Medical Specialties Commons^™

Spatial Immunoprofiling Of Adenoid Cystic Carcinoma Reveals B7-H4 Is A Therapeutic Target For Aggressive Tumors, Luana Guimaraes Sousa, Daniel J Mcgrail, Felippe Lazar Neto, Kaiyi Li, Mario L Marques-Piubelli, Sammy Ferri-Borgogno, Hui Dai, Yoshitsugu Mitani, Nicole Spardy Burr, Zachary A Cooper, Krista Kinneer, Maria Angelica Cortez, Shiaw-Yih Lin, Diana Bell, Adel El Naggar, Jared Burks, Renata Ferrarotto

Faculty, Staff and Student Publications

PURPOSE: Adenoid cystic carcinoma (ACC) is a heterogeneous malignancy, and no effective systemic therapy exists for metastatic disease. We previously described two prognostic ACC molecular subtypes with distinct therapeutic vulnerabilities, ACC-I and ACC-II. In this study, we explored the ACC tumor microenvironment (TME) using RNA-sequencing and spatial biology to identify potential therapeutic targets.

EXPERIMENTAL DESIGN: Tumor samples from 62 ACC patients with available RNA-sequencing data that had been collected as part of previous studies were stained with a panel of 28 validated metal-tagged antibodies. Imaging mass cytometry (IMC) was performed using the Fluidigm Helios CyTOF instrument and analyzed with Visiopharm …

Compass: Joint Copy Number And Mutation Phylogeny Reconstruction From Amplicon Single-Cell Sequencing Data, Etienne Sollier, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel, Katharina Jahn

Faculty, Staff and Student Publications

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including …

Infectious Profiles In Pediatric Anti-N-Methyl-D-Aspartate Receptor Encephalitis, Alexander J Sandweiss, Timothy A Erickson, Yike Jiang, Varun Kannan, Jonathan M Yarimi, Jesse M Levine, Kristen Fisher, Eyal Muscal, Gail Demmler-Harrison, Kristy O Murray, Shannon E Ronca

Faculty, Staff and Students Publications

Anti-N-methyl-d-aspartate receptor autoimmune encephalitis (NMDAR AE) is an antibody-mediated neurological disorder that may be caused by post-herpes simplex virus-1 meningoencephalitis (HSV ME) and ovarian teratomas, although most pediatric cases are idiopathic. We sought to evaluate if other infections precede NMDAR AE by conducting a single-center, retrospective, case-control study of 86 pediatric cases presenting to Texas Children's Hospital between 2006 and 2022. HSV ME (HSV-1 and HSV-2) was a significantly more common preceding infection in the experimental group compared to control patients with idiopathic intracranial hypertension, while there was no difference in remote HSV infection between the two groups. Recent Epstein-Barr …

A Multiparameter Molecular Classifier To Predict Response To Neoadjuvant Lapatinib Plus Trastuzumab Without Chemotherapy In Her2+ Breast Cancer, Jamunarani Veeraraghavan, Carolina Gutierrez, Carmine De Angelis, Robert Davis, Tao Wang, Tomas Pascual, Pier Selenica, Katherine Sanchez, Hiroaki Nitta, Monesh Kapadia, Anne C Pavlick, Patricia Galvan, Brent Rexer, Andres Forero-Torres, Rita Nanda, Anna M Storniolo, Ian E Krop, Matthew P Goetz, Julie R Nangia, Antonio C Wolff, Britta Weigelt, Jorge S Reis-Filho, Susan G Hilsenbeck, Aleix Prat, C Kent Osborne, Rachel Schiff, Mothaffar F Rimawi

Faculty, Staff and Student Publications

PURPOSE: Clinical trials reported 25% to 30% pathologic complete response (pCR) rates in HER2+ patients with breast cancer treated with anti-HER2 therapies without chemotherapy. We hypothesize that a multiparameter classifier can identify patients with HER2-"addicted" tumors who may benefit from a chemotherapy-sparing strategy.

