Medical Biochemistry Commons^™

Repurposing Niclosamide For Targeting Pancreatic Cancer By Inhibiting Hh/Gli Non-Canonical Axis Of Gsk3Β, Jyoti B. Kaushal, Rakesh Bhatia, Ranjana K. Kanchan, Pratima Raut, Surya Mallapragada, Quan P. Ly, Surinder K. Batra, Satyanarayana Rachagani

Journal Articles: Biochemistry & Molecular Biology

Niclosamide (Nic), an FDA-approved anthelmintic drug, is reported to have anti-cancer efficacy and is being assessed in clinical trials for various solid tumors. Based on its ability to target multiple signaling pathways, in the present study, we evaluated the therapeutic efficacy of Nic on pancreatic cancer (PC) in vitro. We observed an anti-cancerous effect of this drug as shown by the G0/G1 phase cell cycle arrest, inhibition of PC cell viability, colony formation, and migration. Our results revealed the involvement of mitochondrial stress and mTORC1-dependent autophagy as the predominant players of Nic-induced PC cell death. Significant reduction of Nic-induced reactive …

Emerging Role Of Mir-345 And Its Effective Delivery As A Potential Therapeutic Candidate In Pancreatic Cancer And Other Cancers, Nagabhishek Sirpu Natesh, Brianna M. White, Maia M. C. White, Metin Uz, Rakhee Rathnam Kalari Kandy, Surinder K. Batra, Surya K. Mallapragada, Satyanarayana Rachagani

Journal Articles: Biochemistry & Molecular Biology

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with high mortality, poor prognosis, and palliative treatments, due to the rapid upregulation of alternative compensatory pathways and desmoplastic reaction. miRNAs, small non-coding RNAs, have been recently identified as key players regulating cancer pathogenesis. Dysregulated miRNAs are associated with molecular pathways involved in tumor development, metastasis, and chemoresistance in PDAC, as well as other cancers. Targeted treatment strategies that alter miRNA levels in cancers have promising potential as therapeutic interventions. miRNA-345 (miR-345) plays a critical role in tumor suppression and is differentially expressed in various cancers, including pancreatic cancer (PC). The underlying …

Mir-212-3p Functions As A Tumor Suppressor Gene In Group 3 Medulloblastoma Via Targeting Nuclear Factor I/B (Nfib), Naveenkumar Perumal, Ranjana K. Kanchan, David Doss, Noah Bastola, Pranita Atri, Ramakanth C. Venkata, Ishwor Thapa, Raghupathy Vengoji, Shailendra K. Maurya, David Klinkebiel, Geoffrey A. Talmon, Mohd W. Nasser, Surinder K. Batra, Sidharth Mahapatra

Journal Articles: Biochemistry & Molecular Biology

Haploinsufficiency of chromosome 17p and c-Myc amplification distinguish group 3 medulloblastomas which are associated with early metastasis, rapid recurrence, and swift mortality. Tumor suppressor genes on this locus have not been adequately characterized. We elucidated the role of miR-212-3p in the pathophysiology of group 3 tumors. First, we learned that miR-212-3p undergoes epigenetic silencing by histone modifications in group 3 tumors. Restoring its expression reduced cancer cell proliferation, migration, colony formation, and wound healing in vitro and attenuated tumor burden and improved survival in vivo. MiR-212-3p also triggered c-Myc destabilization and degradation, leading to elevated apoptosis. We then isolated an …

Disruption Of Fdps/Rac1 Axis Radiosensitizes Pancreatic Ductal Adenocarcinoma By Attenuating Dna Damage Response And Immunosuppressive Signalling, Parthasarathy Seshacharyulu, Sushanta Halder, Rama Krishna Nimmakayala, Satyanarayana Rachagani, Sanjib Chaudhary, Pranita Atri, Ramakanth C. Venkata, Michel M. Ouellette, Joseph Carmicheal, Shailendra K. Gautam, Raghupathy Vengoji, Shuo Wang, Sicong Li, Lynette M. Smith, Geoffrey A. Talmon, Kelsey Klute, Quan P. Ly, Bradley N. Reames, Jean L. Grem, Lyudmyla Berim, James C. Padussis, Sukhwinder Kaur, Sushil Kumar, Moorthy P. Ponnusamy, Maneesh Jain, Chi Lin, Surinder K. Batra

Journal Articles: Biochemistry & Molecular Biology

BACKGROUND: Radiation therapy (RT) has a suboptimal effect in patients with pancreatic ductal adenocarcinoma (PDAC) due to intrinsic and acquired radioresistance (RR). Comprehensive bioinformatics and microarray analysis revealed that cholesterol biosynthesis (CBS) is involved in the RR of PDAC. We now tested the inhibition of the CBS pathway enzyme, farnesyl diphosphate synthase (FDPS), by zoledronic acid (Zol) to enhance radiation and activate immune cells.

