Medical Biochemistry Commons^™

Dna Mismatch Repair And Its Role In Huntington's Disease, Ravi R Iyer, Anna Pluciennik

Department of Biochemistry and Molecular Biology Faculty Papers

DNA mismatch repair (MMR) is a highly conserved genome stabilizing pathway that corrects DNA replication errors, limits chromosomal rearrangements, and mediates the cellular response to many types of DNA damage. Counterintuitively, MMR is also involved in the generation of mutations, as evidenced by its role in causing somatic triplet repeat expansion in Huntington's disease (HD) and other neurodegenerative disorders. In this review, we discuss the current state of mechanistic knowledge of MMR and review the roles of key enzymes in this pathway. We also present the evidence for mutagenic function of MMR in CAG repeat expansion and consider mechanistic hypotheses …

Label‑Free Spectral Imaging To Study Drug Distribution And Metabolism In Single Living Cells, Qamar Alshammari, Rajasekharreddy Pala, Nir Katzir, Surya M. Nauli

Pharmacy Faculty Articles and Research

During drug development, evaluation of drug and its metabolite is an essential process to understand drug activity, stability, toxicity and distribution. Liquid chromatography (LC) coupled with mass spectrometry (MS) has become the standard analytical tool for screening and identifying drug metabolites. Unlike LC/MS approach requiring liquifying the biological samples, we showed that spectral imaging (or spectral microscopy) could provide high-resolution images of doxorubicin (dox) and its metabolite doxorubicinol (dox’ol) in single living cells. Using this new method, we performed measurements without destroying the biological samples. We calculated the rate constant of dox translocating from extracellular moiety into the cell and …

Distinct Mechanisms Control Genome Recognition By P53 At Its Target Genes Linked To Different Cell Fates., Marina Farkas, Hideharu Hashimoto, Yingtao Bi, Ramana V Davuluri, Lois Resnick-Silverman, James J. Manfredi, Erik W. Debler, Steven B. Mcmahon

Department of Biochemistry and Molecular Biology Faculty Papers

The tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate decisions (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to 20-bp response elements (REs) in the genome (RRRCWWGYYYN_0-13RRRCWWGYYY). In general, REs at cell cycle arrest targets (e.g. p21) are of higher affinity than those at apoptosis targets (e.g., BAX). However, the RE sequence code underlying selectivity remains undeciphered. Here, we identify molecular mechanisms mediating p53 binding to high- and low-affinity REs by showing that key determinants of the code are embedded …

A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha

Publications and Research

Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). …

Tumor Microenvironment: An Evil Nexus Promoting Aggressive Head And Neck Squamous Cell Carcinoma And Avenue For Targeted Therapy, Ajaz A. Bhat, Parvaiz Yousuf, Nissar A. Wani, Arshi Rizwan, Shyam S. Chauhan, Mushtaq A. Siddiqi, Davide Bedognetti, Wael El-Rifai, Michael P. Frenneaux, Surinder K. Batra, Mohammad Haris, Muzafar A. Macha

Journal Articles: Biochemistry & Molecular Biology

Head and neck squamous cell carcinoma (HNSCC) is a very aggressive disease with a poor prognosis for advanced-stage tumors. Recent clinical, genomic, and cellular studies have revealed the highly heterogeneous and immunosuppressive nature of HNSCC. Despite significant advances in multimodal therapeutic interventions, failure to cure and recurrence are common and account for most deaths. It is becoming increasingly apparent that tumor microenvironment (TME) plays a critical role in HNSCC tumorigenesis, promotes the evolution of aggressive tumors and resistance to therapy, and thereby adversely affects the prognosis. A complete understanding of the TME factors, together with the highly complex tumor-stromal interactions, …

Insights Into Genome Recoding From The Mechanism Of A Classic +1-Frameshifting Trna., Howard Gamper, Haixing Li, Isao Masuda, D. Miklos Robkis, Thomas Christian, Adam B. Conn, Gregor Blaha, E. James Petersson, Ruben L. Gonzalez, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 …

Myc Regulates Ribosome Biogenesis And Mitochondrial Gene Expression Programs Through Its Interaction With Host Cell Factor-1., Tessa M. Popay, Jing Wang, Clare M. Adams, Gregory Caleb Howard, Simona G. Codreanu, Stacy D. Sherrod, John A. Mclean, Lance R. Thomas, Shelly L. Lorey, Yuichi J. Machida, April M. Weissmiller, Christine M. Eischen, Qi Liu, William P. Tansey

Department of Cancer Biology Faculty Papers

The oncoprotein transcription factor MYC is a major driver of malignancy and a highly validated but challenging target for the development of anticancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here we interrogate how one MYC co-factor, host cell factor (HCF)-1, contributes to MYC activity in a human Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets and demonstrate how modulation of the MYC-HCF-1 interaction influences cell growth, metabolite profiles, global …

