Medical Sciences Commons^™

Tissue-Resident Memory T Cell Signatures From Single-Cell Analysis Associated With Better Melanoma Prognosis, Chongming Jiang, Cheng-Chi Chao, Jianrong Li, Xin Ge, Aidan Shen, Vadim Jucaud, Chao Cheng, Xiling Shen

Faculty, Staff and Students Publications

Tissue-resident memory T cells (TRM) are a specialized T cell population residing in peripheral tissues. The presence and potential impact of TRM in the tumor immune microenvironment (TIME) remain to be elucidated. Here, we systematically investigated the relationship between TRM and melanoma TIME based on multiple clinical single-cell RNA-seq datasets and developed signatures indicative of TRM infiltration. TRM infiltration is associated with longer overall survival and abundance of T cells, NK cells, M1 macrophages, and memory B cells in the TIME. A 22-gene TRM–derived risk score was further developed to effectively classify patients into low- and high-risk categories, distinguishing overall …

Clonal Dominance Defines Metastatic Dissemination In Pancreatic Cancer, I-Lin Ho, Chieh-Yuan Li, Fuchenchu Wang, Li Zhao, Jingjing Liu, Er-Yen Yen, Charles A Dyke, Rutvi Shah, Zhaoliang Liu, Ali Osman Çetin, Yanshuo Chu, Francesca Citron, Sergio Attanasio, Denise Corti, Faezeh Darbaniyan, Edoardo Del Poggetto, Sara Loponte, Jintan Liu, Melinda Soeung, Ziheng Chen, Shan Jiang, Hong Jiang, Akira Inoue, Sisi Gao, Angela Deem, Ningping Feng, Haoqiang Ying, Michael Kim, Virginia Giuliani, Giannicola Genovese, Jianhua Zhang, Andrew Futreal, Anirban Maitra, Timothy Heffernan, Linghua Wang, Kim-Anh Do, Gaetano Gargiulo, Giulio Draetta, Alessandro Carugo, Ruitao Lin, Andrea Viale

Faculty, Staff and Student Publications

Tumors represent ecosystems where subclones compete during tumor growth. While extensively investigated, a comprehensive picture of the interplay of clonal lineages during dissemination is still lacking. Using patient-derived pancreatic cancer cells, we created orthotopically implanted clonal replica tumors to trace clonal dynamics of unperturbed tumor expansion and dissemination. This model revealed the multifaceted nature of tumor growth, with rapid changes in clonal fitness leading to continuous reshuffling of tumor architecture and alternating clonal dominance as a distinct feature of cancer growth. Regarding dissemination, a large fraction of tumor lineages could be found at secondary sites each having distinctive organ growth …

The Digital Transition: Are Adults Aged 65 Years Or Older Willing To Complete Online Forms And Questionnaires In Patient Portals?, Nancy P Gordon, Sherry Zhang, Joan C Lo, Christina F Li

Faculty, Staff and Student Publications

INTRODUCTION: Patients are being encouraged to complete forms electronically using patient portals rather than on paper, but willingness of older adults to make this transition is uncertain.

METHODS: The authors analyzed data for 4105 Kaiser Permanente Northern California 2020 Member Health Survey respondents aged 65-85 years who answered a question about willingness to complete online forms and questionnaires using a patient portal. Data weighted to the Kaiser Permanente Northern California membership were used to estimate percentages of older adults willing to complete patient portal forms and questionnaires. Chi-square tests and log-Poisson regression models that included sociodemographic, internet use, and patient …

Downregulation Of Irf8 In Alveolar Macrophages By G-Csf Promotes Metastatic Tumor Progression, Stephanie L Tzetzo, Elliot D Kramer, Hemn Mohammadpour, Minhyung Kim, Spencer R Rosario, Han Yu, Melissa R Dolan, Chetan C Oturkar, Brian G Morreale, Paul N Bogner, Aimee B Stablewski, Fernando J Benavides, Craig M Brackett, John M L Ebos, Gokul M Das, Mateusz Opyrchal, Michael J Nemeth, Sharon S Evans, Scott I Abrams