METHODS: We investigated the role of FDPS in PDAC RR using the following methods: in vitro cell-based assay, immunohistochemistry, immunofluorescence, immunoblot, cell-based cholesterol assay, RNA sequencing, tumouroids (KPC-murine and PDAC patient-derived), orthotopic models, and PDAC patient's …

Differential Gene Expression-Based Connectivity Mapping Identified Novel Drug Candidate And Improved Temozolomide Efficacy For Glioblastoma, Raghupathy Vengoji, Pranita Atri, Muzafar A. Macha, Parthasarathy Seshacharyulu, Naveenkumar Perumal, Kavita Mallya, Yutong Liu, Lynette M. Smith, Satyanarayana Rachagani, Sidharth Mahapatra, Moorthy P. Ponnusamy, Maneesh Jain, Surinder K. Batra, Nicole Shonka

Journal Articles: Biochemistry & Molecular Biology

BACKGROUND: Glioblastoma (GBM) has a devastating median survival of only one year. Treatment includes resection, radiation therapy, and temozolomide (TMZ); however, the latter increased median survival by only 2.5 months in the pivotal study. A desperate need remains to find an effective treatment.

METHODS: We used the Connectivity Map (CMap) bioinformatic tool to identify candidates for repurposing based on GBM's specific genetic profile. CMap identified histone deacetylase (HDAC) inhibitors as top candidates. In addition, Gene Expression Profiling Interactive Analysis (GEPIA) identified HDAC1 and HDAC2 as the most upregulated and HDAC11 as the most downregulated HDACs. We selected PCI-24781/abexinostat due to …

A Biochemical Characterization Of The Fusion Proteins From Enveloped Rna Viruses, Chelsea T. Barrett

Theses and Dissertations--Molecular and Cellular Biochemistry

Enveloped viruses must bind target cells and then fuse the viral membrane with a cell membrane to enter a host cell. These viruses use one or more surface glycoproteins to carry out these critical functions. The surface glycoprotein that carries out the fusion function, termed a fusion protein, is divided into three classes based on structural similarities. Some of the most studied human viral pathogens, such as human immunodeficiency virus (HIV), Ebola virus, influenza, measles, and the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), possess class I fusion proteins. Following synthesis, class I fusion proteins associate as non-covalently …

Entry And Early Infection Of Non-Segmented Negative Sense Rna Viruses, Jean Mawuena Branttie

Theses and Dissertations--Molecular and Cellular Biochemistry

Paramyxoviruses, pneumoviruses, and other non-segmented negative sense (NNS) RNA viruses have historically been of public health concern. Although their genomes are typically small (up to 19kbs) they are able to inflict large-scale detrimental pathologies on host cells. Human metapneumovirus (HMPV) is a widespread pathogen and is a NNS RNA virus. HMPV results respiratory tract infections and is particularly dangerous for preterm infants, the elderly, and immunocompromised individuals. Other viruses within the NNS RNA virus order include the deadly Ebola, Hendra, and Nipah viruses (EBOV, HeV, and NiV), as well as the re-emerging measles virus (MeV). Despite their public impact, there …

Pre-Clinical Advancements In Biomarkers, Tools, And Therapeutics For A Metabolic Neurodegenerative Disease, Zoë Simmons

Theses and Dissertations--Molecular and Cellular Biochemistry

Glycogen is the storage form of glucose and a highly important substrate for cellular metabolism. Characterization of the enzymes and mechanisms of glycogen metabolism began over 70 years ago and over the last 20 years, a previously unknown protein called laforin has emerged as an important contributor to glycogen metabolism homeostasis. Multiple labs demonstrated that laforin is a glycogen phosphatase and mutations in the gene encoding laforin cause the formation of aberrant glycogen-like aggregates called Lafora bodies (LBs). LBs are cytoplasmic, water-insoluble aggregates that drive neurodegeneration and early death in Lafora disease (LD) patients. The direct relationship between mutated laforin, …

