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Depletion Of Effector Regulatory T Cells Associates With Major Response To Induction Dual Immune Checkpoint Blockade, Xianli Jiang, Nils-Petter Rudqvist, Bo Jiang, Shengbin Ye, Shan He, Qingnan Liang, Jinzhuang Dou, Michelle D Williams, Joe Dan Dunn, Jason M Johnson, Keiko Akagi, Weihong Xiao, Shaoheng Liang, Satvik Elayavalli, Baohua Sun, Edwin R Parra, Renata Ferrarotto, Adam S Garden, Clifton David Fuller, Jay Reddy, Neil D Gross, Miriam N Lango, Cheuk Hong Leung, Suyu Liu, Diane D Liu, Meng Li, J Jack Lee, Michael A Curran, Jack Phan, Ken Chen, Maura L Gillison Aug 2025

Depletion Of Effector Regulatory T Cells Associates With Major Response To Induction Dual Immune Checkpoint Blockade, Xianli Jiang, Nils-Petter Rudqvist, Bo Jiang, Shengbin Ye, Shan He, Qingnan Liang, Jinzhuang Dou, Michelle D Williams, Joe Dan Dunn, Jason M Johnson, Keiko Akagi, Weihong Xiao, Shaoheng Liang, Satvik Elayavalli, Baohua Sun, Edwin R Parra, Renata Ferrarotto, Adam S Garden, Clifton David Fuller, Jay Reddy, Neil D Gross, Miriam N Lango, Cheuk Hong Leung, Suyu Liu, Diane D Liu, Meng Li, J Jack Lee, Michael A Curran, Jack Phan, Ken Chen, Maura L Gillison

Faculty, Staff and Student Publications

In a phase II trial, patients with local-regionally advanced human papillomavirus-positive oropharyngeal carcinoma (n = 35) received ipilimumab (anti-CTLA4) and nivolumab (anti-PD-1) as induction immunotherapy and concurrently with radiotherapy (NCT03799445). Coprimary endpoints included 6-month complete metabolic response rate (94%) and 2-year progression-free survival (84%). Induction yielded a 46% major histopathologic response rate. Single-cell profiling revealed responders had higher baseline intratumoral CD8+ T cells with a tumor-reactive, tissue-resident memory (TRM) phenotype and a treatment-related decrease in effector regulatory T (eTreg) cells. The eTreg decrease correlated with CD8+ T-cell clonotype transitioning from TRM to effector memory and IFNG+ effector cells. …


The Effect Of Hcv On Methadone Dose During Pregnancy, Sarah Boudova, Neel S. Iyer, Danielle M. Tholey, Jonathan M. Fenkel, Rupsa C. Boelig Aug 2025

The Effect Of Hcv On Methadone Dose During Pregnancy, Sarah Boudova, Neel S. Iyer, Danielle M. Tholey, Jonathan M. Fenkel, Rupsa C. Boelig

Department of Obstetrics and Gynecology Faculty Papers

Pregnancy is a time of high patient motivation to initiate treatment for opioid use disorder (OUD). Hepatic drug metabolism can be altered by pregnancy and hepatitis C virus (HCV) infection. We aimed to examine the impact of HCV during pregnancy on methadone dosing. Retrospective chart review of all pregnant patients with OUD admitted for initiation of methadone from 1/2020-6/2022. Associations were examined using Student's T-tests, chi-squared tests, Fisher's exact tests and univariate and multivariate linear regression. We identified 191 pregnancies initiated on methadone, of which 188 were screened for HCV. 111 (59.0%) were HCV Antibody (Ab)+, of whom 108 were …


Nemvaleukin Alfa Monotherapy In Patients With Advanced Melanoma And Renal Cell Carcinoma: Results From The Phase 1/2 Non-Randomized Artistry-1 Trial, Emiliano Calvo, Valentina Boni, Olivier Dumas, Sang Joon Shin, Seth D Rosen, Arvind Chaudhry, Philip R Debruyne, Xiaomin He, Ulka N Vaishampayan, David F Mcdermott Aug 2025

Nemvaleukin Alfa Monotherapy In Patients With Advanced Melanoma And Renal Cell Carcinoma: Results From The Phase 1/2 Non-Randomized Artistry-1 Trial, Emiliano Calvo, Valentina Boni, Olivier Dumas, Sang Joon Shin, Seth D Rosen, Arvind Chaudhry, Philip R Debruyne, Xiaomin He, Ulka N Vaishampayan, David F Mcdermott

School of Nursing and Midwifery

BACKGROUND: Despite improved outcomes with immune checkpoint inhibitors (ICIs) and their combinations in advanced solid tumors, a subset of patients remains unresponsive or progresses, highlighting an unmet need for novel treatments with durable benefit. Nemvaleukin alfa (nemvaleukin, ALKS 4230) demonstrated manageable safety and antitumor activity, alone and in combination with pembrolizumab, across heavily pretreated advanced solid tumors in the ARTISTRY-1 study. We report in-depth antitumor activity, safety, pharmacokinetics, and pharmacodynamics of nemvaleukin monotherapy at the recommended phase 2 dose (RP2D) in advanced melanoma and renal cell carcinoma (RCC) cohorts from ARTISTRY-1.