Faculty, Staff and Student Publications

Tissue-resident macrophages (TRMs) are abundant immune cells within pre-metastatic sites, yet their functional contributions to metastasis remain incompletely understood. Here, we show that alveolar macrophages (AMs), the main TRMs of the lung, are susceptible to downregulation of the immune stimulatory transcription factor IRF8, impairing anti-metastatic activity in models of metastatic breast cancer. G-CSF is a key tumor-associated factor (TAF) that acts upon AMs to reduce IRF8 levels and facilitate metastasis. Translational relevance of IRF8 downregulation was observed among macrophage precursors in breast cancer and a

Phase I Study Of Oric-101, A Glucocorticoid Receptor Antagonist, In Combination With Enzalutamide In Patients With Metastatic Castration-Resistant Prostate Cancer Progressing On Enzalutamide, Wassim Abida, Andrew W Hahn, Neal Shore, Neeraj Agarwal, Paul Sieber, Matthew R Smith, Tanya Dorff, Paul Monk, Matthew Rettig, Rupal Patel, Anne Page, Maureen Duff, Rongda Xu, Jian Wang, Shravani Barkund, Aleksandr Pankov, Amber Wang, Melissa R Junttila, Pratik S Multani, Anneleen Daemen, Edna Chow Maneval, Christopher J Logothetis, Michael J Morris

Faculty, Staff and Student Publications

Purpose: Increased glucocorticoid receptor (GR) signaling is a proposed compensatory mechanism of resistance to androgen receptor (AR) inhibition in metastatic castration-resistant prostate cancer (mCRPC). ORIC-101 is a potent and selective orally-bioavailable GR antagonist.

Patients and methods: Safety, pharmacokinetic/pharmacodynamic, and antitumor activity of ORIC-101 in combination with enzalutamide were studied in patients with mCRPC progressing on enzalutamide. ORIC-101 doses ranging from 80 to 240 mg once daily were tested in combination with enzalutamide 160 mg once daily. Pharmacokinetics/pharmacodynamics was assessed after a single dose and at steady state. Disease control rate (DCR) at 12 weeks was evaluated at the recommended phase …

Validation Of A Multiomic Model Of Plasma Extracellular Vesicle Pd-L1 And Radiomics For Prediction Of Response To Immunotherapy In Nsclc, Diego De Miguel-Perez, Murat Ak, Priyadarshini Mamindla, Alessandro Russo, Serafettin Zenkin, Nursima Ak, Vishal Peddagangireddy, Luis Lara-Mejia, Muthukumar Gunasekaran, Andres F Cardona, Aung Naing, Fred R Hirsch, Oscar Arrieta, Rivka R Colen, Christian Rolfo

Faculty, Staff and Student Publications

BACKGROUND: Immune-checkpoint inhibitors (ICIs) have showed unprecedent efficacy in the treatment of patients with advanced non-small cell lung cancer (NSCLC). However, not all patients manifest clinical benefit due to the lack of reliable predictive biomarkers. We showed preliminary data on the predictive role of the combination of radiomics and plasma extracellular vesicle (EV) PD-L1 to predict durable response to ICIs.

MAIN BODY: Here, we validated this model in a prospective cohort of patients receiving ICIs plus chemotherapy and compared it with patients undergoing chemotherapy alone. This multiparametric model showed high sensitivity and specificity at identifying non-responders to ICIs and outperformed …

Toward Clinical-Grade Evaluation Of Large Language Models, Amy C Moreno, Danielle S Bitterman

Faculty, Staff and Student Publications

No abstract provided.