Development Of Novel Point-Of-Care-Testing For Oxalate Detection In Urine Based On Oxalate-Binding Ligands, Naruerat Joybumrung

Chulalongkorn University Theses and Dissertations (Chula ETD)

Kidney stone disease is the third most common urinary tract disease worldwide that is more prevalent in the tropics. In Thailand, the highest stone prevalence up to 17% is reported in the Northeast. The disease is highly recurrent with a recurrence rate of about 50% within 5-10 years. The most common type of kidney stones is calcium oxalate (CaOx), and an increased urinary oxalate excretion is an important risk factor. Most of kidney stone patients have a hyperoxaluria condition (urinary oxalate >40 mg/day or >0.46 mmol/day). Therefore, urinary oxalate measurement has been widely used for estimating the risk of CaOx …

Epigenetic Regulation Of Reactive Oxygen Species-Induced Tumor Progression In Hepatocellular Carcinoma, Suchittra Phoyen

Chulalongkorn University Theses and Dissertations (Chula ETD)

Oxidative stress is a consequence of an imbalance of antioxidants and reactive species. The most common form of reactive species is derived from oxygen, called reactive oxygen species (ROS). ROS involve in pathogenesis of several diseases including cancers. Cancer genesis and progression are contributed through both genetic and epigenetic mechanisms. Histone modification, a post-translational modification at histone tails, is one of the epigenetic mechanisms known to participate in carcinogenesis and tumor progression. Although the ROS-induced histone modification alteration has been demonstrated in some cancers, the change in histone methylation and gene expression by ROS in hepatocellular carcinoma (HCC) is scarcely …

Integrative Transcriptomic Analysis And Validation Of Non-Coding Rna In Liver Cancers, Varunya Virushkul

Chulalongkorn University Theses and Dissertations (Chula ETD)

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) are the most common and cause cancer-related deaths. Due to the lack of sensitivity and specificity of conventional markers, such as AFP, CA19-9 and CEA. Thus, this study aimed to identify miRNAs as a diagnostic biomarker for HCC and iCCA. First, in discovery set, RNA sequencing and small RNA sequencing data of 992 HCC and adjacent tissues and 116 iCCA and adjacent tissues were downloaded from the GEO database. After that, the lncRNA-miRNA-mRNA network was constructed and analyzed for the differential expression of lncRNA (DElncRNA), miRNA (DEmiRNA), and mRNA (DEmRNA). Then, the significant …

บทบาทของ Advanced Glycation End Products และภาวะเครียดออกซิเดชันในโรคกระดูกสันหลังส่วนเอวเสื่อม, มนัสนันท์ จิตรจำนงค์