METHODS: ARTISTRY-1 was a three-part (A, B, and C), …


Detection Of Brain Cancer Using Genome-Wide Cell-Free Dna Fragmentomes, Dimitrios Mathios, Et Al. Aug 2025

Detection Of Brain Cancer Using Genome-Wide Cell-Free Dna Fragmentomes, Dimitrios Mathios, Et Al.

2020-Current year OA Pubs

UNLABELLED: Diagnostic delays in patients with brain cancer are common and can impact patient outcome. Development of a blood-based assay for detection of brain cancers could accelerate brain cancer diagnosis. In this study, we analyzed genome-wide cell-free (cfDNA) fragmentomes, including fragmentation profiles and repeat landscapes, from the plasma of individuals with (n = 148) or without (n = 357) brain cancer. Machine learning analyses of cfDNA fragmentome features detected brain cancer across all-grade gliomas (AUC = 0.90; 95% confidence interval, 0.87-0.93), and these results were validated in an independent prospectively collected cohort. cfDNA fragmentome changes in patients with gliomas represented …


Enhancing Patient Positioning Accuracy: Evaluating Daily Cone Beam Computed Tomography In The Halcyon System., Duong Thanh Tai, Luong Tien Phat, Tran Trung Kien, Nguyen Ngoc Anh, Nguyen Xuan Hai, Peter Sandwall, David Bradley, James C L Chow Aug 2025

Enhancing Patient Positioning Accuracy: Evaluating Daily Cone Beam Computed Tomography In The Halcyon System., Duong Thanh Tai, Luong Tien Phat, Tran Trung Kien, Nguyen Ngoc Anh, Nguyen Xuan Hai, Peter Sandwall, David Bradley, James C L Chow

Oncology Articles

BACKGROUND: Precise patient positioning is crucial for successful radiotherapy, ensuring accurate delivery of radiation to tumors while minimizing exposure to healthy tissues. Positional errors can significantly impact treatment efficacy and increase side effects. This study evaluates the effectiveness of daily cone beam computed tomography (CBCT) imaging in the Halcyon system for detecting and correcting patient misalignments across various cancer types and treatment sites.

METHODS: A retrospective analysis was conducted on 411 patients treated with the Varian Halcyon linear accelerator from August 2022 to August 2024. Patients were grouped based on tumor location: Head and Neck (118 patients), Chest (188 patients), …


Stem Cell-Derived Corneal Epithelium: Engineering Barrier Function For Ocular Surface Repair, Emily Elizabeth Fresenko, Jian-Xing Ma, Matthew Giegengack, Atalie Carina Thompson, Anthony Atala, Andrew J W Huang, Yuanyuan Zhang Aug 2025

Stem Cell-Derived Corneal Epithelium: Engineering Barrier Function For Ocular Surface Repair, Emily Elizabeth Fresenko, Jian-Xing Ma, Matthew Giegengack, Atalie Carina Thompson, Anthony Atala, Andrew J W Huang, Yuanyuan Zhang

2020-Current year OA Pubs

The cornea, the transparent anterior window of the eye, critically refracts light and protects intraocular structures. Corneal pathologies, including trauma, infection, chemical injury, metabolic diseases, genetic conditions, and age-related degeneration, can lead to significant visual impairment. While penetrating keratoplasty or full-thickness corneal transplantation remains a standard and effective intervention for severe corneal dysfunction, limitations in donor tissue availability and the risk of immunogenic graft rejection necessitate alternative therapeutic strategies. Furthermore, for cases of isolated epithelial disfunction, a full-thickness cornea graft may not be required or effective. This review examines the potential of corneal epithelial constructs derived from autologous stem cells …


Sporadic Als Induced Pluripotent Stem Cell Derived Neurons Reveal Hallmarks Of Tdp-43 Loss Of Function, Jeffrey D Rothstein, Olivia Keeley, Caroline Warlick, Timothy M Miller, Cindy V Ly, Jonathan D Glass, Alyssa N Coyne Aug 2025

Sporadic Als Induced Pluripotent Stem Cell Derived Neurons Reveal Hallmarks Of Tdp-43 Loss Of Function, Jeffrey D Rothstein, Olivia Keeley, Caroline Warlick, Timothy M Miller, Cindy V Ly, Jonathan D Glass, Alyssa N Coyne

2020-Current year OA Pubs

Nuclear loss and cytoplasmic buildup of the RNA-binding protein TDP-43 is a hallmark of ALS and related disorders. While studies using artificial TDP-43 depletion in neurons have revealed changes in gene expression and splicing, their relevance to actual patients remained unclear. Induced pluripotent stem cell (iPSC)-derived neurons (iPSNs) from 180 individuals, including controls, C9orf72 ALS/FTD, and sporadic ALS (sALS) patients were used to generate and analyze ~32,500 qRT-PCR data points across 20 genes which identified variable, time-dependent signatures of TDP-43 loss of function in individual lines. Notably, the same changes were also seen in postmortem brain tissue from the same …


Quantile Index Predictors Using R Package Hyper.Gam, Tingting Zhan, Misung Yi, Inna Chervoneva Aug 2025

Quantile Index Predictors Using R Package Hyper.Gam, Tingting Zhan, Misung Yi, Inna Chervoneva

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

MOTIVATION: Evaluation of single-cell protein expression from immunohistochemistry images is used increasingly in biomedical research. Many proteins are used solely for phenotyping cells in the tumor microenvironment. Other proteins with meaningfully quantitative expression levels provide so-called functional protein biomarkers. There is still a limited number of methods and software tools available for utilizing the entire distributions of single-cell expression levels.