Role Of Thymidine Phosphorylase In Type 2 Diabetes-Associated High-Risk Of Thrombosis, Adam Belcher

Theses, Dissertations and Capstones

Cardiovascular diseases (CVDs), such as ischemic heart disease and stroke, are the leading causes of death globally that disproportionally affects patients with type 2 diabetes mellitus (T2DM) at a 2-4-fold rate compared to non-diabetic patients. These CVDs result from a blood clot, also known as a thrombus, formed in arteries that can block blood flow resulting in tissue damage and death. Antiplatelet drugs, such as aspirin and clopidogrel, used to prevent thrombosis have been found to be less effective in diabetics and increase the risk of hemorrhagic events. The T2DM epidemic has made it imperative to find therapies that decrease …

Treatments For The Mitigation Of Immunotherapy-Related Neurotoxicities In Patients With Non-Small Cell Lung Cancer, Gautam Chiang

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Lung cancer is the most common cancer type worldwide, with one of the highest mortality rates across all cancer types. Cancer immunotherapeutics such as immune checkpoint inhibitors (ICIs) have improved cancer treatment by promoting the body’s natural immune response to tumor development while avoiding toxic effects associated with traditional cytotoxic chemotherapy. However, immunotherapies have been associated with unique toxic effects similar to autoimmune disorders known as immune-related adverse events (irAEs). 4.2% of immunotherapy-treated cancer patients reportedly developed neurological irAEs. In this review, different immunotherapies were studied, including ICIs and mechanism-specific novel therapies, in order to determine a combination therapy to …

Contribution Of The Human Microbiome And Proteus Mirabilis To Onset And Progression Of Rheumatoid Arthritis: Potential For Targeted Therapy, Jessica Kerpez, Marc Kesselman, Michelle Demory Beckler

Internet Journal of Allied Health Sciences and Practice

The human microbiome has been shown to play a role in the regulation of human health, behavior, and disease. Data suggests that microorganisms that co-evolved within humans have an enhanced ability to prevent the development of a large spectrum of immune-related disorders but may also lead to the onset of conditions when homeostasis is disrupted. In many conditions, a link between dysbiosis (microbial imbalance or microbiome upset) has been identified and associated with immune conditions such as rheumatoid arthritis (RA). This review provides insight into how an individual’s unique microbiome, combined with a genetic predisposition and environmental factors may lead …

Growth In A Biofilm Sensitizes Cutibacterium Acnes To Nanosecond Pulsed Electric Fields, Asia Poudel, Adenrele Oludiran, Esin B. Sözer, Maura Casciola, Erin B. Purcell, Claudia Muratori

Bioelectrics Publications

The Gram-positive anaerobic bacterium Cutibacterium acnes (C. acnes) is a commensal of the human skin, but also an opportunistic pathogen that contributes to the pathophysiology of the skin disease acne vulgaris. C. acnes can form biofilms; cells in biofilms are more resilient to antimicrobial stresses. Acne therapeutic options such as topical or systemic antimicrobial treatments often show incomplete responses. In this study we measured the efficacy of nanosecond pulsed electric fields (nsPEF), a new promising cell and tissue ablation technology, to inactivate C. acnes. Our results show that all tested nsPEF doses (250 to 2000 pulses, 280 ns pulses, …

การตรวจสอบการกลายพันธุ์บริเวณ Basal Core Promoter ในผู้ป่วยที่ติดเชื้อไวรัสตับอักเสบบี ด้วยเทคนิคปฏิกิริยาลูกโซ่พอลิเมอเรสแบบดรอปเลทดิจิตอล, ชวิศ พลพงษ์

Chulalongkorn University Theses and Dissertations (Chula ETD)

