Medical Biochemistry Commons^™

Molecular Signaling Network And Therapeutic Developments In Breast Cancer Brain Metastasis, Mercilena Benjamin, Pushkar Malakar, Rohit Anthony Sinha, Mohd Wasim Nasser, Surinder K. Batra, Jawed A. Siddiqui, Bandana Chakravarti

Journal Articles: Biochemistry & Molecular Biology

Breast cancer (BC) is one of the most frequently diagnosed cancers in women worldwide. It has surpassed lung cancer as the leading cause of cancer-related death. Breast cancer brain metastasis (BCBM) is becoming a major clinical concern that is commonly associated with ER-ve and HER2+ve subtypes of BC patients. Metastatic lesions in the brain originate when the cancer cells detach from a primary breast tumor and establish metastatic lesions and infiltrate near and distant organs via systemic blood circulation by traversing the BBB. The colonization of BC cells in the brain involves a complex interplay in the tumor microenvironment (TME), …

Elevated Paf1-Rad52 Axis Confers Chemoresistance To Human Cancers, Sanchita Rauth, Koelina Ganguly, Pranita Atri, Seema Parte, Rama Krishna Nimmakayala, Venkatesh Varadharaj, Palanisamy Nallasamy, Raghupathy Vengoji, Ayoola O. Ogunleye, Imayavaramban Lakshmanan, Ramakanth Chirravuri, Mika Bessho, Jesse L. Cox, Jason M. Foster, Geoffrey A. Talmon, Tadayoshi Bessho, Apar Kishor Ganti, Surinder K. Batra, Moorthy P. Ponnusamy

Journal Articles: Biochemistry & Molecular Biology

Cisplatin- and gemcitabine-based chemotherapeutics represent a mainstay of cancer therapy for most solid tumors; however, resistance limits their curative potential. Here, we identify RNA polymerase II-associated factor 1 (PAF1) as a common driver of cisplatin and gemcitabine resistance in human cancers (ovarian, lung, and pancreas). Mechanistically, cisplatin- and gemcitabine-resistant cells show enhanced DNA repair, which is inhibited by PAF1 silencing. We demonstrate an increased interaction of PAF1 with RAD52 in resistant cells. Targeting the PAF1 and RAD52 axis combined with cisplatin or gemcitabine strongly diminishes the survival potential of resistant cells. Overall, this study shows clinical evidence that the expression …

Molecular And Metabolic Regulation Of Immunosuppression In Metastatic Pancreatic Ductal Adenocarcinoma, Shailendra K. Gautam, Surinder K. Batra, Maneesh Jain

Journal Articles: Biochemistry & Molecular Biology

Immunosuppression is a hallmark of pancreatic ductal adenocarcinoma (PDAC), contributing to early metastasis and poor patient survival. Compared to the localized tumors, current standard-of-care therapies have failed to improve the survival of patients with metastatic PDAC, that necessecitates exploration of novel therapeutic approaches. While immunotherapies such as immune checkpoint blockade (ICB) and therapeutic vaccines have emerged as promising treatment modalities in certain cancers, limited responses have been achieved in PDAC. Therefore, specific mechanisms regulating the poor response to immunotherapy must be explored. The immunosuppressive microenvironment driven by oncogenic mutations, tumor secretome, non-coding RNAs, and tumor microbiome persists throughout PDAC progression, …

Chimeric Antibody Targeting Unique Epitope On Onco-Mucin16 Reduces Tumor Burden In Pancreatic And Lung Malignancies, Ashu Shah, Sanjib Chaudhary, Imayavaramban Lakshmanan, Abhijit Aithal, Sophia G. Kisling, Claire Sorrell, Saravanakumar Marimuthu, Shailendra K. Gautam, Sanchita Rauth, Prakash Kshirsagar, Jesse L. Cox, Gopalakrishnan Natarajan, Rakesh Bhatia, Kavita Mallya, Satyanarayana Rachagani, Mohd W. Nasser, Apar Kishor Ganti, Ravi Salgia, Sushil Kumar, Maneesh Jain, Moorthy P. Ponnusamy, Surinder K. Batra