RESULTS: We present the R package hyper.gam, providing a supervised learning framework for deriving biomarkers based on single-cell distribution quantiles. The single-cell data are first converted into sample quantile functions, which are then used as predictors in scalar-on-function regression models …


Trauma Resuscitation With Low-Titer Group O Whole Blood Or Products: Study Protocol For A Randomized Clinical Trial (The Troop Trial), Jan O Jansen, Claudia Pedroza, Luis Leon Novelo, Tianyao Hao, Gina R Dewildt, Charles F Coton, Kiran Mansoor, Shannon W Stephens, Marisa B Marques, James R Stubbs, Jillian R Richter, Henry E Wang, John B Holcomb, Stacia M Desantis Aug 2025

Trauma Resuscitation With Low-Titer Group O Whole Blood Or Products: Study Protocol For A Randomized Clinical Trial (The Troop Trial), Jan O Jansen, Claudia Pedroza, Luis Leon Novelo, Tianyao Hao, Gina R Dewildt, Charles F Coton, Kiran Mansoor, Shannon W Stephens, Marisa B Marques, James R Stubbs, Jillian R Richter, Henry E Wang, John B Holcomb, Stacia M Desantis

Faculty, Staff and Student Publications

Background: Hemorrhage is the most common cause of potentially preventable death after injury. Balanced transfusion with red blood cells, plasma, and platelets (component therapy, CT) has been shown to reduce mortality, and is the standard of care. Low-Titer Group O Whole Blood (LTOWB) is an attractive alternative to CT, but existing evidence comprises observational studies, and a small single center pilot randomized controlled trial, which evaluated a type of whole blood that is no longer in use. The aim of the "Trauma Resuscitation with Low-Titer Group O Whole Blood Or Products" (TROOP) trial is to compare the effectiveness and safety …


Rsph4a-Pcdx: An Index To Predict Lung Function Decline In Primary Ciliary Dyskinesia, Gabriel Román-Ríos, Gabriel Rosario-Ortiz, Marcos J Ramos-Benitez, Ricardo A Mosquera, Wilfredo De Jesús-Rojas Aug 2025

Rsph4a-Pcdx: An Index To Predict Lung Function Decline In Primary Ciliary Dyskinesia, Gabriel Román-Ríos, Gabriel Rosario-Ortiz, Marcos J Ramos-Benitez, Ricardo A Mosquera, Wilfredo De Jesús-Rojas

Faculty, Staff and Student Publications

Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous disorder that impairs mucociliary clearance and leads to progressive lung disease. This study aimed to characterize lung function decline in a genetically homogeneous cohort of Puerto Rican patients with


Rna Sequencing And Immunohistochemistry Jointly Improve Tumor Biomarker Interpretation, Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K Lennerz, Funda Meric-Bernstam, Alexander Bagaev Aug 2025

Rna Sequencing And Immunohistochemistry Jointly Improve Tumor Biomarker Interpretation, Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K Lennerz, Funda Meric-Bernstam, Alexander Bagaev

Faculty, Staff and Student Publications

This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers-ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20-were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman's correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to …


Inhibition Of Epithelial Cell Yap-Tead/Lox Signaling Attenuates Pulmonary Fibrosis In Preclinical Models, Darcy Elizabeth Wagner, Hani N Alsafadi, Nilay Mitash, Aurelien Justet, Qianjiang Hu, Ricardo Pineda, Claudia Staab-Weijnitz, Martina Korfei, Nika Gvazava, Kristin Wannemo, Ugochi Onwuka, Molly Mozurak, Adriana Estrada-Bernal, Juan Cala-Garcia, Katrin Mutze, Rita Costa, Deniz Bölükbas, John Stegmayr, Wioletta Skronska-Wasek, Stephan Klee, Chiharu Ota, Hoeke A Baarsma, Jingtao Wang, John Sembrat, Anne Hilgendorff, Jun Ding, Andreas Günther, Rachel Chambers, Ivan Rosas, Stijn De Langhe, Naftali Kaminski, Mareike Lehmann, Oliver Eickelberg, Melanie Königshoff Aug 2025

Inhibition Of Epithelial Cell Yap-Tead/Lox Signaling Attenuates Pulmonary Fibrosis In Preclinical Models, Darcy Elizabeth Wagner, Hani N Alsafadi, Nilay Mitash, Aurelien Justet, Qianjiang Hu, Ricardo Pineda, Claudia Staab-Weijnitz, Martina Korfei, Nika Gvazava, Kristin Wannemo, Ugochi Onwuka, Molly Mozurak, Adriana Estrada-Bernal, Juan Cala-Garcia, Katrin Mutze, Rita Costa, Deniz Bölükbas, John Stegmayr, Wioletta Skronska-Wasek, Stephan Klee, Chiharu Ota, Hoeke A Baarsma, Jingtao Wang, John Sembrat, Anne Hilgendorff, Jun Ding, Andreas Günther, Rachel Chambers, Ivan Rosas, Stijn De Langhe, Naftali Kaminski, Mareike Lehmann, Oliver Eickelberg, Melanie Königshoff

