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Performance Analysis Of Computational Methods For Predicting Protein Function In Rare Diseases, Aichetou Mohamed Sidiya, Hanin Alzaher, Razan Almahdi, Tayeb Brahimi

Effat Undergraduate Research Journal

Protein function prediction is crucial for understanding the underlying mechanisms of rare diseases. With the increasing availability of computational methods including machine learning-based approaches, network-based methods, and sequence-based methods, predicting protein functions has become more accessible. However, it is not clear which of these methods performs better or how they compare to each other in terms of accuracy, efficiency, and scalability. In this study, we evaluate several computational methods for predicting protein functions in rare diseases using key performance indicators (KPIs). We analyze the strengths and weaknesses of each method and provide recommendations for researchers and clinicians interested in using …

The Effects Of Exercise Training In A Novel Full-Body Compression Garment On Anaerobic Performance In Healthy Men, Benjamin W. Cunningham, Mikayla M. Reese, Jesse M. Jansen, Benjamin S. Minier, Curtis A. Cornell, Faith C. Benedict, Joshua T. Mayne, Justin A. O'Dell, Gabriel M. Lysak, James R. Sackett

International Journal of Exercise Science

International Journal of Exercise Science 18(8): 836-851, 2025. Although acutely donning compression garments improves several markers of athletic performance, the effects of training in compression garments remains largely unexplored. Thus, this study aimed to determine the effects of exercise training while donning a novel full-body compression garment on multiple measures of anaerobic performance. Sixteen sedentary males (age: 21±3 y; BMI: 25±3 kg/m²) completed 4 weeks of training with (CG; n=8) or without (CON; n=8) a novel full-body compression garment. Subjects performed a 40m sprint (time and velocity), a 5-repetition maximum barbell back squat (barbell weight and serratus anterior …

Change In Free-Living Daily Steps Does Not Affect Vo2max Adaptation In Response To A Supervised Aerobic Walking Program In Females Ages 18-45, Catherine L. Jarrett, Brandon J. Sawyer, Wesley Tucker, Dharini M. Bhammar, Justin R. Ryder, Siddhartha Angadi, Glenn A. Gaesser

International Journal of Exercise Science

International Journal of Exercise Science 18(5): 852-863, 2025. We hypothesized that an increase in nonexercise physical activity (NEPA), assessed by daily steps outside of steps accrued during supervised exercise training sessions, would be positively correlated with the change in VO_2max. Females ages 18-45 yr (n = 44; 30 ± 7 yr; 67.7 ± 18.3 kg; 24.9 ± 6.4 kg/m²) completed 36 supervised training sessions on a motorized treadmill (3 sessions/week, 30 min/session) over 12 weeks, at 70% VO_2max (80% max heart rate). VO_2max was assessed at baseline, 4, 8, and 12 weeks, and …

Advancing Rfid Systems: From Head Orientation To Robotic Localization Using Passive Tags, Guilherme Ricardo Mendes Da Silva Barreto De Figueiredo

Doctoral Dissertations

No abstract provided.

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Blood And Neuronal Extracellular Vesicle Mitochondrial Disruptions In Schizophrenia, A Ankeeta, Ashutosh Tripathi, Bindu Pillai, Yizhou Ma, Joshua J Chiappelli, Jessica N Jernberg, Keiko Kunitoki, Xiaoming Du, Si Gao, Bhim M Adhikari, Consuelo Walss-Bass, Giselli Scaini, Peter Kochunov, Anilkumar Pillai, L Elliot Hong

Faculty, Staff and Student Publications

The high energy demand of the human brain obligates robust mitochondrial energy metabolism, while mitochondrial dysfunctions have been linked to neuropsychiatric disorders, including schizophrenia spectrum disorders (SSD). However, in vivo assessments that can directly inform brain mitochondrial functioning and its etiopathophysiological path to SSD remain difficult to obtain. We hypothesized that system and brain mitochondrial dysfunctions in SSD may be indexed by elevated cell-free mitochondrial DNA (cf-mtDNA) levels in the blood and in neuronal extracellular vesicles (nEVs). We also explored if these mtDNA marker elevations were associated with brain metabolites as measured by magnetic resonance spectroscopy (MRS). We examined blood …

Predicting Regional Cerebral Blood Flow Using Voxel-Wise Resting-State Functional Mri, Hongjie Ke, Bhim M Adhikari, Yezhi Pan, David B Keator, Daniel Amen, Si Gao, Yizhou Ma, Paul M Thompson, Neda Jahanshad, Jessica A Turner, Theo G M Van Erp, Mohammed R Milad, Jair C Soares, Vince D Calhoun, Juergen Dukart, L Elliot Hong, Tianzhou Ma, Peter Kochunov

Faculty, Staff and Student Publications

Background: Regional cerebral blood flow (rCBF) is a putative biomarker for neuropsychiatric disorders, including major depressive disorder (MDD).