Journal Articles: Biochemistry & Molecular Biology

Aberrantly expressed onco-mucin 16 (MUC16) and its post-cleavage generated surface tethered carboxy-terminal (MUC16-Cter) domain are strongly associated with poor prognosis and lethality of pancreatic (PC) and non-small cell lung cancer (NSCLC). To date, most anti-MUC16 antibodies are directed towards the extracellular domain of MUC16 (CA125), which is usually cleaved and shed in the circulation hence obscuring antibody accessibility to the cancer cells. Herein, we establish the utility of targeting a post-cleavage generated, surface-tethered oncogenic MUC16 carboxy-terminal (MUC16-Cter) domain by using a novel chimeric antibody in human IgG1 format, ch5E6, whose epitope expression directly correlates with disease severity in both cancers. …

Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis And Ameliorates Colitis, Emily Jean Wilson, Nagabhishek Sirpu Natesh, Parsa Ghadermazi, Ramesh Pothuraju, Dipakkumar R. Prajapati, Sanjit Pandey, Jussuf T. Kaifi, John R. Dodam, Jeffrey N. Bryan, Christian L. Lorson, Aude A. Watrelot, Jason M. Foster, Thomas J. Mansell, Siu Hung Joshua Chan, Surinder K. Batra, Jeyamkondan Subbiah, Satyanarayana Rachagani

Journal Articles: Biochemistry & Molecular Biology

Gut microbiota plays a crucial role in inflammatory bowel diseases (IBD) and can potentially prevent IBD through microbial-derived metabolites, making it a promising therapeutic avenue. Recent evidence suggests that despite an unclear underlying mechanism, red cabbage juice (RCJ) alleviates Dextran Sodium Sulfate (DSS)-induced colitis in mice. Thus, the study aims to unravel the molecular mechanism by which RCJ modulates the gut microbiota to alleviate DSS-induced colitis in mice. Using C57BL/6J mice, we evaluated RCJ's protective role in DSS-induced colitis through two cycles of 3% DSS. Mice were daily gavaged with PBS or RCJ until the endpoint, and gut microbiota composition …

Protein S In Coagulation And Inflammation, Martha Mega Silvia Sim

Theses and Dissertations--Molecular and Cellular Biochemistry

Protein S (PS) is a key regulator, which links inflammation and coagulation and performs multiple proposed functions in both processes. PS exists in the blood as a free soluble form (~40%), bound to complement component 4b-binding protein/ C4BP (~60%), and packaged in platelet α-granules (~2.5%). Subendothelial tissue factor (TF), upon exposure to blood, initiates coagulation, a proteolytic cascade which results in the activation of thrombin, the enzyme responsible for formation of a fibrin clot. PS is a critical anticoagulant that inhibits multiple steps of this process. Only the free fraction of PS has full anticoagulant properties, as C4BP blocks this …

Analysis Of Plasma Extracellular Vesicle-Derived Micrornas From Patients With Nonalcoholic Fatty Liver Disease And Hepatocellular Carcinoma, Bootsakorn Boonkaew

Chulalongkorn University Theses and Dissertations (Chula ETD)

Extracellular vesicle-derived microRNAs (EV-miRNAs) are promising circulating biomarkers for chronic liver disease. In this study, we explored the potential significance of plasma EV-miRNAs in non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). We compared plasma EV-miRNA profiles between NBNC-HCC and control groups including non-alcoholic fatty liver disease (NAFLD) and healthy controls using NanoString method. The differentially expressed EV-miRNAs were validated in another set of plasma samples by qRT-PCR. Five plasma EV-miRNAs were significantly elevated in HCC, which included miR-19-3p, miR-16-5p, miR-223-3p, miR-30d-5p, and miR-451a. Among them, EV-miR-19-3p exhibited the best diagnostic performance and displayed a high sensitivity for detecting AFP-negative HCC and …

Immunogenicity And Allergenicity Of A Major Shrimp Allergen Displayed On The Surface Of Virus-Like Particles (Vlps), Supapich Chanasit

Chulalongkorn University Theses and Dissertations (Chula ETD)

Frequencies of shrimp-induced anaphylaxis are particularly important in Asia; Asian countries consume more than 60% of the global seafood production. Currently, approved allergen-specific immunotherapy (AIT) for shrimp allergy is lacking. Shrimp sensitizations are only managed by strict avoidance and treatment with adrenaline. Clinical studies showed that oral immunotherapy (OIT), oral administrations of increasing amounts of food allergen extracts, can be now recognized as an alternative active treatment to strict food avoidance in certain patients with IgE-mediated food allergy. Up to now, the only FDA-approved OIT is for desensitization of peanut-allergic patients. Recently, sustained unresponsiveness to peanuts by OIT was shown …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Autodocking Studies Of Oxygenated Fullerenes As Inhibitors Of The Hiv Protease, Michael Kaminski