Faculty, Staff and Students Publications

Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX …


A Phase 2 Trial Of Niraparib Plus Bevacizumab Maintenance Therapy Following First-Line Platinum-Based Chemotherapy With Bevacizumab In Advanced Ovarian Cancer: Final Analysis And Overall Survival Results From Ovario., Melissa M Hardesty, Thomas C Krivak, Gail S Wright, Erika Hamilton, Evelyn L Fleming, Jimmy Belotte, Shelby Gorman, Natalie Compton, Aine Clements, Heidi J Gray, Gottfried E Konecny, Richard G Moore, Debra L Richardson Aug 2025

A Phase 2 Trial Of Niraparib Plus Bevacizumab Maintenance Therapy Following First-Line Platinum-Based Chemotherapy With Bevacizumab In Advanced Ovarian Cancer: Final Analysis And Overall Survival Results From Ovario., Melissa M Hardesty, Thomas C Krivak, Gail S Wright, Erika Hamilton, Evelyn L Fleming, Jimmy Belotte, Shelby Gorman, Natalie Compton, Aine Clements, Heidi J Gray, Gottfried E Konecny, Richard G Moore, Debra L Richardson

Oncology Articles

OBJECTIVE: To report long-term outcomes from the OVARIO trial of niraparib plus bevacizumab maintenance following first-line platinum-based chemotherapy with bevacizumab in advanced ovarian cancer.

METHODS: The phase 2, single-arm, open-label trial enrolled adult patients with stage IIIB-IV epithelial ovarian, fallopian tube, or primary peritoneal cancer (NCT03326193). Patients were required to have attempted debulking surgery and have a complete or partial response or no evidence of disease following first-line, platinum-based chemotherapy with ≥3 cycles of bevacizumab. The primary endpoint was 18-month progression-free survival (PFS) rate, per RECIST. Secondary endpoints included PFS, overall survival (OS), safety, and health-related quality of life (HRQOL) …


Management Approaches To Spastic Gait Disorders, Sheng Li, Tulsi Pandat, Bradley Chi, Daniel Moon, Manuel Mas Aug 2025

Management Approaches To Spastic Gait Disorders, Sheng Li, Tulsi Pandat, Bradley Chi, Daniel Moon, Manuel Mas

Faculty, Staff and Student Publications

Spastic gait presents clinically as the net mechanical consequence of neurological impairments of spasticity, weakness, and abnormal synergies and their interactions with the ground reaction force in patients with upper motor neuron syndromes and with some neuromuscular diseases. It is critical to differentiate whether the primary problem is weakness or spasticity, thus better understanding different phenotypes of spastic gait disorders. Pelvic girdle abnormality plays a pivotal role in determining the clinical presentation of gait disorders, since it determines the body vector and compensatory kinetic chain reactions in the knee and ankle joints. Knee joint abnormality can be a mechanical compensation …


Patient-Specific Preoperative Plans Can Optimize Femoral Head Coverage And Range Of Motion After Periacetabular Osteotomies, Shuyang Han, Carey A Clark, Nicholas J Dunbar, Madison Brenner, Alexis H Aboulafia, Alfred A Mansour Iii, Philip C Noble Aug 2025

Patient-Specific Preoperative Plans Can Optimize Femoral Head Coverage And Range Of Motion After Periacetabular Osteotomies, Shuyang Han, Carey A Clark, Nicholas J Dunbar, Madison Brenner, Alexis H Aboulafia, Alfred A Mansour Iii, Philip C Noble

Faculty, Staff and Student Publications

Background: The goal of a periacetabular osteotomy is to increase the coverage of the femoral head, primarily in the antero-lateral region, through rotation of the acetabulum in three anatomical planes. The present study was undertaken to determine whether specific combinations of lateral rotation, anterior rotation, and anteversion of the acetabular fragment can be targeted to provide the best balance between femoral head coverage and joint motion.

Methods: Three-dimensional patient-specific hip models were reconstructed from preoperative computerized tomography scans of 15 patients diagnosed with hip dysplasia. Each model was placed in a standard coordinate system with neutral pelvic tilt and femoral …


Mitochondrial Complex I Deficiency Induces Alzheimer's Disease-Like Signatures That Are Reversible By Targeted Therapy., Huanyao Gao, Kate Jensen, Jarred Nesbitt, Mark Ostroot, Gregory Cary, Jesse Wiley, Sergey Trushin, Jens O Watzlawik, Wolfdieter Springer, Alexander Galkin, Priyanka Baloni, Cory Funk, Eugenia Trushina Aug 2025

Mitochondrial Complex I Deficiency Induces Alzheimer's Disease-Like Signatures That Are Reversible By Targeted Therapy., Huanyao Gao, Kate Jensen, Jarred Nesbitt, Mark Ostroot, Gregory Cary, Jesse Wiley, Sergey Trushin, Jens O Watzlawik, Wolfdieter Springer, Alexander Galkin, Priyanka Baloni, Cory Funk, Eugenia Trushina

Faculty Research 2025

INTRODUCTION: Mitochondrial dysfunction is implicated in Alzheimer's disease (AD), but whether it drives AD-associated changes is unclear. We assessed transcriptomic alterations in the brains of Ndufs4

METHODS: Cortico-hippocampal tissue from Ndufs4

RESULTS: Knockout of Ndufs4-mediated mtCI deficiency disrupted mitochondrial homeostasis, energy metabolism, and synaptic gene expression, recapitulating transcriptomic signatures of AD. CP2 treatment partially reversed these changes, with female Ndufs4