Methods: Here, we show that rCBF can be predicted from resting-state functional MRI (rsfMRI) at the voxel level while correcting for partial volume averaging (PVA) artifacts. Cortical patterns of MDD-related CBF differences decoded from rsfMRI using a PVA-corrected approach showed excellent agreement with CBF measured using single-photon emission computed tomography (SPECT) and arterial spin labeling (ASL). A support vector machine algorithm was trained to decode cortical voxel-wise CBF from temporal and power-spectral features of voxel-level rsfMRI time series while accounting for PVA. …

Placental Polycyclic Aromatic Hydrocarbon (Pah) Levels Are Associated With Spontaneous Preterm Birth, Gwendolynn Hummel, Sohini Banerjee, Vasanta Putluri, Inaara Malick, Grace Johnson, Abu Hena Mostafa Kamal, Chandra Shekar R Ambati, Nagireddy Putluri, Lori Showalter, Cynthia D Shope, Joseph Hagan, Kjersti M Aagaard, Bhagavatula Moorthy, Melissa A Suter

Faculty, Staff and Students Publications

While the cause of preterm birth (PTB) (i.e., delivery before 37 weeks of gestation) is likely multifactorial, ambient exposure to environmental chemicals has been postulated to play a role in its etiology. Our prior studies of exposure to polycyclic aromatic hydrocarbons (PAHs) in pregnancy have shown an increased level of placental PAH-induced bulky DNA adducts with increasing levels of PAH exposures. In this investigation, we hypothesized that higher levels of placental PAHs would be associated with an increased risk of PTB. Using gas chromatography and mass spectrometry (GC-MS/MS), we measured levels of benzo(a)pyrene (BaP), benzo(b)fluoranthene (BbF) and dibenz(a,h)anthracene (DBA) from …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

Host, Microbiome, And Parasite: How Apicomplexan Microorganisms Interact With Gut Microbiota, Senia Bu, Andrew T. Ozga

Mako: NSU Undergraduate Student Journal

The gut microbiome, a complex ecosystem of microorganisms residing in the human gastrointestinal tract, plays a crucial role in maintaining overall health. It functions in immune system regulation, digestion, and protection against pathogens. Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., and Cryptosporidium spp., are major pathogens that can significantly disrupt the gut microbiota, leading to alterations in microbial composition and function. This review explores the bidirectional interactions between Apicomplexan parasites and the gut microbiome, focusing on how these parasites influence microbial diversity, immune responses, and host metabolism. It examines the mechanisms by which infection-induced inflammation, altered …

From Infection To Restoration: A Case Study On Dental Extraction In The Maxilla Anterior, Melanie Ramirez

Mako: NSU Undergraduate Student Journal

A dental implant is a restorative surgical procedure that serves as a solution to replace missing teeth that imitate the function, sensation, and appearance of natural teeth. The objective of this dental case study is to examine the diagnosis, treatment, and post-operation of a patient with a history of tooth loss and infection in the anterior maxilla. This case follows a 55-year-old patient, Jorge Marquez, name changed for confidentiality, who presented a severe tooth abscess on tooth #10 on the anterior maxilla which had previously undergone root canal treatment (Figure 1B). Radiographic evaluations illustrated the severity of the abscess the …

Effects Of Storage Temperatures On Quality And Phytochemical Properties Of The Hawthorn (Crataegus Azarolus L.) During Storage And Shelf Life, Ahmet Erhan Özdemi̇r, Oğuzhan Çalişkan, Safder Bayazit, Kazi̇m Gündüz, Nurdan Tuna Güneş, Zafer Karaşahi̇n, Derya Kiliç, Ramazan Bestami̇ Karahan