EXPERIMENTAL DESIGN: Baseline HER2+ breast cancer specimens from the TBCRC023 and PAMELA trials, which included neoadjuvant treatment with lapatinib and trastuzumab, were used. In the case of estrogen receptor-positive (ER+) tumors, endocrine therapy was also administered. HER2 protein and gene amplification (ratio), HER2-enriched (HER2-E), and PIK3CA mutation status were assessed by dual gene protein assay (GPA), research-based …

Impact Of Geroscience On Therapeutic Strategies For Older Adults With Cardiovascular Disease: Jacc Scientific Statement, Daniel E Forman, George A Kuchel, John C Newman, James L Kirkland, Elena Volpi, George E Taffet, Nir Barzilai, Ambarish Pandey, Dalane W Kitzman, Peter Libby, Luigi Ferrucci

Faculty, Staff and Students Publications

Geroscience posits that cardiovascular disease (CVD) and other chronic diseases result from progressive erosion of the effectiveness of homeostatic mechanisms that oppose age-related accumulation of molecular damage. This hypothetical common root to chronic diseases explains why patients with CVD are often affected by multimorbidity and frailty and why older age negatively affects CVD prognosis and treatment response. Gerotherapeutics enhance resilience mechanisms that counter age-related molecular damage to prevent chronic diseases, frailty, and disability, thereby extending healthspan. Here, we describe the main resilience mechanisms of mammalian aging, with a focus on how they can affect CVD pathophysiology. We next present novel …

Oleoylethanolamide Facilitates Pparα And Tfeb Signaling And Attenuates Aβ Pathology In A Mouse Model Of Alzheimer’S Disease, Michele M Comerota, Manasee Gedam, Wen Xiong, Feng Jin, Lisheng Deng, Meng C Wang, Jin Wang, Hui Zheng

Faculty, Staff and Students Publications

BACKGROUND: Age is the strongest risk factor for the development of Alzheimer's disease (AD). Besides the pathological hallmarks of β-amyloid (Aβ) plaques and neurofibrillary tangles, emerging evidence demonstrates a critical role of microglia and neuroinflammation in AD pathogenesis. Oleoylethanolamide (OEA) is an endogenous lipid amide that has been shown to promote lifespan and healthspan in C. elegans through regulation of lysosome-to-nucleus signaling and cellular metabolism. The goal of our study was to determine the role of OEA in the mediation of microglial activity and AD pathology using its stable analog, KDS-5104.

METHODS: We used primary microglial cultures and genetic and …

Spatial Organization Of The Mouse Retina At Single Cell Resolution By Merfish, Jongsu Choi, Jin Li, Salma Ferdous, Qingnan Liang, Jeffrey R Moffitt, Rui Chen

Faculty, Staff and Students Publications

The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing …

Insight Into The Mechanism Of H+-Coupled Nucleobase Transport, Jun Weng, Xiaoming Zhou, Pattama Wiriyasermkul, Zhenning Ren, Kehan Chen, Eva Gil-Iturbe, Ming Zhou, Matthias Quick

Faculty, Staff and Students Publications

The nucleobase/ascorbic acid transporter (NAT) family comprises proteins in all kingdoms of life. Their substrates, nucleobases and their analogs, have special attention in therapeutic applications, such as the treatment of solid tumors, lymphoproliferative diseases, viral infections, and inflammatory diseases. Here, we present the crystal structure of a bacterial NAT member, PurT of Colwellia psychrerythraea (PurTCp) at 2.80 Å resolution that, together with functional data, provide insight into the transport mechanism of NAT family members.

Bi-Atrial Thrombus Via Patent Foramen Ovale With Medical Noncompliance: A Case Report, Reid Mccullough, Ayesha Cheema, Owesh Contractor, Krystal Tomsky-Jackson

Advances in Clinical Medical Research and Healthcare Delivery

Numerous diagnoses in the hospital setting require anticoagulation. With different etiologies, certain specific assessments may not have a treatment plan that is studied extensively in evidence-based medical texts. In these uncommon situations, management may not have clear medical guidelines for successful treatment. We present a case of bi-atrial thrombus via PFO with concurrent pulmonary embolism, extensive clot burden history, and the plan to move forward with Angiovac. In patients with this specific history and pathology, modern procedures like Angiovac should be considered and discussed.

Encephalopathy Tango: When Beta-Lactam Antibiotics Waltz With Gaba Receptor, Ali Mohamed, Nagesh Jadhav, Mohamed Elbathani, Abubaker Farah

Advances in Clinical Medical Research and Healthcare Delivery

Beta-lactam antibiotics are a class of drugs that are widely used to treat a variety of infections. They are generally well-tolerated, but they can cause a variety of side effects, including allergic reactions, acute interstitial nephritis (AIN) and neurotoxicity.