DISCUSSION: Loss of mtCI activity alone is sufficient to induce AD-like molecular changes in the brain, independent of amyloid beta or phosphorylated tau. CP2-mediated rescue highlights the potential of targeting mitochondria as a therapeutic strategy for AD. Sex-specific responses suggest …


Lonp1 Regulation Of Mitochondrial Protein Folding Provides Insight Into Beta Cell Failure In Type 2 Diabetes., Jin Li, Yamei Deng, Marie Gasser, Jie Zhu, Emily M Walker, Vaibhav Sidarala, Emma C Reck, Dre L Hubers, Mabelle B Pasmooij, Chun-Shik Shin, Khushdeep Bandesh, Efthymios Motakis, Siddhi Nargund, Romy Kursawe, Venkatesha Basrur, Alexey I Nesvizhskii, Michael L. Stitzel, David C Chan, Guy A Rutter, Scott A Soleimanpour Aug 2025

Lonp1 Regulation Of Mitochondrial Protein Folding Provides Insight Into Beta Cell Failure In Type 2 Diabetes., Jin Li, Yamei Deng, Marie Gasser, Jie Zhu, Emily M Walker, Vaibhav Sidarala, Emma C Reck, Dre L Hubers, Mabelle B Pasmooij, Chun-Shik Shin, Khushdeep Bandesh, Efthymios Motakis, Siddhi Nargund, Romy Kursawe, Venkatesha Basrur, Alexey I Nesvizhskii, Michael L. Stitzel, David C Chan, Guy A Rutter, Scott A Soleimanpour

Faculty Research 2025

Protein misfolding is a contributor to the development of type 2 diabetes (T2D), but the specific role of impaired proteostasis is unclear. Here we show a robust accumulation of misfolded proteins in the mitochondria of human pancreatic islets from patients with T2D and elucidate its impact on β cell viability through the mitochondrial matrix protease LONP1. Quantitative proteomics studies of protein aggregates reveal that islets from donors with T2D have a signature resembling mitochondrial rather than endoplasmic reticulum protein misfolding. Loss of LONP1, a vital component of the mitochondrial proteostatic machinery, with reduced expression in the β cells of donors …


Sustained Lung Inflammation Post-Sars-Cov-2 Infection In Mice Is Associated With Increased Pulmonary T Cells., Sophie Y Guan, Patricia P Ogger, Ana Farias, Minerva Garcia Martín, Joy Nakawesi, Olivia Bedard, Candice N Baker, Nadia Rosenthal, Cecilia Johansson Aug 2025

Sustained Lung Inflammation Post-Sars-Cov-2 Infection In Mice Is Associated With Increased Pulmonary T Cells., Sophie Y Guan, Patricia P Ogger, Ana Farias, Minerva Garcia Martín, Joy Nakawesi, Olivia Bedard, Candice N Baker, Nadia Rosenthal, Cecilia Johansson

Faculty Research 2025

Many SARS-CoV-2 patients experience chronic pulmonary symptoms and long-term inflammation despite viral clearance. While these clinical manifestations have been linked to the dysregulation of the adaptive immune response, the underlying immunopathology remains poorly understood due to a lack of suitable animal models. To investigate long-term pulmonary consequences of SARS-CoV-2 infection, we used a genetic cross of 129 mice and C57BL/6 (B6)-K18-hACE2 transgene mice, a model previously shown to survive infection. 129xB6-K18-hACE2 mice or littermate controls were infected with a low dose (5 × 102 PFU) of ancestral SARS-CoV-2. Complete viral clearance and full recovery from weight loss …


Complex Genetic Variation In Nearly Complete Human Genomes., Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, Dongahn Yoo, Carolyn Paisie, William T Harvey, Xuefang Zhao, Gianni V Martino, Mir Henglin, Katherine M Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Stephan Scholz, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J Norman, Keisuke K Oshima, Benedict Paten, Adam M Phillippy, Nicholas R Pollock, Tobias Rausch, Mikko Rautiainen, Yuwei Song, Arda Söylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C Zody, Ryan E Mills, Scott E Devine, Xinghua Shi, Michael E Talkowski, Mark J P Chaisson, Alexander T Dilthey, Miriam K Konkel, Jan O Korbel, Charles Lee, Christine R Beck, Evan E Eichler, Tobias Marschall Aug 2025

Complex Genetic Variation In Nearly Complete Human Genomes., Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, Dongahn Yoo, Carolyn Paisie, William T Harvey, Xuefang Zhao, Gianni V Martino, Mir Henglin, Katherine M Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Stephan Scholz, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J Norman, Keisuke K Oshima, Benedict Paten, Adam M Phillippy, Nicholas R Pollock, Tobias Rausch, Mikko Rautiainen, Yuwei Song, Arda Söylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C Zody, Ryan E Mills, Scott E Devine, Xinghua Shi, Michael E Talkowski, Mark J P Chaisson, Alexander T Dilthey, Miriam K Konkel, Jan O Korbel, Charles Lee, Christine R Beck, Evan E Eichler, Tobias Marschall

Faculty Research 2025

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps1,2 and reaching telomere-to-telomere status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8 and AMY1/AMY2, and fully resolve 1,852 complex structural variants. In addition, we completely assemble and validate 1,246 human centromeres. We find up …