All Student Theses and Dissertations

In a previous study, several oxygenated fullerene compounds were produced by ozonation of C60 (Buckminsterfullerene) and were identified by elemental analysis and by SALI (surface analysis by laser ionization). Some of these compounds, especially a batch, SK-5, a mixture of C60O1-8, were shown to inhibit activities of HIV-Protease with IC50 (concentration for 50% inhibition) of 1 mg/mol in the in-vitro studies. The oxygenated fullerenes were shown to have epoxide, ketones, and hydroxyl functionalities. As expected, C60 interacted with ozone with alkene functionality and not as an aromatic compound. It was postulated that C60O had epoxide functionality, as a product of …

Effects Of Atrazine Exposure On Human Bone Marrow-Derived Mesenchymal Stromal Cells Assessed By Combinatorial Assay Matrix, Crystal C Uwazie, Bonnie M Pirlot, Tyler U Faircloth, Mihir Patel, Rhett N Parr, Halie M Zastre, Peiman Hematti, Guido Moll, Devi Rajan, Raghavan Chinnadurai

Faculty, Staff and Student Publications

INTRODUCTION: Mesenchymal Stromal/Stem cells (MSCs) are an essential component of the regenerative and immunoregulatory stem cell compartment of the human body and thus of major importance in human physiology. The MSCs elicit their beneficial properties through a multitude of complementary mechanisms, which makes it challenging to assess their phenotype and function in environmental toxicity screening. We here employed the novel combinatorial assays matrix approach/technology to profile the MSC response to the herbicide Atrazine, which is a common environmental xenobiotic, that is in widespread agricultural use in the US and other countries, but banned in the EU. Our here presented approach …

การแสดงออกและระดับการเติมหมู่เมทิลของยีนตัวรับวิตามินดีในโรคกระดูกสันหลังส่วนเอวเสื่อม, ลดาวัลย์ วัชรินทรางกูร

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคกระดูกสันหลังส่วนเอวเสื่อม (lumbar degenerative disease, LDD) เป็นสาเหตุสำคัญที่ทำให้ผู้สูงอายุไม่สามารถทำกิจกรรมต่าง ๆ ได้ตามปกติจึงส่งผลต่อการดำเนินชีวิตประจำวัน ในปัจจุบันการวินิจฉัย ตรวจติดตามและรักษาโรค อาศัยภาพถ่ายคลื่นแม่เหล็กไฟฟ้า (magnetic resonance imaging, MRI) เพื่อช่วยตรวจหมอนรองกระดูกสันหลังเสื่อม การรักษาประกอบด้วยการให้ยาไปจนถึงการผ่าตัด ซึ่งทำให้เกิดบาดแผลและใช้เวลาในการฟื้นฟู โรคกระดูกสันหลังเสื่อมมีส่วนเกี่ยวข้องกับวิตามินดีที่มีบทบาทเสริมสร้างความแข็งแรงให้กับกระดูก ดังนั้นในงานวิจัยนี้จึงมีความสนใจศึกษาความสัมพันธ์ของระดับวิตามินดี การแสดงออกยีนและโปรตีนตัวรับวิตามินดี (vitamin D receptor, VDR) และระดับการเติมหมู่เมทิลของ VDR (VDR promoter methylation) ในเซลล์เม็ดเลือดขาวและเนื้อเยื่อ nucleus pulposus (NP) จากในผู้ป่วย LDD จำนวน 35 ราย เทียบกับกลุ่มควบคุม จำนวน 15 ราย จากการวิจัยพบว่ากลุ่ม LDD มีภาวะการทำกิจกรรมถูกจำกัด (40.00 %) จากการประเมิน Oswestry disability index (ODI) มากกว่ากลุ่มควบคุม (13.33 %) อย่างมีนัยสำคัญ (P < 0.001) และกลุ่ม LDD มีระดับ serum vitamin D เท่ากับ 24.30 ng/mL สูงกว่ากลุ่มควบคุม (16.20 ng/mL) อย่างมีนัยสำคัญ (P = 0.039) ส่วนระดับการแสดงออกของยีน VDR ทั้งในเซลล์เม็ดเลือดขาวและเนื้อเยื่อ NP ของทั้งสองกลุ่มไม่แตกต่างกัน แต่ระดับของโปรตีน VDR ในเลือดนั้น พบว่ากลุ่มควบคุมมีโปรตีน VDR เท่ากับ 53.28 ng/mg protein ต่ำกว่ากลุ่ม LDD ที่มีระดับการแสดงออกเท่ากับ 64.60 ng/mg protein อย่างมีนัยสำคัญ (P = 0.02) นอกจากนี้กลุ่ม LDD มีระดับ VDR promoter methylation เท่ากับ 22.02 % ในขณะที่กลุ่มควบคุมมีเพียง 14.18 % ซึ่งกลุ่ม LDD มีการเติมหมู่เมทิลสูงกว่ากลุ่มควบคุมอย่างมีนัยสำคัญ (P < 0.001) นอกจากนี้เมื่อศึกษาความสัมพันธ์ของระดับความรุนแรงของโรคที่แบ่งตาม Pfirrmann grade พบว่ามีความสัมพันธ์กันแปรผันกับระดับวิตามินดี (r = 0.588, P < 0.001) และมีความสัมพันธ์แปรผันกับ VDR promoter methylation (r = 0.377, P = 0.026) อีกทั้งพบความสัมพันธ์แปรผันของ VDR mRNA ในเซลล์เม็ดเลือดขาวกับระดับโปรตีน VDR ใน serum (r = 0.420, P = 0.012) นอกจากนี้ได้พบความสัมพันธ์แปรผกผันของระดับวิตามินดีกับ ODI ของผู้ป่วย LDD (r = -0.359, P = 0.034) และความสัมพันธ์แปรผันของ VDR promoter methylation กับดัชนีมวลกาย (r = 0.348, P = 0.041) ดังนั้นสรุปได้ว่าระดับ VDR promoter methylation อาจนำมาประยุกต์และพัฒนาเพื่อนำไปใช้เป็นตัวบ่งชี้ทางชีวภาพในการพยากรณ์ระดับความรุนแรงของโรคได้ในอนาคต