We present a patient who developed neurotoxicity after being treated with cephalosporin and carbapenem antibiotics. A 76-year-old female was admitted to the hospital with osteomyelitis of the right foot. She was initially treated with cefepime and daptomycin. She was discharged and then began to experience delirium with visual hallucinations and acute kidney injury. After common causes of confusion were excluded, the …

Persistent Foci Of Infection: A Case Of Two Mycotic Aneurysms Separated In Time In A Patient With Infective E. Faecalis Endocarditis, Julia C. Stone, Joel Thompson, Joseph Hatem, Evan Basha

Advances in Clinical Medical Research and Healthcare Delivery

This is a case report of a patient who presented with mycotic aneurysms of two different blood vessels at separate hospital visits following a diagnosis of infective endocarditis.

Cystic Fibrosis - An Ever Evolving Challenge, Abdullah A. Orakzai, Osama Sherjeel Khan, Syeda Sarah Raza, Muhammad H. Sharif, Mehr A. Orakzai

Advances in Clinical Medical Research and Healthcare Delivery

Cystic fibrosis (CF) is a genetic disease that results from mutations in a large single gene located on chromosome 7. More than 2000 different mutations in the gene have been identified to have caused the disease. Most of these mutations are exceedingly rare and therefore not a part of CF screening or all testing panels. This case discusses an adult female with a history of asthma, bronchiectasis, pseudomonas colonization, and respiratory failure on chronic oxygen who presented to the ED with sudden onset shortness of breath, fever, chills, body aches, nonproductive cough, and headache. The patient's condition clinically improved with …

Pseudo-Wellens Syndrome: A Rare Entity Associated With Cocaine Use, Mohamed Salah Mohamed, Syed Hamza Waheed, Amir Mahmoud, Anas Hashem, Bipul Baibhav, Abdullah M. Firoze Ahmed

Advances in Clinical Medical Research and Healthcare Delivery

Wellens syndrome usually indicates critical left anterior descending artery (LAD) occlusion. Pseudo-Wellens syndrome consists of criteria of Wellens syndrome in the absence of critical LAD occlusion. We report a case of Pseudo-Wellens syndrome related to cocaine use. A 52-year-old male with a medical history of hypertension and diabetes, presented with acute retrosternal chest pain of 3 days duration. Physical examination was unremarkable. EKG on presentation showed deep T-wave inversions in leads V2 to V5. Highly sensitive troponin was elevated. The patient admitted to using cocaine daily for the past two months. Due to concerns for Wellens syndrome, the patient had …

Hydroxychloroquine Induced Cardiomyopathy, Mohamed Salah Mohamed, Katrina Wojciechowski, Scott Feitell, Muhammad Osama, Anas Hashem, Jayesh Patel, Amir Mahmoud, Ali Abdelhay, Prakash Upreti, Soidjon Khodjaev

Advances in Clinical Medical Research and Healthcare Delivery

Hydroxychloroquine (HCQ) is one of the immunomodulatory medications used in treatment of autoimmune diseases. Rarely, HCQ can cause serious complications, such as cardiotoxicity. We present a rare case of HCQ-induced cardiomyopathy. 60-year-old female patient with a medical history of SLE on chronic HCQ therapy for 28 years, preexisting non-ischemic cardiomyopathy and heart failure with reduced ejection fraction for 7 years, and complete heart block status post pacemaker insertion presented with acute chest pain and severe weight loss. Patient underwent coronary angiogram that showed normal coronaries and right-sided heart catheterization that showed acute heart failure. Echocardiogram showed LVEF of 30% with …

Median Arcuate Ligament Syndrome: A Rare Cause Of Abdominal Pain That Is Difficult To Identify, Mark E. Eskander, Matthew Thrall, Joel P. Thompson

Advances in Clinical Medical Research and Healthcare Delivery

Median arcuate ligament syndrome (MALS) is a rare disease that occurs when the celiac artery is compressed by the median arcuate ligament. Patients with MALS typically present with non-specific symptoms that overlap with more common diseases. As a result, patients may undergo extensive workup and unnecessary treatments before being properly diagnosed with MALS. In this case we present a 23-year-old female with chronic postprandial abdominal pain that persisted despite undergoing a cholecystectomy. This case highlights the symptoms and imaging findings needed to diagnose MALS and thus prevent unnecessary surgical interventions.