Use Of Cognitive-Behavioral Therapy In A Nation-Wide Veterans Health Administration Sample: The Role Of Clinic, Therapist, And Patient Factors., Alan Mcguire, Mindy Flanagan, Madison E Stout, Jessica Coffing, Marina Kukla, Morgan Traylor, Laura Myers, Nancy Henry, Jessica Carter, Marianne Matthias Aug 2025

Use Of Cognitive-Behavioral Therapy In A Nation-Wide Veterans Health Administration Sample: The Role Of Clinic, Therapist, And Patient Factors., Alan Mcguire, Mindy Flanagan, Madison E Stout, Jessica Coffing, Marina Kukla, Morgan Traylor, Laura Myers, Nancy Henry, Jessica Carter, Marianne Matthias

Health Services and Informatics Research

OBJECTIVE: To examine the use of CBT-CP (Cognitive-behavioral therapy for chronic pain) by CBT-CP-trained therapists to treat patients with pain over a five-year period (October 2015-February 2020).

DATA SOURCES AND STUDY SETTING: CBT-CP is a core evidence-based practice that is central to multidisciplinary chronic pain care. However, research suggests that CBT-CP is underused. The current study used national Veterans Health Administration data to examine the use of CBT-CP by CBT-CP-trained therapists to treat patients with pain over a five-year period.

STUDY DESIGN: Multilevel modeling was used to evaluate clinic, therapist, and patient-level factors as predictors of CBT-CP receipt.

DATA COLLECTION: …


Association Of Epigenetic Aging With Plasma Cbiomarkers Of Amyloid, Tau, Neurodegeneration, And Neuroinflammation In Hispanic/Latino Adults, Myriam Fornage, Wassim Tarraf, Martha L Daviglus, Charles Decarli, Kevin A Gonzalez, Carmen R Isasi, Sayaka Kuwayama, Melissa Lamar, Bonnie E Levin, Humberto Parada, Alberto R Ramos, Tatjana Rundek, Bharat Thyagarajan, Hector M González Aug 2025

Association Of Epigenetic Aging With Plasma Cbiomarkers Of Amyloid, Tau, Neurodegeneration, And Neuroinflammation In Hispanic/Latino Adults, Myriam Fornage, Wassim Tarraf, Martha L Daviglus, Charles Decarli, Kevin A Gonzalez, Carmen R Isasi, Sayaka Kuwayama, Melissa Lamar, Bonnie E Levin, Humberto Parada, Alberto R Ramos, Tatjana Rundek, Bharat Thyagarajan, Hector M González

The Brown Foundation: Institute of Molecular Medicine

Background: Blood-based biomarkers hold significant promise for the early detection and diagnosis of Alzheimer's disease (AD) and other dementias. Age-related changes in blood levels of AD biomarkers are well-documented but poorly understood. Epigenetic clocks are mathematical models based on DNA methylation patterns that reflect various aspects of the multidimensional aging process. We investigated the associations of epigenetic aging with five blood-based AD biomarkers in 2656 Hispanic/Latino adults (mean age 62.5 years; 65% females) from the Hispanic Community Health Study/Study of Latinos. We used multivariable linear regression models to estimate the associations of acceleration in each of five epigenetic clocks with …


Summit Max: A Randomized Trial Of The Super Large Bore Hipoint Reperfusion System Versus Vecta System For Aspiration Thrombectomy., Thanh N Nguyen, Guilherme Dabus, Ben Mcguinness, James Caldwell, Ryan Priest, Ansaar T Rai, Osama O Zaidat, Bradley A Gross, Ricardo Hanel, Shane Lee, Shazam Hussain, Hamza Shaikh, Mohamad Abdalkader, Ronald Budzik, Craig Kilburg, Keith Woodward, Marco Colasurdo, Jesse Liu, Albert J Yoo, Priyank Khandelwal, Sohyun Boo, Phong Vu, Eugene Lin, Mohammad Almajali, Jasmeet Singh, Alhamza Al-Bayati, Michael J Lang, Michael Abraham, Ameer E Hassan, Peter Pema, Coleman Martin, Ramesh Grandhi, Daniel A Tonetti, Harry R Hixson, Amin Aghaebrahim, Eric Sauvageau, Santiago Ortega-Gutierrez, Dileep R Yavagal, Esteban Cheng-Ching, Jane Khalife, Italo Linfante, Volodymyr Vulkanov, Jazba Soomro, Johanna T Fifi, Lucien Maidan, Alexander Copelan, Clemens M Schirmer, Mark Bain, Gabor Toth, Mahesh Jayaraman, Roberta Novakovic-White, Sudhakar Satti, Nicolas Villelli, Pascal Jabbour, Matthew Page, Davina J Mcallister, Robert Araujo Contreras, Edgar A Samaniego, David S Liebeskind, Steven W Hetts, Raul G Nogueira, Joey English, Ajit S Puri Aug 2025