Safety And Efficacy Of Ibrutinib In Combination With Rituximab And Lenalidomide In Previously Untreated Follicular And Marginal Zone Lymphoma: An Open Label, Phase 2 Study, Max J Gordon, Lei Feng, Paolo Strati, Hun Ju Lee, Fredrick B Hagemeister, Jason R Westin, Felipe Samaniego, Mario L Marques-Piubelli, Francisco Vega Vazquez, Edwin R Parra Cuentas, Luisa M Solis-Soto, Wencai Ma, Jing Wang, Linda Claret, Barbara Averill, Karina Ibanez, Luis E Fayad, Christopher R Flowers, Michael R Green, R Eric Davis, Sattva S Neelapu, Nathan H Fowler, Loretta J Nastoupil

Faculty, Staff and Student Publications

Background: Follicular lymphoma (FL) and marginal zone lymphoma (MZL) are indolent non-Hodgkin lymphomas (iNHL). Median survival for iNHL is approximately 20 years. Because standard treatments are not curative, patients often receive multiple lines of therapy with associated toxicity-rationally designed, combination therapies with curative potential are needed. The immunomodulatory drug lenalidomide was evaluated in combination with rituximab for the frontline treatment of FL in the phase 3 RELEVANCE study. Ibrutinib, an oral Bruton tyrosine kinase inhibitor, is active in NHL and was evaluated in combination with lenalidomide, rituximab, and ibrutinib (IRR) in a phase 1 study.

Methods: The authors conducted an …

Sabr For Sarcoma Lung Metastases: Indications For Treatment And Guidance For Patient Selection, Ahsan S Farooqi, Alison K Yoder, Heather Y Lin, Dario Pasalic, Jeremy Erasmus, Sonia Betancourt, Cort Wernz, Devarati Mitra, Maria A Zarzour, Neeta Somaiah, Anthony Conley, Ravin Ratan, Andrew Livingston, Dejka M Araujo, Christina Roland, Christopher Scally, Emily Keung, Saumil N Gandhi, B Ashleigh Guadagnolo, Quynh-Nhu Nguyen, Andrew J Bishop

Faculty, Staff and Student Publications

Purpose: The lungs are the most common site of metastasis for patients with soft tissue sarcoma. SABR is commonly employed to treat lung metastases among select patients with sarcoma with limited disease burden. We sought to evaluate outcomes and patterns of failure among patients with sarcoma treated with SABR for their lung metastases.

Methods and materials: We performed a retrospective review of patients treated at a tertiary cancer center between 2006 and 2020. Patient disease status at the time of SABR was categorized as either oligorecurrent or oligoprogressive. The Kaplan-Meier method was used to estimate disease outcomes. Uni- and multivariable …

Deep Learning Approaches For Cancer Prognosis Prediction Using Histopathological, Omics, And Clinical Data, Shuai Jiang

Dartmouth College Ph.D Dissertations

Accurate prediction of patient outcomes is crucial for shared clinical decision-making, treatment planning, and patients' psychological adjustment. Histopathological features of cancer, including tumor size, lymph node involvement, and metastasis, are commonly incorporated into survival prediction models, underscoring the prognostic value of whole slide images (WSIs). Concurrently, studies have highlighted the significance of omics data, such as transcriptomics, in providing valuable insights into cancer prognosis.

The emerging deep learning methods have brought new opportunities in biomedical informatics. Despite a growing body of studies on the application of deep learning methods for predicting prognosis using WSIs, the results are varied, primarily due …

Viscosity Flow Curves Of Agar And The Bounded Ripening Growth Model Of The Gelation Onset, Vincenzo Villani

Faculty, Staff and Student Publications

The gelation kinetics of agar aqueous solutions were studied by means of the viscosity flow curves using a coaxial Couette cylinder viscometer. The viscosity curves show an unusual sigmoidal trend or an exponential decay to a viscous steady state. An original theory of gelation kinetics was developed considering the coarsening of increasingly larger and more stable clusters due to Ostwald ripening and the breakup of clusters that were too large due to the instability of rotating large particles induced by the shear rate. The developed

A Novel Spatiotemporal Graph Convolutional Network Framework For Functional Connectivity Biomarkers Identification Of Alzheimer’S Disease, Ying Zhang, Le Xue, Shuoyan Zhang, Jiacheng Yang, Qi Zhang, Min Wang, Luyao Wang, Mingkai Zhang, Jiehui Jiang, Yunxia Li

Faculty, Staff and Student Publications

BACKGROUND: Functional connectivity (FC) biomarkers play a crucial role in the early diagnosis and mechanistic study of Alzheimer's disease (AD). However, the identification of effective FC biomarkers remains challenging. In this study, we introduce a novel approach, the spatiotemporal graph convolutional network (ST-GCN) combined with the gradient-based class activation mapping (Grad-CAM) model (STGC-GCAM), to effectively identify FC biomarkers for AD.