Role Of Suction-Based Airway Clearance Devices In Pediatric Foreign Body Airway Obstruction, Rebecca Braver

Master of Science in Physician Assistant Studies Capstone Presentations (Center City)

Introduction

• Foreign body airway obstruction (FBAO) represents a significant cause of morbidity and mortality in the pediatric population. Factors including pediatric anatomy, chewing and swallowing difficulties, developmental stages, habits and behaviors, and children’s toys and foods increase risk of FBAO in children.^1,2
• BLS guidelines for FBAO management in responsive children ages 1-8 call for a series of subdiaphragmatic abdominal thrusts, which increase intrathoracic pressure to force air and the foreign body out of the airway.^3,4 Abdominal thrusts have higher reports of injury compared to all other FBAO interventions, with risk of thoracic, vascular, and gastro-esophageal injury.^5-7
• Novel …

Electric Field Navigated 1-Hz Rtms For Poststroke Motor Recovery: The E-Fit Randomized Controlled Trial, Dylan J. Edwards, Charle Y. Liu, Kari Dunning, Felipe Fregni, Jarmo Laine, Benjamin E. Leiby, Lynn M. Rogers, Richard L. Harvey

Moss-Magee Rehabilitation Papers

BACKGROUND: To determine if low-frequency repetitive transcranial magnetic stimulation targeting the primary motor cortex contralateral (M1_CL) to the affected corticospinal tract in patients with hemiparetic stroke augments intensive training–related clinical improvement; an extension of the NICHE trial (Navigated Inhibitory rTMS to Contralesional Hemisphere Trial) using an alternative sham coil.

METHODS: The present E-FIT trial (Electric Field Navigated 1Hz rTMS for Post-stroke Motor Recovery Trial) included 5 of 12 NICHE trial outpatient US rehabilitation centers. The stimulation protocol remained identical (1 Hz repetitive transcranial magnetic stimulation, M1_CL, preceding 60-minute therapy, 18 sessions/6 wks; parallel arm randomized clinical …

The Role Of Repetitive Transcranial Magnetic Stimulation (Rtms) V. Electroconvulsive Therapy (Ect) In Geriatric Depression Treatment: Efficacy & Tolerability, Madeleine Sarro

Master of Science in Physician Assistant Studies Capstone Presentations (Center City)

Background

• Geriatric depression, or depression in a population over the age of 60, is a highly debilitating mental health condition with a prevalence of 25% versus 10% in the general population.^{1, 2} Increasing prevalence is expected in the next 30 years with a rise in the population size for adults over 60 from 12% to 22%.³
• Limiting variables in the treatment of geriatric depression include polypharmacy, intolerable adverse effects, medical comorbidities, drug resistance and atypical symptom presentation.^2-7
• Due to uniformity in underlying pathophysiology, current treatment guidelines for geriatric depression are the same as for the general population. …

The Impact Of Intralesional 5-Fluorouracil In The Treatment Of Keloid Scars, Madeline Derham

Master of Science in Physician Assistant Studies Capstone Presentations (Center City)

Background

- The American Academy of Dermatology (AAD) defines a keloid scar as a type of raised scar extending past the initial area of injury¹

- Approximately 10% of the general population affected - significant risk factors include +family history, darker skin tones, mechanism of injury (burn, surgical)³

- Symptom presentation: pain, pruritus, burning, increased sensitivity³

- Varying existing treatment methods with high resistance and recurrence rates leading to no agreed upon standard approach⁵

• Most widely adopted method currently : intralesional (ILS) steroid ^injection5

Immunological Monitoring In Hepatitis C Virus Controlled Human Infection Model, Naglaa H Shoukry, Andrea L Cox, Christopher M Walker

Faculty, Staff and Student Publications

Controlled human infection model trials for hepatitis C virus represent an important opportunity to identify correlates of protective immunity against a well-characterized inoculum of hepatitis C virus and how such responses are modified by vaccination. In this article, we discuss the approach to immunological monitoring during such trials, including a set of recommendations for optimal sampling schedule and preferred immunological assays to examine the different arms of the immune response. We recommend that this approach be adapted to different trial designs. Finally, we discuss how these studies can provide surrogate predictors of the success of candidate vaccines.

Successful Return To Sport And Daily Activities After Suture Augmentation Of Both The Anterior Talofibular Ligament And Calcaneofibular Ligament, S Ali Ghasemi, Jetha Tallapaneni, Benjamin C Murray, Clark Yin, James Raphael, Zachary Vaupel, Allan Grant, Paul Fortin

Department of Orthopaedic Surgery Faculty Papers

PURPOSE: To evaluate the return to sport and daily activities in addition to clinical outcomes after modification of the Brostöm repair, specifically using suture augmentation for concomitant fixation of both the anterior talofibular ligament and calcaneofibular ligament.