Summit Max: A Randomized Trial Of The Super Large Bore Hipoint Reperfusion System Versus Vecta System For Aspiration Thrombectomy., Thanh N Nguyen, Guilherme Dabus, Ben Mcguinness, James Caldwell, Ryan Priest, Ansaar T Rai, Osama O Zaidat, Bradley A Gross, Ricardo Hanel, Shane Lee, Shazam Hussain, Hamza Shaikh, Mohamad Abdalkader, Ronald Budzik, Craig Kilburg, Keith Woodward, Marco Colasurdo, Jesse Liu, Albert J Yoo, Priyank Khandelwal, Sohyun Boo, Phong Vu, Eugene Lin, Mohammad Almajali, Jasmeet Singh, Alhamza Al-Bayati, Michael J Lang, Michael Abraham, Ameer E Hassan, Peter Pema, Coleman Martin, Ramesh Grandhi, Daniel A Tonetti, Harry R Hixson, Amin Aghaebrahim, Eric Sauvageau, Santiago Ortega-Gutierrez, Dileep R Yavagal, Esteban Cheng-Ching, Jane Khalife, Italo Linfante, Volodymyr Vulkanov, Jazba Soomro, Johanna T Fifi, Lucien Maidan, Alexander Copelan, Clemens M Schirmer, Mark Bain, Gabor Toth, Mahesh Jayaraman, Roberta Novakovic-White, Sudhakar Satti, Nicolas Villelli, Pascal Jabbour, Matthew Page, Davina J Mcallister, Robert Araujo Contreras, Edgar A Samaniego, David S Liebeskind, Steven W Hetts, Raul G Nogueira, Joey English, Ajit S Puri

Neuroscience Articles

BACKGROUND: Rapid and complete recanalization is a primary goal in the endovascular treatment of large vessel occlusion stroke. The effectiveness and safety of super large bore aspiration catheters (0.088″ inner diameter) for the treatment of large vessel occlusion stroke have not been demonstrated in a randomized trial.

METHODS: SUMMIT MAX (A Prospective, Randomized, Controlled, Interventional Clinical Trial to Evaluate the Safety and Effectiveness of the Route 92 Medical MonoPoint Reperfusion System for Aspiration Embolectomy in Acute Ischemic Stroke Patients) was a prospective, randomized, controlled, open-label clinical trial of patients with internal carotid artery and middle cerebral artery M1 occlusions, comparing …


The Importance Of Imperfect Pre-Clinical Models In Adolescent Idiopathic Scoliosis, Diane S Sepich, Ryan S Gray, Nadav Ahituv, Christina A Gurnett, Jonathan J Rios, Lila Solnica-Krezel, Carol A Wise Aug 2025

The Importance Of Imperfect Pre-Clinical Models In Adolescent Idiopathic Scoliosis, Diane S Sepich, Ryan S Gray, Nadav Ahituv, Christina A Gurnett, Jonathan J Rios, Lila Solnica-Krezel, Carol A Wise

2020-Current year OA Pubs

Adolescent idiopathic scoliosis (AIS) is a twisting spinal deformity that occurs in otherwise healthy children at the time of rapid pre-pubescent growth. AIS affects ∼3% of children worldwide and is the most common musculoskeletal diagnosis in pediatric populations, posing a significant physiological, psychosocial and financial burden to patients. Genetic predisposition is a clear and major contributor to AIS, and insights from genomic discoveries are inspiring translational studies ultimately aimed at developing novel diagnostics and therapies. Pre-clinical animal models of AIS are now essential to validate human genetic findings, understand gene-by-environment interactions, and speed etiologic and therapeutic discovery. In this Perspective, …


Sex-Related Measurement Bias In Autism Spectrum Disorder Symptoms In The Baby Siblings Research Consortium, Catherine A Burrows, Natasha Marrus, Et Al. Aug 2025

Sex-Related Measurement Bias In Autism Spectrum Disorder Symptoms In The Baby Siblings Research Consortium, Catherine A Burrows, Natasha Marrus, Et Al.

2020-Current year OA Pubs

IMPORTANCE: Disparities exist in age of diagnosis and prevalence of autism spectrum disorder (ASD) for female compared with male children. Correcting for sources of bias is critical for improving equitable ASD identification.

OBJECTIVE: To determine whether sex differences exist in measurement of ASD symptoms using the Autism Diagnostic Observation Schedule (ADOS) among young children at high familial likelihood (HFL) and low familial likelihood (LFL) of ASD.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study collected longitudinal, prospective data from the Baby Siblings Research Consortium between January 1, 2003, and December 31, 2021. Participants included 3106 children who had an older sibling …


Benefit Of Early Oseltamivir Therapy For Adults Hospitalized With Influenza A: An Observational Study, Nathaniel M Lewis, Jennie H Kwon, Et Al. Aug 2025

Benefit Of Early Oseltamivir Therapy For Adults Hospitalized With Influenza A: An Observational Study, Nathaniel M Lewis, Jennie H Kwon, Et Al.

2020-Current year OA Pubs

BACKGROUND: Clinical guidelines recommend initiation of antiviral therapy as soon as possible for patients hospitalized with confirmed or suspected influenza.