METHODS: This multi-center cross-racial retrospective study involved 2,272 participants, including 1,105 cognitively normal (CN) subjects, 790 mild cognitive impairment (MCI) individuals, and 377 AD patients. All participants underwent functional magnetic resonance imaging (fMRI) and T1-weighted MRI scans. In this study, …

Outpatient Covid-19 Convalescent Plasma Recipient Antibody Thresholds Correlated To Reduced Hospitalizations Within A Randomized Trial, Han-Sol Park, Anna Yin, Caelan Barranta, John S Lee, Christopher A Caputo, Jaiprasath Sachithanandham, Maggie Li, Steve Yoon, Ioannis Sitaras, Anne Jedlicka, Yolanda Eby, Malathi Ram, Reinaldo E Fernandez, Owen R Baker, Aarthi G Shenoy, Giselle S Mosnaim, Yuriko Fukuta, Bela Patel, Sonya L Heath, Adam C Levine, Barry R Meisenberg, Emily S Spivak, Shweta Anjan, Moises A Huaman, Janis E Blair, Judith S Currier, James H Paxton, Jonathan M Gerber, Joann R Petrini, Patrick B Broderick, William Rausch, Marie Elena Cordisco, Jean Hammel, Benjamin Greenblatt, Valerie C Cluzet, Daniel Cruser, Kevin Oei, Matthew Abinante, Laura L Hammitt, Catherine G Sutcliffe, Donald N Forthal, Martin S Zand, Edward R Cachay, Jay S Raval, Seble G Kassaye, Christi E Marshall, Anusha Yarava, Karen Lane, Nichol A Mcbee, Amy L Gawad, Nicky Karlen, Atika Singh, Daniel E Ford, Douglas A Jabs, Lawrence J Appel, David M Shade, Bryan Lau, Stephan Ehrhardt, Sheriza N Baksh, Janna R Shapiro, Jiangda Ou, Yu Bin Na, Maria D Knoll, Elysse Ornelas-Gatdula, Netzahualcoyotl Arroyo-Curras, Thomas J Gniadek, Patrizio Caturegli, Jinke Wu, Nelson Ndahiro, Michael J Betenbaugh, Alyssa Ziman, Daniel F Hanley, Arturo Casadevall, Shmuel Shoham, Evan M Bloch, Kelly A Gebo, Aaron Ar Tobian, Oliver Laeyendecker, Andrew Pekosz, Sabra L Klein, David J Sullivan

Faculty, Staff and Students Publications

BACKGROUND

COVID-19 convalescent plasma (CCP) virus-specific antibody levels that translate into recipient posttransfusion antibody levels sufficient to prevent disease progression are not defined.

METHODS

This secondary analysis correlated donor and recipient antibody levels to hospitalization risk among unvaccinated, seronegative CCP recipients within the outpatient, double-blind, randomized clinical trial that compared CCP to control plasma. The majority of COVID-19 CCP arm hospitalizations (15/17, 88%) occurred in this unvaccinated, seronegative subgroup. A functional cutoff to delineate recipient high versus low posttransfusion antibody levels was established by 2 methods: (i) analyzing virus neutralization–equivalent anti–Spike receptor-binding domain immunoglobulin G (anti-S-RBD IgG) responses in donors …

Utility Of Peripheral Protein Biomarkers For The Prediction Of Incident Interstitial Features: A Multicentre Retrospective Cohort Study, Samuel Ash, Tracy J Doyle, Bina Choi, Ruben San Jose Estepar, Victor Castro, Nicholas Enzer, Ravi Kalhan, Gabrielle Liu, Russell Bowler, David O Wilson, Raul San Jose Estepar, Ivan O Rosas, George R Washko

Faculty, Staff and Students Publications

INTRODUCTION/RATIONALE: Protein biomarkers may help enable the prediction of incident interstitial features on chest CT.