METHODS: Patients who had grade III ankle sprains and lateral ankle instability, all of whom failed supervised conservative management, were included. Patients underwent a modified Broström procedure consisting of suture augmentation for both the anterior talofibular ligament and calcaneofibular ligament. For clinical outcome evaluation, Foot and Ankle Ability Measure (FAAM) and Karlsson-Peterson Scoring System for Ankle Function questionnaires coupled with questions regarding time …

Evolution Of Immune And Stromal Cell States And Ecotypes During Gastric Adenocarcinoma Progression, Ruiping Wang, Shumei Song, Jiangjiang Qin, Katsuhiro Yoshimura, Fuduan Peng, Yanshuo Chu, Yuan Li, Yibo Fan, Jiankang Jin, Minghao Dang, Enyu Dai, Guangsheng Pei, Guangchun Han, Dapeng Hao, Yating Li, Deyali Chatterjee, Kazuto Harada, Melissa Pool Pizzi, Ailing W Scott, Ghia Tatlonghari, Xinmiao Yan, Zhiyuan Xu, Can Hu, Shaowei Mo, Namita Shanbhag, Yang Lu, Matheus Sewastjanow-Silva, Ahmed Adel Fouad Abdelhakeem, Guang Peng, Samir M Hanash, George A Calin, Cassian Yee, Pawel Mazur, Autumn N Marsden, Andrew Futreal, Zhenning Wang, Xiangdong Cheng, Jaffer A Ajani, Linghua Wang

Faculty, Staff and Student Publications

Understanding tumor microenvironment (TME) reprogramming in gastric adenocarcinoma (GAC) progression may uncover novel therapeutic targets. Here, we performed single-cell profiling of precancerous lesions, localized and metastatic GACs, identifying alterations in TME cell states and compositions as GAC progresses. Abundant IgA+ plasma cells exist in the premalignant microenvironment, whereas immunosuppressive myeloid and stromal subsets dominate late-stage GACs. We identified six TME ecotypes (EC1–6). EC1 is exclusive to blood, while EC4, EC5, and EC2 are highly enriched in uninvolved tissues, premalignant lesions, and metastases, respectively. EC3 and EC6, two distinct ecotypes in primary GACs, associate with histopathological and genomic characteristics, and prognosis. …

Loss Of Syncrip Unleashes Apobec-Driven Mutagenesis, Tumor Heterogeneity, And Ar-Targeted Therapy Resistance In Prostate Cancer, Xiaoling Li, Yunguan Wang, Su Deng, Guanghui Zhu, Choushi Wang, Nickolas A Johnson, Zeda Zhang, Carla Rodriguez Tirado, Yaru Xu, Lauren A Metang, Julisa Gonzalez, Atreyi Mukherji, Jianfeng Ye, Yuqiu Yang, Wei Peng, Yitao Tang, Mia Hofstad, Zhiqun Xie, Heewon Yoon, Liping Chen, Xihui Liu, Sujun Chen, Hong Zhu, Douglas Strand, Han Liang, Ganesh Raj, Housheng Hansen He, Joshua T Mendell, Bo Li, Tao Wang, Ping Mu

Faculty, Staff and Student Publications

Tumor mutational burden and heterogeneity has been suggested to fuel resistance to many targeted therapies. The cytosine deaminase APOBEC proteins have been implicated in the mutational signatures of more than 70% of human cancers. However, the mechanism underlying how cancer cells hijack the APOBEC mediated mutagenesis machinery to promote tumor heterogeneity, and thereby foster therapy resistance remains unclear. We identify SYNCRIP as an endogenous molecular brake which suppresses APOBEC-driven mutagenesis in prostate cancer (PCa). Overactivated APOBEC3B, in SYNCRIP-deficient PCa cells, is a key mutator, representing the molecular source of driver mutations in some frequently mutated genes in PCa, including FOXA1, …

Bacteroides Uniformis-Induced Perturbations In Colonic Microbiota And Bile Acid Levels Inhibit Th17 Differentiation And Ameliorate Colitis Developments, Yiting Yan, Yu Lei, Ying Qu, Zhen Fan, Ting Zhang, Yangbin Xu, Qian Du, Daniel Brugger, Yulin Chen, Ke Zhang, Enping Zhang