การกลายพันธุ์บริเวณ Basal core promoter (BCP) ตำแหน่ง A1762T/G1764A ของไวรัสตับอักเสบบี มีความสัมพันธ์กับการดำเนินโรคไวรัสตับอักเสบบีแบบเรื้อรัง(chronic hepatitis B; CHB) อย่างไรก็ตามส่วนใหญ่เป็นการศึกษาด้วย Sanger sequencing ที่ให้ผลเชิงคุณภาพ แต่การศึกษาด้วยเทคนิคอื่นเช่นเทคนิค droplet digital PCR(ddPCR) ที่สามารถบ่งบอกปริมาณร้อยละการกลายพันธุ์ (mutation percentage) ได้ยังคงมีจำกัด การศึกษานี้จึงมีจุดประสงค์เพื่อพัฒนาวิธีการตรวจสอบการกลายพันธุ์บริเวณ BCP โดยใช้ ddPCR เปรียบเทียบกับ Sanger sequencing และ Real- Time PCR และหาความสัมพันธ์ของ mutation percentage กับปัจจัยทางไวรัสและคลินิก ในผู้ป่วย CHB จำนวน 185 คน ผลการศึกษาพบว่าจากจำนวนผู้ป่วยทั้งหมดมีผู้ป่วย 78 รายที่นำมาศึกษาเปรียบเทียบกันได้ทั้ง 3 วิธี โดยพบว่า ddPCR สามารถตรวจพบการกลายพันธุ์ได้มากกว่าSanger sequence(84.6%vs.43.6%,P<0.001) และReal-time PCR(84.6%vs. 60.3%,P<0.001) และพบการกลายพันธุ์ได้(limit of detection(LOD)ตั้งแต่ร้อยละ0.25 การศึกษาด้วย ddPCR พบว่าผู้ป่วย HBeAg-positive มีร้อยละการกลายพันธุ์ต่ำกว่าผู้ป่วย HBeAg-negative (31.36±33.56vs.46.86±27.88 ,P<0.001) นอกจากนี้ยังพบความสัมพันธ์เชิงลบกับระดับ HBcrAg ในเลือดของผู้ป่วย HBeAg-positive(r=-0.286,P=0.070) และพบว่าผู้ป่วยกลุ่ม wild type มีระดับของ HBcrAg สูงสุด และพบระดับ HBcrAg ลดลงเมื่อมีการกลายพันธุ์เพิ่มขึ้น ส่วนในผู้ป่วย HBeAg-negative พบว่าการกลายพันธุ์มีความสัมพันธ์เชิงบวกกับ HBcrAg(r=0.273,P=0.008) ผลการศึกษาสรุปได้ว่า ddPCR เป็นเทคนิคที่มีประสิทธิภาพและมีความไวในการตรวจสอบการกลายพันธุ์บริเวณ BCP ได้ดีที่สุด นอกจากนี้ยังพบความสัมพันธ์กับระดับของ HBcrAg ในเลือดซึ่งเป็นตัวบ่งชี้ใหม่ที่ใช้ในทางคลินิก ดังนั้นเทคนิค ddPCR จึงอาจจะสามารถเป็นวิธีทางเลือกหนึ่งในการตรวจสอบการกลายพันธุ์ของไวรัสตับอักเสบบีได้

The Current Landscape Of Antibody-Based Therapies In Solid Malignancies, Ashu Shah, Sanchita Rauth, Abhijit Aithal, Sukhwinder Kaur, Koelina Ganguly, Catherine Orzechowski, Grish C. Varshney, Maneesh Jain, Surinder K. Batra

Journal Articles: Biochemistry & Molecular Biology

Over the past three decades, monoclonal antibodies (mAbs) have revolutionized the landscape of cancer therapy. Still, this benefit remains restricted to a small proportion of patients due to moderate response rates and resistance emergence. The field has started to embrace better mAb-based formats with advancements in molecular and protein engineering technologies. The development of a therapeutic mAb with long-lasting clinical impact demands a prodigious understanding of target antigen, effective mechanism of action, gene engineering technologies, complex interplay between tumor and host immune system, and biomarkers for prediction of clinical response. This review discusses the various approaches used by mAbs for …

Dynamic Phenotypic Switching And Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy, Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, Srisairam Achuthan, Kishore Hari, Saumya Srivastava, Linlin Guo, Anusha Nathan, Rishov Chatterjee, Maneesh Jain, Mohd W. Nasser, Surinder K. Batra, Govindan Rangarajan, Erminia Massarelli, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi Salgia

Journal Articles: Biochemistry & Molecular Biology

Drug resistance, a major challenge in cancer therapy, is typically attributed to mutations and genetic heterogeneity. Emerging evidence suggests that dynamic cellular interactions and group behavior also contribute to drug resistance. However, the underlying mechanisms remain poorly understood. Here, we present a new mathematical approach with game theoretical underpinnings that we developed to model real-time growth data of non-small cell lung cancer (NSCLC) cells and discern patterns in response to treatment with cisplatin. We show that the cisplatin-sensitive and cisplatin-tolerant NSCLC cells, when co-cultured in the absence or presence of the drug, display dynamic group behavior strategies. Tolerant cells exhibit …

Characterization Of Cucurbitacin-Inspired Estrone Analogues As Novel Inhibitors Of Human Atp- Binding Cassette Proteins (Abcb1 And Abcc1), Jennifer Kyeremateng