Turkish Journal of Agriculture and Forestry

This study aimed to investigate the effects of storage temperature on the quality and phytochemical characteristics in Sultan hawthorn cultivar during cold storage and shelf life. Fruits were stored at 0 ± 0.5 °C and 4 ± 0.5 °C and 90 ± 5% relative humidity (RH) for 6 months in cold storage and were analyzed every month. In addition, hawthorn fruits were kept at 20 ± 0.5 °C and 75 ± 5% RH for 7 days, and their shelf life was investigated at monthly intervals. Weight loss, appearance, the incidence of physiological disorders and fungal decay, fruit skin color, firmness, …

Monitoring The Developmental Stages Of Calendula Officinalis L. Nutrients Efficacy Under Hot Weather Mitigation Through Nutrients In Haripur, Pakistan, Waseem Ahmed, Rafia Azmat, Shah Masaud Khan, Abdul Qayyum, Waseem Hassan, Adnan Noor Shah, Muhammad Hadi Abbas, Fatima M. Abbas, Tahani A.Y. Asseri, Ahmet Hakan Ürüşan

Turkish Journal of Agriculture and Forestry

This study examines the effect of different doses of N and P fertilizer on Calendula officinalis L. (marigold) during the hot weather in summer (May–July) in Pakistan. The aim was to determine whether fertilization can help minimize the impacts of climate change. During the summer peak seasons (May, June, and July), the trial was conducted in potted plants with different N and P application levels to monitor the quality and quantity of C. officinalis. The results showed that the interactive effects (N × P) gave higher values for plant height, number of leaves, fresh weight, leaf length, and number of …

Exploring The Genetic Diversity And Population Structure Of Serbian And Selected European Bread Wheat Cultivars Through Ipbs-Retrotransposon Markers, Rada Šućur, Amjad Ali, Parnaz Mortazavi, Muhammad Tanveer Altaf, Muhammed Tatar, Muhammad Azhar Nadeem, Bojan Jocković, Velimir Mladenov, Sotirios Fragkostefanakis, Yong Suk Chung, Faheem Shehzad Baloch

Turkish Journal of Agriculture and Forestry

Bread wheat is a globally vital crop, sustaining millions and contributing to food security. The present study investigated the molecular characterization of 60 bread wheat accessions, using 12 interprimer binding site (iPBS) retrotransposon markers, which yielded a total of 260 distinct bands. Out of the 260 bands, 42 were monomorphic while the remaining 218 (83.84%) were polymorphic, with polymorphism information content values ranging from 0.38 to 0.45. Genetic diversity indices, including Shannon’s information index (I = 0.01–0.53), effective number of alleles (Ne = 1.00–1.63), gene diversity (He = 0.0037–0.36), and marker index (MI = 0.31– 0.51), revealed moderate variability across …

Green Synthesis Of Silver Nanoparticles From Melanoleuca Grammopodia: Changes In Bioactive Components, Antidiabetic Properties And Bioaccessibility, İsmai̇l Acar, Emi̇ne Okumuş, Arzu Karataş

Turkish Journal of Agriculture and Forestry

Green synthesis of silver nanoparticles (AgNPs) using plant materials allows the production of low-cost and biocompatible nanoparticles without the use of toxic compounds or solvents. In this study, biogenic AgNP/Mg nanoparticles were synthesized using the Melanoleuca grammopodia mushroom. Vitamin C and E contents of the mushroom were 42.6 mg/g and 26.82 mg/g, respectively. FTIR analysis revealed the reducing and stabilizing effects of bioactive components present in M. grammopodia mushroom extract. SEM micrographs showed that the nanoparticles were spherical in form and the EDX spectrum confirmed the presence of the characteristic metallic silver peak at 3.0 keV. A significant reduction in …

The Status Of Agritourism In Bosnia And Herzegovina, Nerma Čolaković-Prguda, Jasna Hasanbegović, Irma Đidelija Čolaković, Lejla Škaljić, Nuray Demi̇r

Turkish Journal of Agriculture and Forestry

Agritourism in Bosnia and Herzegovina has a lot of potential benefit for economic growth and sustainable development in rural regions, as it incorporates local culture and natural beauty into the tourism offerings of the region. Tourism creates opportunities to diversify the economy, retain traditions, improve local income, and protect natural resources. This study covered Međugorje, Ilijaš, Rostovo, Vlašić, Bosanska Krupa, Neum, Olovo, Gornji Vakuf, Sarajevo, and Donji Vakuf. Agritourism can provide authentic experiences like learning about traditional agriculture, fruit harvesting, tasting local products, and environmental preservation in destinations like Međugorje and Neum. Ilijaš and Gornji Vakuf have potential in organic …