Development Of Raman Spectroscopy-Integrated Calcium Oxalate Crystallization Index (Rcoci) Test And Its Clinical Validation For Diagnosing Calcium Oxalate Urolithiasis, Kamonchat Boonkam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Urinary stone disease is mostly formed in the kidney and is highly recurrent. The most common type of urinary stones is calcium oxalate (CaOx). The development of urinary screening tests for estimating risk of CaOx stone formation is still challenging. Recently, we developed a urinary test, called indole-reacted calcium oxalate crystallization index (iCOCI) test, that provided a high diagnostic accuracy for CaOx urolithiasis. However, the iCOCI test is time-consuming and highly acidic chemicals are required for quantifying amount of CaOx. In this study, we proposed to develop a new method, called Raman spectroscopy-integrated calcium oxalate crystallization index (rCOCI) test, that …

Crispr-Cas12a-Based Detection And Differentiation Of Mycobacterium Spp., Peeraphan Compiro

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mycobacterium species cause several vital human diseases, including tuberculosis (TB) and non-tuberculous mycobacterial (NTM) infections. TB is a chronic infectious disease caused by the Mycobacterium tuberculosis complex (MTBC). Additionally, non-tuberculous mycobacteria infections are caused by major NTM species, including Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium intracelulare, are medically necessary. Both groups of infections can lead to outbreaks in immunocompromised individuals and AIDS patients. It is crucial to differentiate between these two groups of mycobacterial infections, as they require distinct treatment approaches. However, initial diagnosis poses limitations in terms of time and diagnostic tools. Therefore, …

Mycobacterium Spp. Identification By Nanopore Technology, Samitanan Sunantawanit

Chulalongkorn University Theses and Dissertations (Chula ETD)

Tuberculosis is caused by infection with Mycobacterium tuberculosis (MTB). Although TB and non-tuberculous mycobacteria (NTM) infection exhibit similar symptoms, their treatments differ significantly. NTM strains need a specific drug regimen and some NTM strains are resistant to anti-TB drugs. Hence, mycobacterial identification is crucial. At present, the culture-based technique is the gold standard in mycobacterium detection, but it is time-consuming (3-6 weeks). Here, this study aimed to develop mycobacterial amplicon-based nanopore sequencing (Myco-ANS) assay for the differentiation of eight reference strains of mycobacteria, as well as to assess the diagnostic accuracy of Myco-ANS compared with reference line probe assay for …