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคกระดูกสันหลังส่วนเอวเสื่อมเป็นโรคที่เกิดจากการเสื่อมสภาพของหมอนรองกระดูกสันหลัง พบได้บ่อยในผู้สูงอายุ ปัจจัยหนึ่งที่เป็นสาเหตุร่วมทำให้เกิดการเสื่อมคือภาวะเครียดออกซิเดชัน การสะสมของสารอนุมูลอิสระ และ advanced glycation end products (AGEs) ซึ่งอาจมีบทบาทสำคัญต่อการเกิดและการดำเนินโรค วัตถุประสงค์ของการศึกษานี้เพื่อศึกษาบทบาทของ AGEs, receptor for AGEs (RAGE) ตัวชี้วัดภาวะเครียดออกซิเดชัน สารต้านอนุมูลอิสระ และความยาวเทโลเมียร์ในเลือดของผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อม การศึกษานี้แบ่งกลุ่มตัวอย่างเป็นสองกลุ่ม กลุ่มคนปกติที่มีสุขภาพดีและกลุ่มผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อม กลุ่มละ 75 ราย ซึ่งใช้ภาพถ่ายคลื่นแม่เหล็กไฟฟ้า (Magnetic Resonance Imaging, MRI) เพื่อแบ่งกลุ่มผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อมตามระดับความรุนแรงของโรค โดยทำการเก็บตัวอย่างเลือดจากอาสาสมัครทั้งสองกลุ่มเพื่อตรวจวัดระดับ AGEs, RAGE, 8-hydroxy-2'-deoxyguanosine (8-OHdG), protein carbonyl, malondialdehyde (MDA), nitrite ในพลาสมา การแสดงออกของยีน inducible nitric oxide synthase (iNOS) ในเลือด ระดับ total antioxidant capacity (TAC), ferric reducing antioxidant power (FRAP) ในพลาสมา ค่า catalase activity ค่า superoxide dismutase (SOD) activity ค่า glutathione peroxidase (GPx) activity และความยาวเทโลเมียร์ในเลือด จากการศึกษาพบว่าระดับ AGEs, RAGE, 8-OHdG, protein carbonyl, MDA, nitrite ในพลาสมา การแสดงออกของยีน iNOS ในเลือดของกลุ่มผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อมมีค่าสูงกว่ากลุ่มควบคุมอย่างมีนัยสำคัญทางสถิติ (P < 0.001, P < 0.001, P = 0.001, P = 0.01, P = 0.02, P < 0.001, P < 0.001 ตามลำดับ) และค่า GPx activity ในเลือดของกลุ่มผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อมมีค่าต่ำกว่ากลุ่มควบคุมอย่างมีนัยสำคัญทางสถิติ (P = 0.04) สำหรับระดับ TAC, FRAP ค่า catalase activity ค่า SOD activity และความยาวเทโลเมียร์ในเลือดพบว่าไม่มีความแตกต่างกันระหว่างกลุ่มผู้ป่วยโรคกระดูกสันหลังส่วนเอวเสื่อมและกลุ่มควบคุม นอกจากนี้ยังพบว่าระดับ protein carbonyl และ nitrite ในพลาสมามีความสัมพันธ์กับระดับความรุนแรงของโรคที่เพิ่มขึ้นจากภาพถ่ายคลื่นแม่เหล็กไฟฟ้า การศึกษานี้สรุปได้ว่าระดับ protein carbonyl และ nitrite ในพลาสมาอาจนำมาประยุกต์ใช้เป็นตัวชี้วัดในการพยากรณ์ระดับความรุนแรงของโรคกระดูกสันหลังส่วนเอวเสื่อมได้

Antioxidative And Lipid-Reducing Activities Of Ficus Deltoidea In Palmitic Acid-Induced Wrl68 Cells, Noor Nazirahanie Abrahim

Student Works (2020-2029)

Non-alcoholic fatty liver disease (NAFLD) is a series of liver disorder caused by deposition of fat without involving alcohol. This chronic liver disease has become a major concern globally due to its high mortality and morbidity rate. This situation leads to the quest of finding natural remedy to overcome this condition. Ficus deltoidea or commonly known as mistletoe fig or Mas Cotek, is a plant that is very well known especially in Malaysia for its blood glucose lowering effect. However, the potential value of F. deltoidea has not been fully evaluated, and no studies have been published on the effects …

Trends And Predictors Of Glycosylated Haemoglobin A1c, Blood Pressure, And Ldl-Cholesterol Among Patients With Type 2 Diabetes In Negeri Sembilan, Malaysia, Wan Kim Sui

Student Works (2020-2029)

Cardiovascular disease and diabetes pose enormous disease burdens globally and in Malaysia. Concurrent attainment of glycosylated haemoglobin A1C, blood pressure (BP), and LDL-cholesterol (LDL-C) goals, or collectively known as the “ABC” goals, help prevent cardiovascular complications in patients with type 2 diabetes (T2D). Numerous studies have reported suboptimal achievement of all three ABC goals, and clinical inertia in diabetes management is one primary reason for poor A1C control. However, such information is lacking in Malaysia. Hence, this study aims to: a) determine the proportion of T2D patients who achieved all three ABC goals at study baseline and exit and the …

Open Problems In Extracellular Rna Data Analysis: Insights From An Ercc Online Workshop, Roger P Alexander, Robert R Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E A Max, Joel Rozowsky, Karolina Elżbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L Van Nostrand, Emily Laplante, Bogdan Mateescu, Brian S White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, Ryan M Spengler