Innovative Approaches To Estimating Sessile Oak Stem Volume: Comparing Additive Models And Ensemble Machine Learning, Maria J. Diamantopoulou, Abbas Şahi̇n, Ramazan Özçeli̇k

Turkish Journal of Agriculture and Forestry

Sessile oak is an important deciduous forest tree species across Türkiye and Europe. Estimating individual tree and stand volumes is essential for growth and yield models, as these predictions play a critical role in assessing forest management, economics, and fire risk. In pursuit of this goal, nonlinear seemingly unrelated regression (NSUR) was used for the simultaneous fitting of stem volume components, and compared to three ensemble machine learning techniques: gradient boosting regression (GBr), XGBoost regression (XGBr), and random forest regression (RFr). NSUR accounts for correlations between error terms across different equations, leading to more efficient parameter estimates than if each …

Effects Of Polyethylene Films With Different Uv-A Transmittance On Quality Parameters And Physiology Of Greenhouse-Grown Tomato, Nefi̇se Yasemi̇n Tezcan, Mustafa Erkan, Ahmet Kurunç

Turkish Journal of Agriculture and Forestry

In this study, the effects of three different polyethylene (PE) greenhouse covering materials (CMs) with varying thicknesses and ultraviolet-A (UV-A) transmittance on greenhouse microclimate, plant growth, yield, fruit quality, and chlorophyll fluorescence parameters (Chl FPs) in tomatoes were investigated. The CMs used in the study were 180 μm thick ultraviolet (UV) + ethylene vinyl acetate (EVA) + long-wave infrared (IR) + light diffuser (LD) + antifog (AF) added PE (CM1), 160 μm thick PLUS UV + EVA + IR + LD + AF added PE (CM2), and 200 μm thick UV + EVA + IR + LD added PE (CM3). …

Assessment Of Bat Species (Mammalia: Chiroptera) In Canubas Cave, Kibawe, Bukidnon, Philippines, Jurriel Mari D. Alce, Jasmine Rouida M. Abenes, Leo Gabriel Cervantes, Matthew Eli K. Llacer, Von Zhyrus P. Oche, Ian Jay P. Saldo, Jhovel Roy D. Calo

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Bats, flying mammals, are essential to ecosystems, playing vital roles in pollination, seed dispersal, and insect control. Despite their ecological importance, no prior bat research exists for Canubas Cave, Kibawe, Bukidnon. This study aimed to assess the bat species at the site, documenting their morphometric data, diversity and richness indices, and conservation statuses. A purposive sampling design was implemented by setting up mist nets inside and outside the cave. A total of 13 individuals were identified, comprising three species from two families: Rousettus amplexicaudatus and Eonycteris spelaea (family Pteropodidae, fruit bats), and Miniopterus schreibersii (family Miniopteridae, bent-winged bats). Based on …

Muscarinic Acetylcholine Receptor 1: Implications For Precision Medicine And Rett Syndrome Therapeutics, Mackenzie Smith

Dissertations

Rett syndrome (RTT) is a rare neurodevelopmental disorder caused by mutations in the gene coding for methyl-CpG binding protein 2 (MeCP2). Currently, there is no cure for RTT and few effective treatment options to address the social, cognitive, motor, and respiratory symptoms that patients face. With the goal of identifying novel targets, our lab performed RNA-sequencing experiments in human autopsy samples and found decreased levels of the M1 muscarinic acetylcholine receptor. We have established that potentiation of this receptor in a Mecp2+/- mouse model of RTT rescues social, cognitive, and respiratory phenotypes, providing support for using drugs that act on …

Biophysical Effects Of Altered Myosin Binding Protein Stoichiometry In Atrial Myofilaments, Kelly N. Araujo

Dissertations

Cardiomyopathies, such as hypertrophic and dilated subtypes, are leading causes of heart failure and are often driven by genetic mutations that disrupt the structure and function of the cardiac sarcomere. While much of the research has focused on ventricular involvement, the role of atrial sarcomere dysfunction remains unexplored. The regulation of contractile function by sarcomeric proteins in the atria remains poorly understood, especially the impact of protein stoichiometry among myosin binding proteins. Cardiac myosin binding protein-C (cMyBP-C) and its atrial paralog, myosin binding protein H-like (MyBP-HL), have been shown to have a stoichiometric relationship within the atrial sarcomere. These two …