Development Of Sensors For Bacteria And Wound Environment Monitoring, Pannawich Thirabowonkitphithan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Diabetes mellitus (DM) is a leading cause of death and reduces life expectancy. Complications from diabetes have wreaked havoc not only on patients' quality of life, but also on the global burdens of public health and socioeconomic development. The most frequent complication among patients with diabetes mellitus is diabetic wounds, particularly diabetic foot ulcers because of the damage to sensory nerves and blood vessel issues brought on by elevated blood glucose levels. As a result, chronic wounds eventually develop and are prone to infection. In this study, several novel analytical devices for the detection of wound infections and the wound …

Association Of Smoking With Total Oxidant And Antioxidant Levels In Breast Milk, Nesibe Yildiz, Adnan Yilmaz

Makara Journal of Health Research

Background: Breast milk is a natural food that contains all the fluids, energy, and nutrients necessary for the optimum growth and development of newborns. Smoking is a public health problem that has harmful effects on the mother and baby. This study aimed to examine the association of exposure to smoking with total oxidant status (TOS) and total antioxidant status (TAS) in breast milk.

Methods: Healthy mothers without any health problems during their pregnancy and lactation periods were selected as subjects. Eighty-eight milk samples (44 in the smoking group and 44 in the nonsmoking group) were examined. TOS and …

Kras Inhibitor That Simultaneously Inhibits Nucleotide Exchange Activity And Effector Engagement, Cynthia V Pagba, Amit K Gupta, Ali K Naji, Dharini Van Der Hoeven, Kelly Churion, Xiaowen Liang, Jacob Jakubec, Magnus Hook, Yan Zuo, Marisela Martinez De Kraatz, Jeffrey A Frost, Alemayehu A Gorfe

Faculty, Staff and Student Publications

We describe a small molecule ligand ACA-14 (2-hydroxy-5-{[(2-phenylcyclopropyl) carbonyl] amino} benzoic acid) as an initial lead for the development of direct inhibitors of KRAS, a notoriously difficult anticancer drug target. We show that the compound binds to KRAS near the switch regions with affinities in the low micromolar range and exerts different effects on KRAS interactions with binding partners. Specifically, ACA-14 impedes the interaction of KRAS with its effector Raf and reduces both intrinsic and SOS-mediated nucleotide exchange rates. Likely as a result of these effects, ACA-14 inhibits signal transduction through the MAPK pathway in cells expressing mutant KRAS and …

In Silico Identification Of A Β2-Adrenoceptor Allosteric Site That Selectively Augments Canonical Β2ar-Gs Signaling And Function, Sushrut D Shah, Christoffer Lind, Francesco De Pascali, Raymond B Penn, Alexander D Mackerell, Deepak A Deshpande

Department of Biochemistry and Molecular Biology Faculty Papers

Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. However, the therapeutic efficacy of β-agonists is limited by agonist-induced β2AR desensitization and noncanonical β2AR signaling involving β-arrestin that is shown to promote asthma pathophysiology. Accordingly, we undertook the identification of an allosteric site on β2AR that could modulate the activity of β-agonists to overcome these limitations. We employed the site identification by ligand competitive saturation (SILCS) computational method to comprehensively map the entire 3D structure of in silico-generated β2AR intermediate conformations and identified …

Unilateral ‘Crazy-Paving’ Pattern: An Exceptional Presentation Of Squamous Cell Carcinoma Of The Lung, Sumeera Banday, Shamim U Khan, Sabina Khan, Surinderpal S Anand, Ashok Shah

Faculty, Staff and Student Publications

The 'crazy-paving' pattern on high resolution computed tomography (HRCT) is a distinct imaging appearance that is still considered to be a radiological hallmark of pulmonary alveolar proteinosis. However, since its first description about three decades ago, more than 40 different clinical entities presenting as 'crazy-paving' patterns have been documented. This rather remarkable but uncommon imaging appearance is now considered to be a non-specific manifestation. A 62-year-old male referred for evaluation of productive cough, breathlessness and fever presented with 'crazy-paving' pattern on HRCT. Endobronchial biopsy done on presentation was consistent with the diagnosis of squamous cell carcinoma. This report highlights this …