, Hongzheng Dai, Jill Rosenfeld, Gladys E Zapata, Shenglan Li, Patricia A Ward, Christiana Wang, Chunjing Qu, Becky Maywald, Brendan Lee, Christine Eng, Pengfei Liu

Faculty, Staff and Students Publications

Despite rapid advancements in clinical sequencing, over half of diagnostic evaluations still lack definitive results. RNA sequencing (RNA-seq) has shown promise in research settings for bridging this gap by providing essential functional data for accurate interpretation of diagnostic sequencing results. However, despite advanced research pipelines, clinical translation of diagnostic RNA-seq has not yet been realized. We have developed and validated a clinical diagnostic RNA-seq test for individuals with suspected genetic disorders who have existing or concurrent comprehensive DNA diagnostic testing. This diagnostic RNA-seq test processes RNA samples from fibroblasts or blood and derives clinical interpretations based on the analytical detection …

Open Access Dataset And Common Data Model For Pulse Oximeter Performance Data, Nicholas Fong, Michael S Lipnick, Ella Behnke, Yu Chou, Seif Elmankabadi, Lily Ortiz, Christopher S Almond, Isabella Auchus, Garrett W Burnett, Ronald Bisegerwa, Desireé R Conrad, Carolyn M Hendrickson, Shubhada Hooli, Robert Kopotic, Gregory Leeb, Daniel Martin, Eric D Mccollum, Ellis P Monk, Kelvin L Moore, Leonid Shmuylovich, J Brady Scott, An-Kwok Ian Wong, Tianyue Zhou, Romain Pirracchio, Philip E Bickler, John Feiner, Tyler J Law

Peninsula Medical School

The OpenOximetry Dataset stores clinical and lab pulse oximetry data. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.g., arterial blood pressure, end-tidal carbon dioxide), and arterial blood gas parameters (e.g., acid-base balance, hemoglobin concentration). All data, from desaturation studies to clinical trials, are collected prospectively to ensure accuracy. A common data model and standardized protocols for consistent archival and interpretation ensure consistent data archival and interpretation. The dataset aims to facilitate …

The Role Of Non-Statin Lipid Lowering Therapies To Reduce Ascvd Events In Primary Prevention, Chukwuemezie Mamanu, Dean Karalis

Division of Cardiology Faculty Papers

PURPOSE OF REVIEW: Atherosclerotic cardiovascular disease (ASCVD) remains a leading global health challenge, with low-density lipoprotein (LDL) cholesterol a pivotal risk factor. While statins are cornerstone therapy for lowering LDL cholesterol, many high-risk primary prevention patients are unable to tolerate statin therapy and do not achieve their guideline directed LDL cholesterol goal. For these patients, non-statin therapies offer complementary and alternative approaches to LDL cholesterol reduction.

RECENT FINDINGS: Recent advancements in non-statin therapies have expanded the options available to clinicians to lower LDL cholesterol in high-risk primary prevention patients. Yet these medications are often under-utilized in clinical practice. Observational studies, …

Methylome-Wide Association Analyses Of Lipids And Modifying Effects Of Behavioral Factors In Diverse Race And Ethnicity Participants, Yao Hu, Jeff Haessler, Jessica I Lundin, Burcu F Darst, Eric A Whitsel, Megan Grove, Weihua Guan, Rui Xia, Mindy Szeto, Laura M Raffield, Scott Ratliff, Yuxuan Wang, Xuzhi Wang, Alison E Fohner, Megan T Lynch, Yesha M Patel, S Lani Park, Huichun Xu, Braxton D Mitchell, Joshua C Bis, Nona Sotoodehnia, Jennifer A Brody, Bruce M Psaty, Gina M Peloso, Michael Y Tsai, Stephen S Rich, Jerome I Rotter, Jennifer A Smith, Sharon L R Kardia, Alex P Reiner, Leslie Lange, Myriam Fornage, James S Pankow, Mariaelisa Graff, Kari E North, Charles Kooperberg, Ulrike Peters

Faculty, Staff and Student Publications

Circulating lipid concentrations are clinically associated with cardiometabolic diseases. The phenotypic variance explained by identified genetic variants remains limited, highlighting the importance of searching for additional factors beyond genetic sequence variants. DNA methylation has been linked to lipid concentrations in previous studies, although most of the studies harbored moderate sample sizes and exhibited underrepresentation of non-European ancestry populations. In addition, knowledge of nongenetic factors on lipid profiles is extremely limited. In the Population Architecture Using Genomics and Epidemiology (PAGE) Study, we performed methylome-wide association analysis on 9,561 participants from diverse race and ethnicity backgrounds for HDL-c, LDL-c, TC, and TG …