Development, Validation, And Applicability Of A Race-Specific Insulin Sensitivity Estimator (Rise) In Youth And Young Adults, Wonhee Cho

Dissertations - ALL

Parallel to the escalating rate of overweight and obesity in the youth and young adult population, the incidence and prevalence of type 2 diabetes are also mounting, presenting significant public health problems. Among the various pathophysiological factors, insulin sensitivity has emerged as a critical risk factor for impaired glucose tolerance (IGT) and type 2 diabetes in youth. Despite the pivotal role of insulin sensitivity in the development and progression of these conditions, current methodologies for its assessment, such as the hyperinsulinemic-euglycemic clamp and intravenous glucose tolerance test, are limited by their invasive methods, high cost, and unsuitability for use in …

Caf-Macrophage Crosstalk Fuels Immunotherapy Resistance, Yang Liu, Linghua Wang

Faculty, Staff and Student Publications

No abstract provided.

Safety Of Contemporary Radiation Therapy In Patients With Cardiac Implantable Electronic Devices: Implications For Clinical Practice, Kaveh Karimzad, Shalin Shah, Stephen F Kry, Christopher Peeler, Julianne Pollard-Larkin, Amit Koduri, Martin Chacon Portillo, Siddharth Chauhan, Atia Amatullah, Chase Miller, Amanda Strang, Juhee Song, Khatera Mir Zaman Shah, Donelo Lopez, Darla Wagner, January Tsai, Shital Vachhani, Dilip Thakar, Cezar Iliescu, Jean-Bernard Durand, Anne H Dougherty, Bharat Kantharia, Anita Deswal

Faculty, Staff and Student Publications

Background: Radiation therapy (RT) can cause cardiac implantable electronic device (CIED) malfunction, primarily reset. Given changes in RT and CIED technologies, large observational studies examining malfunction of contemporary CIEDs during modern-day RT are needed to guide clinical practice.

Methods: Electronic medical records of all consecutive patients with CIEDs who underwent RT at a large tertiary cancer center between January 2015 and January 2022 were reviewed. All patients had CIED interrogation before and after completion of RT. Device-related data and RT-specific variables were collected. Statistical analyses were performed at the RT course level.

Results: Over a period of 7 years, 677 …

A Multimodal Approach To Assess A Liposomal Carrier’S Biodistribution, Stability, And Clearance, Cayla A Wood, Claire E Jones, Ananthakrishnan Soundaram Jeevarathinam, Riley Watson, Sangheon Han, Jennifer Meyer, Konstantin V Sokolov, Richard R Bouchard

Faculty, Staff and Student Publications

Liposomal carriers, used for site-specific drug delivery, are being investigated for diagnostic approaches by replacing the therapeutic with an imaging contrast agent, exploring potential for selective treatment planning. There remains a critical need to improve in vivo assessment of biodistribution, stability, and clearance kinetics of liposomal carriers. This pilot study presents a multimodal approach in which liposome-encapsulated J-aggregated indocyanine green (ICG) dye (Lipo-JICG) is imaged with high spatial resolution using both in vivo photoacoustic (PA) imaging, to assess the absorbance characteristics of JICG and monomeric ICG, and ex vivo cryofluorescence tomography (CFT), to measure ICG fluorescence. An in vitro assay …

In Silico Investigation Of The Anticancer Activity Of Natural Isoquinoline Alkaloids Targeting The Monoamine Oxidase A Enzyme, Reham A. Al-Anssari, Anwar H. Ali, Ola Adel Al-Saad, Shaker A.N. Al-Jadaan

AUIQ Complementary Biological System

Monoamine oxidase A (MAO-A) has recently been identified as a candidate for cancer therapy due to its roles in tumor development and growth. Conventional approaches for the discovery of MAO-A inhibitors are both costly and time-consuming. The objective of this work was to apply in silico methods to predict natural isoquinoline alkaloids capable of acting as potent MAO-A inhibitors, and to establish this class of compounds as potential sources of a cost-effective anticancer therapy. Twenty-one natural isoquinoline alkaloids were subjected to a multistep computer-aided drug discovery protocol. The compounds were initially screened for pharmacokinetic (ADME), toxicity, and drug-likeliness properties by …

Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing, Danielle Ireland, L. J. Word, Eva-Maria S. Collins

Biology Faculty Works

There is an urgent need for high-throughput screening (HTS) models to replace, refine, and/or reduce (“3Rs”) vertebrate toxicity testing. Replacing in vivo animal studies is challenging for neurotoxicity and developmental neurotoxicity (DNT), where the functional relevancy of adverse outcomes needs to be assessed on the whole organism. We previously screened the NTP 87-compound library (NTP87), consisting of known and suspected developmental neurotoxicants, and showed that planarian HTS can identify known (developmental) neurotoxicants. Because analysis methods can impact screening results, and our original analysis used the lowest-observed-effect-level (LOEL) only, we hypothesized that the use of state-of-the-art statistical analysis would increase the …

Prefrontal Cortex Astrocytes Modulate Distinct Neuronal Populations To Control Anxiety-Like Behavior, Eunyoung Kim, Hairuo Du, Yanqi Tan, Brandon L Brown, Yaowen Chang, Blanca Díaz-Castro, Jonathan V Sweedler, Xinzhu Yu

Faculty, Staff and Student Publications

Accumulating evidence has supported diverse regulatory functions of astrocytes in different neural circuits as well as various aspects of complex behaviors. However, little is known about how astrocytes regulate different neuronal subpopulations that are linked to specific behavioral aspects within a single brain region. Here, we show that astrocytes in the medial prefrontal cortex (mPFC) encode anxiogenic environmental cues in freely behaving mice. Silencing mPFC astrocyte Ca

Phase 1/2 Trial Of Encorafenib, Cetuximab, And Nivolumab In Microsatellite Stable Brafv600e Metastatic Colorectal Cancer, Van K Morris, Christine M Parseghian, Vahid Bahrambeigi, Nourhan Abdelfattah, Lianchun Xiao, Anjali Agrawal, Kangyu Lin, Kanwal P S Raghav, Robert A Wolff, Arvind Dasari, Ryan W Huey, Bryan K Kee, Michael J Overman, Jason A Willis, Phat H Le, Michelle Escano, Yunyu C Baig, Kelsey Pan, David Menter, Alda L Tam, Wai C Foo, Li Shen, Hey Min Lee, Thomas D Gallup, Cori Margain, Dave Gallup, Kimal I Rajapakshe, Paola A Guerrero, Jing Wang, Ryan B Corcoran, Anirban Maitra, Kyuson Yun, Scott Kopetz

Faculty, Staff and Student Publications

The BRAF inhibitor encorafenib and anti-epidermal growth factor receptor (EGFR) antibody cetuximab modestly improve survival for patients with microsatellite stable (MSS) BRAFV600E metastatic colorectal cancer (mCRC), characterized by higher immune activation than MSS BRAFwild-type colorectal cancer (CRC). In this phase 1/2 study (NCT04017650) of 26 participants with MSS BRAFV600E mCRC who received encorafenib, cetuximab, and anti-PD-1 antibody nivolumab, we report an overall response rate of 50% (95% confidence interval [CI] 29–71) and median progression-free survival of 7.4 months (95% CI, 5.6–9.6). Transcriptomic profiling of pretreatment biopsies and extracellular vesicle RNA (evRNA) isolated from plasma show …

Circzfr/Ythdf3 Axis Drives Lymph Node Metastasis In Cervical Cancer Via Fasn Translation, Mingyi Zhou, Yan Gao, Yong Zhang, Lian He, Bo Gao, Yue Zhang, Francois X Claret, George A Calin, Danbo Wang

Faculty, Staff and Student Publications

Background: Lymph node metastasis is a key driver of poor outcomes in cervical cancer. However, the molecular mechanisms of circular RNAs (circRNAs) driving cervical cancer lymph node metastasis remain unclear.

Methods: We identified circZFR, fatty acid synthase (FASN) and YTH N6-methyladenosine RNA binding protein F3 (YTHDF3) protein expression in the cervical cancer patients with long and short disease-free survival (DFS). Functional experiments were performed to investigate the function of circZFR, FASN and YTHDF3 on cell migration and invasion. MeRIP-qPCR, RNA pulldown, RNA Immunoprecipitation (RIP), and Co-Immunoprecipitation (Co-IP) assays were executed to investigate the mechanism of circZFR regulating FASN protein expression. …