METHODS: We identified which protein biomarkers in a cohort of smokers (COPDGene) differed between those with and without objectively measured interstitial features at baseline using a univariate screen (t-test false discovery rate, FDR p

RESULTS: In COPDGene, 1305 biomarkers were available and 20 differed between those with and without interstitial features at baseline. Of these, 11 were associated with feature progression over a mean of 5.5 years of follow-up, and of these 4 were available in PLuSS, (angiopoietin-2, matrix metalloproteinase 7, macrophage inflammatory protein 1 …

Btn1a1 Is A Novel Immune Checkpoint Mutually Exclusive To Pd-L1, Young-Seung Kim, Seung-Hoon Lee, Andrew H Park, Chunai Wu, Bong-Ki Hong, Hyunjin Jung, Steven H Lin, Stephen S Yoo

Faculty, Staff and Student Publications

BACKGROUND: While Programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) blockade is a potent antitumor treatment strategy, it is effective in only limited subsets of patients with cancer, emphasizing the need for the identification of additional immune checkpoints. Butyrophilin 1A1 (BTN1A1) has been reported to exhibit potential immunoregulatory activity, but its ability to function as an immune checkpoint remains to be systematically assessed, and the mechanisms underlying such activity have yet to be characterized.

METHODS: BTN1A1 expression was evaluated in primary tumor tissue samples, and its ability to suppress T-cell activation and T cell-dependent tumor clearance was examined. …

Opportunities And Challenges For The Use Of Deep Brain Stimulation In The Treatment Of Refractory Major Depression, Prashin Unadkat, Joao Quevedo, Jair Soares, Albert Fenoy

Faculty, Staff and Student Publications

Major Depressive Disorder continues to remain one of the most prevalent psychiatric diseases globally. Despite multiple trials of conventional therapies, a subset of patients fail to have adequate benefit to treatment. Deep brain stimulation (DBS) is a promising treatment in this difficult to treat population and has shown strong antidepressant effects across multiple cohorts. Nearly two decades of work have provided insights into the potential for chronic focal stimulation in precise brain targets to modulate pathological brain circuits that are implicated in the pathogenesis of depression. In this paper we review the rationale that prompted the selection of various brain …

Effect Of Neutralizing Monoclonal Antibody Treatment On Early Trajectories Of Virologic And Immunologic Biomarkers In Patients Hospitalized With Covid-19, Tomas O Jensen, Greg A Grandits, Mamta K Jain, Thomas A Murray, Birgit Grund, Kathryn Shaw-Saliba, Michael A Matthay, Mahsa Abassi, Magdalena Ardelt, Jason V Baker, Peter Chen, Robin L Dewar, Anna L Goodman, Timothy J Hatlen, Helene C Highbarger, Mark Holodniy, Perrine Lallemand, Sylvain Laverdure, Bradley G Leshnower, David Looney, Charalampos D Moschopoulos, Henry Mugerwa, Daniel D Murray, Eleftherios Mylonakis, Stephanie Nagy-Agren, M Tauseef Rehman, Adam Rupert, Randy A Stevens, Stuart Turville, Amy Weintrob, Katherine Wick, Jens Lundgren, Emily R Ko, Activ-3/Tico Study Group

Faculty, Staff and Student Publications

BACKGROUND: Neutralizing monoclonal antibodies (nmAbs) failed to show clear benefit for hospitalized patients with coronavirus disease 2019 (COVID-19). Dynamics of virologic and immunologic biomarkers remain poorly understood.

METHODS: Participants enrolled in the Therapeutics for Inpatients with COVID-19 trials were randomized to nmAb versus placebo. Longitudinal differences between treatment and placebo groups in levels of plasma nucleocapsid antigen (N-Ag), anti-nucleocapsid antibody, C-reactive protein, interleukin-6, and D-dimer at enrollment, day 1, 3, and 5 were estimated using linear mixed models. A 7-point pulmonary ordinal scale assessed at day 5 was compared using proportional odds models.