Faculty, Staff and Students Publications

We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These extracellular RNA (exRNA) play a role in intercellular signaling, serve as biomarkers of disease, and form the basis of new strategies for disease treatment. The Extracellular RNA Communication Consortium (ERCC) hosted a two-day online workshop (April 19–20, 2021) on the unique challenges of exRNA data analysis. The goal was to foster an open dialog about best practices and discuss open problems in the field, focusing initially on small exRNA sequencing data. Video recordings of workshop …

Protein-Functionalized Poly(Ethylene Glycol) Hydrogels As Scaffolds For Monolayer Organoid Culture, Reid L Wilson, Ganesh Swaminathan, Khalil Ettayebi, Carolyn Bomidi, Xi-Lei Zeng, Sarah E Blutt, Mary K Estes, K Jane Grande-Allen

Faculty, Staff and Students Publications

Stem cell-derived, organotypic in vitro models, known as organoids, have emerged as superior alternatives to traditional cell culture models due to their unparalleled ability to recreate complex physiological and pathophysiological processes. For this reason, they are attractive targets of tissue-engineering efforts, as constructs that include organoid technology would be expected to better simulate the many functions of the desired tissue or organ. While the 3D spheroidal architecture that is the default architecture of most organoid models may be preferred for some applications, 2D monolayer arrangements remain the preferred organization for many applications in tissue engineering. Therefore, in this work, we …

Goblet Cell Carcinoma Of The Appendix: A Case Report On Goblet Cell Carcinoid, Sheliza Kabani, Aubtin Saedi, Austin Lehr, Lina O'Brien

HCA Healthcare Journal of Medicine

Goblet cell carcinoid of the appendix is a rare neoplasm with histological features of both neuroendocrine and adenocarcinomas. The combination of its aggressive behavior, infrequent occurrence, and variable clinical presentation convolutes the management of this tumor. We report the case of a 75-year-old female presenting with acute appendicitis. A laparoscopic appendectomy was performed. The pathology report showed goblet cell carcinoid at the base of the appendix with involvement of the proximal surgical margins. At her postoperative visit, the patient’s pathology report and options for management were reviewed, and the patient agreed to proceed with a right hemicolectomy 8-10 weeks after …

Purification And Use Of Trna For Enzymatic Post-Translational Addition Of Amino Acids To Proteins., Irem Avcilar-Kucukgoze, Howard Gamper, Ya-Ming Hou, Anna Kashina

Department of Biochemistry and Molecular Biology Faculty Papers

Post-translational addition of amino acids to proteins by enzymes using aminoacyl-tRNA is an emerging regulatory mechanism. Examples include Arg transfer in eukaryotes, Leu/Phe transfer in bacteria, and tRNA-synthetase-mediated addition of amino acids to Lys side chains. Here, we present a method of purification and use of tRNA for such reactions, focusing on tRNA^Arg and its use for arginylation. This method can also be used for other tRNA-mediated reactions. For complete details on the use and execution of this protocol, please refer to Avcilar-Kucukgoze et al. (2020).

Impact Of Endangered Animal Protection Rights, Policies, And Practices On Zoonotic Disease Spread, Daniella Fedak-Lengel

Honors Projects

Building on field research in Costa Rica and Belize, this honors project analyzes environmental and endangered animal protection policies, rights, and practices in Central America and the Caribbean, and assesses the impact of veterinary science and biological research and practice, particularly conservation biology, on animal welfare concerns. Informed by the recent surge in awareness regarding zoonoses and zoonotic disease transmission, prevention and control, resulting from the current global pandemic of SARS-CoV-2, the project assesses the need for new and innovative types of collaboration, particularly involving conservation biologists, environmental scientists, public health experts, law and policy makers, and global trade and …

Design Of Hfgf1 Variant(S) With Increased Stability And Enhanced Bioactivity, Shilpi P. Agrawal

Graduate Theses and Dissertations

Fibroblast growth factors (FGFs) are involved in various cellular processes such as cell growth,proliferation, differentiation, migration, angiogenesis, wound healing and embryonic development. Human acidic fibroblast growth factor (hFGF1) binds non-selectively to all the four FGF-receptors and is therefore considered as a powerful mitogen with broadest specificity. However, pharmacological applications of hFGF1 are restricted due to the low thermal stability of the growth factor. hFGF1 has low thermodynamic stability under physiological temperatures which leads to impairment of cellular signaling process thereby preventing its potential mitogenic properties. hFGF1 has a heparin binding pocket at the C-terminus which comprises of positively charges residues. …