Electronic Theses and Dissertations

ATP-binding cassette (ABC) transporters are a large class of integral membrane proteins that contribute to key physiological functions in all organisms by utilizing ATP binding and hydrolysis to transport diverse substrates across membrane barriers. P-glycoprotein (P-gp/ ABCB1) and Multidrug Resistance protein 1 (MRP1/ABCC1) are widely reported ABC transporters associated with multidrug resistance in cancer. Multidrug resistance (MDR) mediated by P-gp and MRP1 is responsible for treatment failures of many metastatic cancers as a result of reduced accumulation, bioavailability and diminished potency of anticancer drugs. Currently, known P-gp and MRP1 inhibitors are limited due to toxicity, lack of selectivity and low …

The Role Of Vascular Endothelial Growth Factor In Leukemia Trafficking, Shaw Powell

Theses and Dissertations--Medical Sciences

Vascular endothelial growth factor (VEGF) is a signaling protein involved in inducing and regulating endothelial cell proliferation and function (Duffy et al 2000). VEGF is also involved in cancer progression, as it induces vascular permeability and promotes angiogenesis to tumor laden areas, giving cancer cells critical oxygen and nutrients (Hoeppner et al.,2012. Studies indicate VEGF prevents lymphoblast apoptosis, which may contribute to leukemia formation and enable the proliferation of leukemic cells (Duffy et al 2000). Ongoing research seeks to further examine VEGF in leukemia, using a rag2:GFP-Myc expressing transgenic zebrafish as the animal model of T-cell Acute Lymphoblastic Leukemia (T-ALL). …

Carnosic Acid Differentially Modulates The Nrf2- Antioxidant Response In Male And Female Mice Following Experimental Traumatic Brain Injury, Jacob A. Dunkerson

Theses and Dissertations--Neuroscience

Traumatic brain injury (TBI) is a leading cause of death and disability in the United States. Each year, an estimated 2.8 million Americans are diagnosed with a TBI due to falling, motor vehicle collisions, gun violence, and sports related concussions. Although inflicted by a single event, the post-traumatic effects of TBI often develop into a life-long disease. Survivors often experience cognitive decline, memory loss, emotional instability, changes in personality, and physical disabilities. A single TBI, and more-so repetitive TBI's, place an individual at a greater risk of developing chronic neurological disorders, such as dementia or Alzheimer’s disease, earlier in life. …

Notch Signaling Regulates Perivascular Adipose Tissue (Pvat) Function During Diet-Induced Obesity, C Yang, A Harrington, L Ryzhova, L Liaw

Costas T. Lambrew Research Retreat 2021

Objectives:

-To test the hypothesis that canonical Notch signaling influence vascular function by regulating PVAT-derived vascular relaxation factors.

-To determine how overexpression of Notch signaling or loss of the key Notch signaling component influence PVAT function.

Monopolar Gene Electrotransfer Enhances Plasmid Dna Delivery To Skin, Anna Bulysheva, Loree Heller, Michael Francis, Frency Varghese, Carly Boye, Richard Heller

Electrical & Computer Engineering Faculty Publications

A novel monopolar electroporation system and methodologies were developed for in vivo electroporation intended for potential clinical applications such as gene therapy. We hypothesized that an asymmetric anode/cathode electrode applicator geometry could produce favorable electric fields for electroporation, without the typical drawback associated with traditional needle and parallel plate geometries. Three monopolar electrode applicator prototypes were built and tested for gene delivery of reporter genes to the skin in a guinea pig model. Gene expression was evaluated in terms of kinetics over time and expression distribution within the treatment site. Different pulsing parameters, including pulse amplitude, pulse duration, and pulse …

Evaluation Of Somatic Mutations In Solid Metastatic Pan-Cancer Patients, Moom R. Roosan, Isa Mambetsariev, Rebecca Pharaon, Jeremy Fricke, Angel R. Baroz, Joseph Chao, Chen Chen, Mohd W. Nasser, Ramakanth C. Venkata, Maneesh Jain, Lynette M. Smith, Susan E. Yost, Karen L. Reckamp, Raju Pillai, Leonidas Arvanitis, Michelle Afkhami, Edward W. Wang, Vincent Chung, Mihaela Cristea, Marwan Fakih, Marianna Koczywas, Erminia Massarelli, Joanne Mortimer, Yuan Yuan, Surinder K. Batra, Sumanta Pal, Ravi Salgia

Journal Articles: Biochemistry & Molecular Biology

Metastasis continues to be the primary cause of all cancer-related deaths despite the recent advancements in cancer treatments. To evaluate the role of mutations in overall survival (OS) and treatment outcomes, we analyzed 957 metastatic patients with seven major cancer types who had available molecular testing results with a FoundationOne CDx^® panel. The most prevalent genes with somatic mutations were TP53, KRAS, APC, and LRP1B. In this analysis, these genes had mutation frequencies higher than in publicly available datasets. We identified that the somatic mutations were seven mutually exclusive gene pairs and an additional fifty-two co-occurring gene pairs. Mutations …