RESULTS: Analysis included 2149 participants enrolled between …

A Road Map Of Relapse In Mds After Allo-Hsct, Juan Jose Rodriguez-Sevilla, Simona Colla

Faculty, Staff and Student Publications

No abstract provided.

Label-Aware Distance Mitigates Temporal And Spatial Variability For Clustering And Visualization Of Single-Cell Gene Expression Data, Shaoheng Liang, Jinzhuang Dou, Ramiz Iqbal, Ken Chen

Faculty, Staff and Student Publications

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Label-Aware Distance (LAD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate LAD on simulated data as well as apply it to a mouse retina development dataset and a lung dataset. We also found the utility of our …

Gene Editing-Based Targeted Integration For Correction Of Wiskott-Aldrich Syndrome, Melissa Pille, John M Avila, So Hyun Park, Cuong Q Le, Haipeng Xue, Filomeen Haerynck, Lavanya Saxena, Ciaran Lee, Elizabeth J Shpall, Gang Bao, Bart Vandekerckhove, Brian R Davis

The Brown Foundation: Institute of Molecular Medicine

Wiskott-Aldrich syndrome (WAS) is a severe X-linked primary immunodeficiency resulting from a diversity of mutations distributed across all 12 exons of the WAS gene. WAS encodes a hematopoietic-specific and developmentally regulated cytoplasmic protein (WASp). The objective of this study was to develop a gene correction strategy potentially applicable to most WAS patients by employing nuclease-mediated, site-specific integration of a corrective WAS gene sequence into the endogenous WAS chromosomal locus. In this study, we demonstrate the ability to target the integration of WAS2-12-containing constructs into intron 1 of the endogenous WAS gene of primary CD34+ hematopoietic stem and progenitor …

Safety And Efficacy Of Dynamic Catheter-Directed Cerebral Digital Subtraction Angiography For Diagnosis Of Bowhunter Syndrome Spectrum Disorders: A Systematic Review Of The Literature, Joo Won Choi, Yang Qiao, Tej I Mehta, Jessica N Wilson, Trevor H Torigoe, Samuel Tsappidi, Y Jonathan Zhang, Stacy C Brown, Ferdinand K Hui, Todd Abruzzo

Faculty, Staff and Student Publications

Introduction: Dynamic catheter-directed cerebral digital subtraction angiography (dcDSA) is the gold standard for diagnosing dynamic vascular occlusion syndromes such as bowhunter syndrome (BHS). Nonetheless, concerns about its safety exist and no standardized protocols have been published to date.

Methods: We describe our methodology and insights regarding the use of dcDSA in patients with BHS. We also perform a systematic literature review to identify cases of typical and atypical presentations of BHS wherein dcDSA was utilized and report on any procedural complications related to dcDSA.

Results: Our study included 104 cases wherein dcDSA was used for the diagnosis of BHS. There …

Short Cell Cycle Duration Is A Phenotype Of Human Epidermal Stem Cells, Tong Xiao, Ugomma C Eze, Alex Charruyer-Reinwald, Tracy Weisenberger, Ayman Khalifa, Brook Abegaze, Gabrielle K Schwab, Rasha H Elsabagh, T Richard Parenteau, Karl Kochanowski, Merisa Piper, Yumin Xia, Jeffrey B Cheng, Raymond J Cho, Ruby Ghadially

Staff and Researcher Publications

Background: A traditional view is that stem cells (SCs) divide slowly. Meanwhile, both embryonic and pluripotent SCs display a shorter cell cycle duration (CCD) in comparison to more committed progenitors (CPs).

Methods: We examined the in vitro proliferation and cycling behavior of somatic adult human cells using live cell imaging of passage zero keratinocytes and single-cell RNA sequencing.