METHODS: A multicenter US observational sentinel surveillance network prospectively enrolled adults (aged ≥18 years) hospitalized with laboratory-confirmed influenza at 24 hospitals during 1 October 2022-21 July 2023. A multivariable proportional odds model was used to compare peak pulmonary disease severity (no oxygen support, standard supplemental oxygen, high-flow oxygen/non-invasive ventilation, invasive mechanical ventilation, or death) after the day of hospital admission among patients starting oseltamivir treatment on the day of admission (early) versus those who did not (late or not treated), …


Combination Effect Of Finerenone And Empagliflozin In Participants With Chronic Kidney Disease And Type 2 Diabetes Using A Uacr Endpoint (Confidence) Trial: Baseline Clinical Characteristics, Rajiv Agarwal, Janet B Mcgill, Et Al. Aug 2025

Combination Effect Of Finerenone And Empagliflozin In Participants With Chronic Kidney Disease And Type 2 Diabetes Using A Uacr Endpoint (Confidence) Trial: Baseline Clinical Characteristics, Rajiv Agarwal, Janet B Mcgill, Et Al.

2020-Current year OA Pubs

BACKGROUND: Finerenone, a selective nonsteroidal mineralocorticoid receptor antagonist, and sodium-glucose cotransporter 2 inhibitors (SGLT2is) both reduce chronic kidney disease (CKD) progression and improve kidney/cardiovascular (CV) outcomes. The CONFIDENCE (COmbinatioN effect of FInerenone anD EmpaglifloziN in participants with chronic kidney disease and type 2 diabetes using a UACR Endpoint) study (NCT05254002; EudraCT 2021-003037-11) hypothesis is that early combination of finerenone and empagliflozin, an SGLT2i, is superior to either drug alone in reducing urine albumin-to-creatinine ratio (UACR) over 6 months.

METHODS: CONFIDENCE is an ongoing, fully enrolled, randomized, controlled, double-blind, multicentre phase 2 clinical trial in adults (≥18 years of age) with …


Tau Pet Positivity In Individuals With And Without Cognitive Impairment Varies With Age, Amyloid-Β Status, Apoe Genotype And Sex, Rik Ossenkoppele, Tammy L S Benzinger, Et Al. Aug 2025

Tau Pet Positivity In Individuals With And Without Cognitive Impairment Varies With Age, Amyloid-Β Status, Apoe Genotype And Sex, Rik Ossenkoppele, Tammy L S Benzinger, Et Al.

2020-Current year OA Pubs

Tau positron emission tomography (PET) imaging allows in vivo detection of tau proteinopathy in Alzheimer's disease, which is associated with neurodegeneration and cognitive decline. Understanding how demographic, clinical and genetic factors relate to tau PET positivity will facilitate its use for clinical practice and research. Here we conducted an analysis of 42 cohorts worldwide (N = 12,048), including 7,394 cognitively unimpaired (CU) participants, 2,177 participants with mild cognitive impairment (MCI) and 2,477 participants with dementia. We found that from age 60 years to 80 years, tau PET positivity in a temporal composite region increased from 1.1% to 4.4% among CU …


Human Thalamocortical Structural Connectivity Develops In Line With A Hierarchical Axis Of Cortical Plasticity, Valerie J Sydnor, Deanna M Barch, Et Al. Aug 2025

Human Thalamocortical Structural Connectivity Develops In Line With A Hierarchical Axis Of Cortical Plasticity, Valerie J Sydnor, Deanna M Barch, Et Al.

2020-Current year OA Pubs

Human cortical development follows a hierarchical, sensorimotor-to-association sequence. The brain's capacity to enact this sequence indicates that it relies on unknown mechanisms to regulate regional differences in the timing of cortical maturation. Given evidence from animal systems that thalamic axons mechanistically regulate periods of cortical plasticity, here we evaluate in humans whether the development of structural connections between the thalamus and cortex aligns with cortical maturational heterochronicity. By deriving a new tractography atlas of human thalamic connections and applying it to diffusion data from three youth samples (8-23 years; total n = 2,676), we demonstrate that thalamocortical connectivity matures in …


Do Risk Factors For Hcc Impact The Association Of Ct/Mri Lirads Major Features With Hcc? An Individual Participant Data Meta-Analysis, Robert G Adamo, Daniel R Ludwig, Tyler J Fraum, Et Al. Aug 2025

Do Risk Factors For Hcc Impact The Association Of Ct/Mri Lirads Major Features With Hcc? An Individual Participant Data Meta-Analysis, Robert G Adamo, Daniel R Ludwig, Tyler J Fraum, Et Al.

2020-Current year OA Pubs

No abstract provided.


Building Capacity And Equity In Implementation Science: Evaluation Of A National Mentored Training Program, Ross C Brownson, Shelly J Kannuthurai, Rebekah R Jacob, Leopoldo J Cabassa, Lisa M Klesges, Rachel G Tabak, Debra Haire-Joshu, Et Al. Aug 2025

Building Capacity And Equity In Implementation Science: Evaluation Of A National Mentored Training Program, Ross C Brownson, Shelly J Kannuthurai, Rebekah R Jacob, Leopoldo J Cabassa, Lisa M Klesges, Rachel G Tabak, Debra Haire-Joshu, Et Al.

2020-Current year OA Pubs

BACKGROUND: As implementation science evolves, it is essential to expand training capacity to build intellectual capital continually. The demand for training in implementation science far outstrips the current supply. This paper presents the methods and findings from the Institute for Implementation Science Scholars (IS-2) national training program (2020-2024).

METHODS: The IS-2 was a US-based, two-year training program that provided mentored training for early- and mid-career researchers interested in applying implementation science principles to reduce the burden of chronic disease disparities. Scholars attended two annual, 2.5-day intensive training sessions, received ongoing remote and in-person mentoring, and were supported by other activities …