Faculty, Staff and Student Publications

Inflammatory bowel disease (IBD) is associated with gut dysbiosis and can lead to colitis-associated malignancies. Bacteroides uniformis (Bu) regulates animal intestinal homeostasis; however, the mechanism by which it alleviates colitis in mice remains unknown. We investigated the effects of B. uniformis JCM5828 and its metabolites on female C57BL/6J mice with dextran sulfate sodium salt (DSS) induced colitis. Treatment with Bu considerably alleviated colitis progression and restored the mechanical and immune barrier protein expression. Additionally, Bu increased the abundance of the symbiotic bacteria Bifidobacterium and Lactobacillus vaginalis while decreasing that of pathogenic Escherichia-Shigella, and modulated intestinal bile acid metabolism. Bu largely …

Proteogenomic Data And Resources For Pan-Cancer Analysis, Yize Li, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P Calinawan, François Aguet, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieslik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J Domagalski, Myvizhi Esai Selvan, David Fenyö, Steven M Foltz, Alicia Francis, Tania Gonzalez-Robles, Zeynep H Gümüş, David Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A Ketchum, Robert J Klein, Jonathan T Lei, Wen-Wei Liang, Yuxing Liao, Caleb M Lindgren, Weiping Ma, Lei Ma, Michael J Maccoss, Fernanda Martins Rodrigues, Wilson Mckerrow, Ngoc Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul Rudnick, Kelly V Ruggles, Dmitry Rykunov, Sara R Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V Terekhanova, Ratna R Thangudu, Mathangi Thiagarajan, Liang-Bo Wang, Joshua M Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A Wyczalkowski, Yi Xin, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I Nesvizhskii, Pei Wang, Ana I Robles, Bing Zhang, Samuel H Payne

Faculty, Staff and Students Publications

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry …

Predicting Pediatric Tuberculosis: The Need For Age-Specific Host Biosignatures, Sara Suliman, Devan Jaganath, Andrew Dinardo

Faculty, Staff and Students Publications

No abstract provided.

Variant Characterization Of A Representative Large Pedigree Suggests “Variant Risk Clusters” Convey Varying Predisposition Of Risk To Lynch Syndrome, Mouadh Barbirou, Amanda A. Miller, Amel Mezlini, Balkiss Bouhaouala-Zahar, Peter J. Tonellato

Department of Medical Oncology Faculty Papers

Recently, worldwide incidences of young adult aggressive colorectal cancer (CRC) have rapidly increased. Of these incidences diagnosed as familial Lynch syndrome (LS) CRC, outcomes are extremely poor. In this study, we seek novel familial germline variants from a large pedigree Tunisian family with 12 LS-affected individuals to identify putative germline variants associated with varying risk of LS. Whole-genome sequencing analysis was performed to identify known and novel germline variants shared between affected and non-affected pedigree members. SNPs, indels, and structural variants (SVs) were computationally identified, and their oncological influence was predicted using the Genetic Association of Complex Diseases and Disorders, …

Hepatitis A Virus And Hepatitis E Virus As Food- And Waterborne Pathogens—Transmission Routes And Methods For Detection In Food, Katalin Nemes, Sofia Persson, Magnus Simonsson

Faculty, Staff and Student Publications

Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses …

Characterizing Cancer Metabolism From Bulk And Single-Cell Rna-Seq Data Using Metaflux, Yuefan Huang, Vakul Mohanty, Merve Dede, Kyle Tsai, May Daher, Li Li, Katayoun Rezvani, Ken Chen

Faculty, Staff and Student Publications

Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) …

New Onset, Refractory Hyperglycemia With Diabetic Ketoacidosis After Enfortumab Vedotin Treatment: A Case Report, Ross E. Heinrich, Marie Caldwell

Journal of Maine Medical Center

Introduction: A patient with no prior diagnosis of diabetes presented with diabetic ketoacidosis (DKA) and severe insulin resistance after being treated with enfortumab vedotin (EV). EV-associated DKA is uncommon—described in only a few case reports—and has unknown pathophysiology. This case characterizes the unique features of DKA in this patient and an unusual amount of insulin resistance not typically seen in patients with diabetes.

Clinical Findings: A 71-year-old male presented with fatigue, xerostomia, and increased thirst. He had a history of obesity, hypertension, and invasive, high-grade papillary urothelial carcinoma. His laboratory results were consistent with DKA.

Clinical Course: The patient was …