Results: We found two populations of keratinocytes: those with short CCD and protracted near exponential growth, and those with long CCD and terminal differentiation. Applying the ergodic principle, the comparative numbers of cycling cells in S phase in an enriched population of …

Apparent Diffusion Coefficient Values Predict Response To Brachytherapy In Bulky Cervical Cancer, Elizabeth E Dong, Junqian Xu, Joo-Won Kim, Jason Bryan, Jewel Appleton, Daniel A Hamstra, Michelle S Ludwig, Alexander N Hanania

Faculty, Staff and Students Publications

BACKGROUND: Diffusion-weighted magnetic resonance imaging (DWI) provides a measurement of tumor cellularity. We evaluated the potential of apparent diffusion coefficient (ADC) values obtained from post-external beam radiation therapy (EBRT) DWI and prior to brachytherapy (BT) to predict for complete metabolic response (CMR) in bulky cervical cancer.

METHODS: Clinical and DWI (b value = 500 s/mm2) data were obtained from patients undergoing interstitial BT with high-risk clinical target volumes (HR-CTVs) > 30 cc. Volumes were contoured on co-registered T2 weighted images and 90th percentile ADC values were calculated. Patients were stratified by CMR (defined by PET-CT at three months post-BT). Relation of …

Genomic Evolution Shapes Prostate Cancer Disease Type, Dan J Woodcock, Atef Sahli, Ruxandra Teslo, Vinayak Bhandari, Andreas J Gruber, Aleksandra Ziubroniewicz, Gunes Gundem, Yaobo Xu, Adam Butler, Ezequiel Anokian, Bernard J Pope, Chol-Hee Jung, Maxime Tarabichi, Stefan C Dentro, J Henry R Farmery, Cruk Icgc Prostate Group, Peter Van Loo, Anne Y Warren, Vincent Gnanapragasam, Freddie C Hamdy, G Steven Bova, Christopher S Foster, David E Neal, Yong-Jie Lu, Zsofia Kote-Jarai, Michael Fraser, Robert G Bristow, Paul C Boutros, Anthony J Costello, Niall M Corcoran, Christopher M Hovens, Charlie E Massie, Andy G Lynch, Daniel S Brewer, Rosalind A Eeles, Colin S Cooper, David C Wedge

Faculty, Staff and Student Publications

The development of cancer is an evolutionary process involving the sequential acquisition of genetic alterations that disrupt normal biological processes, enabling tumor cells to rapidly proliferate and eventually invade and metastasize to other tissues. We investigated the genomic evolution of prostate cancer through the application of three separate classification methods, each designed to investigate a different aspect of tumor evolution. Integrating the results revealed the existence of two distinct types of prostate cancer that arise from divergent evolutionary trajectories, designated as the Canonical and Alternative evolutionary disease types. We therefore propose the evotype model for prostate cancer evolution wherein Alternative-evotype …

Cytoplasmic Genome Contributions To Domestication And Improvement Of Modern Maize, Shuai Cao, Huanhuan Zhang, Yang Liu, Yi Sun, Z Jeffrey Chen

Faculty, Staff and Student Publications

Background: Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated.

Results: Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the …

Synchrony In Networks Of Type 2 Interneurons Is More Robust To Noise With Hyperpolarizing Inhibition Compared To Shunting Inhibition In Both The Stochastic Population Oscillator And The Coupled Oscillator Regimes, Roman Baravalle, Carmen C. Canavier

School of Medicine Faculty Publications

Synchronization in the gamma band (25–150 Hz) is mediated by PV+ inhibitory interneurons, and evidence is accumulating for the essential role of gamma oscillations in cognition. Oscillations can arise in inhibitory networks via synaptic interactions between individual oscillatory neurons (mean-driven) or via strong recurrent inhibition that destabilizes the stationary background firing rate in the fluctuation-driven balanced state, causing an oscillation in the population firing rate. Previous theoretical work focused on model neurons with Hodgkin’s Type 1 excitability (integrators) connected by current-based synapses. Here we show that networks comprised of simple Type 2 oscillators (resonators) exhibit a supercritical Hopf bifurcation between …

Novel Lipid Mediator 7s,14r-Docosahexaenoic Acid: Biogenesis And Harnessing Mesenchymal Stem Cells To Ameliorate Diabetic Mellitus And Retinal Pericyte Loss, Yan Lu, Haibin Tian, Hongying Peng, Quansheng Wang, Bruce A. Bunnell, Nicolas G. Bazan, Song Hong

School of Medicine Faculty Publications

Introduction: Stem cells can be used to treat diabetic mellitus and complications. ω3-docosahexaenoic acid (DHA) derived lipid mediators are inflammation-resolving and protective. This study found novel DHA-derived 7S,14R-dihydroxy-4Z,8E,10Z,12E,16Z,19Z-docosahexaenoic acid (7S,14R-diHDHA), a maresin-1 stereoisomer biosynthesized by leukocytes and related enzymes. Moreover, 7S,14R-diHDHA can enhance mesenchymal stem cell (MSC) functions in the amelioration of diabetic mellitus and retinal pericyte loss in diabetic db/db mice. Methods: MSCs treated with 7S,14R-diHDHA were delivered into db/db mice i.v. every 5 days for 35 days. Results: Blood glucose levels in diabetic mice were lowered by 7S,14R-diHDHA-treated MSCs compared to control and untreated MSC groups, accompanied by …

Ensuring Successful Biomarker Studies In Bladder Preservation Clinical Trials For Non-Muscle Invasive Bladder Cancer, David J. Mcconkey, Brian C. Baumann, Stephanie Cooper Greenberg, David J. Degraff, Scott E. Delacroix, Jason A. Efstathiou, Jared Foster, Susan Groshen, Edward E. Kadel, Francesca Khani, William Y. Kim, Seth P. Lerner, Trevor Levin, Joseph C. Liao, Matthew I. Milowsky, Joshua J. Meeks, David T. Miyamoto, Kent W. Mouw, Eugene J. Pietzak, David B. Solit, Debasish Sundi, Abdul Tawab-Amiri, Pamela J. West, Sara E. Wobker, Alexander W. Wyatt, Andrea B. Apolo, Peter C. Black

School of Medicine Faculty Publications

Recent technological advances have created new opportunities for performing biomarker studies within the National Cancer Institute’s (NCI’s) National Clinical Trials Network (NCTN) clinical trials. These new platforms yield more robust measurements when tissue and blood handling is optimized. At the same time, there is a strong interest in banking tissue and derivatives, such as DNA and RNA, for future biomarker studies using novel platforms that may emerge during the intervening time to trial completion. The NCI recently hosted a Clinical Trials Planning Meeting focused on two trial concepts for bladder preservation in patients with high-risk non-muscle invasive bladder cancer (NMIBC) …

Trends In Us Public Confidence In Science And Opportunities For Progress, Arthur Lupia, David B Allison, Kathleen Hall Jamieson, Jennifer Heimberg, Magdalena Skipper, Susan M Wolf

Children’s Nutrition Research Center Staff Publications

In recent years, many questions have been raised about whether public confidence in science is changing. To clarify recent trends in the public's confidence and factors that are associated with these feelings, an effort initiated by the National Academies' Strategic Council for Research Excellence, Integrity, and Trust (the Strategic Council) analyzed findings from multiple survey research organizations. The Strategic Council's effort, which began in 2022, found that U.S. public confidence in science, the scientific community, and leaders of scientific communities is high relative to other civic, cultural, and governmental institutions for which researchers regularly collect such data. However, confidence in …

Distributed Neural Representations Of Conditioned Threat In The Human Brain, Zhenfu Wen, Edward F Pace-Schott, Sara W Lazar, Jörgen Rosén, Fredrik Åhs, Elizabeth A Phelps, Joseph E Ledoux, Mohammed R Milad

Faculty, Staff and Student Publications

Detecting and responding to threat engages several neural nodes including the amygdala, hippocampus, insular cortex, and medial prefrontal cortices. Recent propositions call for the integration of more distributed neural nodes that process sensory and cognitive facets related to threat. Integrative, sensitive, and reproducible distributed neural decoders for the detection and response to threat and safety have yet to be established. We combine functional MRI data across varying threat conditioning and negative affect paradigms from 1465 participants with multivariate pattern analysis to investigate distributed neural representations of threat and safety. The trained decoders sensitively and specifically distinguish between threat and safety …