Medical Biochemistry Commons^™

Semi-Quantitative Detection Of Pseudouridine Modifications And Type I/Ii I/Ii Hypermodifications In Human Mrnas Using Direct Long-Read Sequencing, Sepideh Tavakoli, Mohammad Nabizadeh, Amr Makhamreh, Howard Gamper, Caroline A Mccormick, Neda K Rezapour, Ya-Ming Hou, Meni Wanunu, Sara H Rouhanifard

Department of Biochemistry and Molecular Biology Faculty Papers

Here, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identify many known sites of pseudouridylation and uncover previously unreported uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites are validated using 1000-mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating systematic …

Sgc-Camkk2-1: A Chemical Probe For Camkk2, Carrow Wells, Yi Liang, Thomas L Pulliam, Chenchu Lin, Dominik Awad, Benjamin Eduful, Sean O'Byrne, Mohammad Anwar Hossain, Carolina Moura Costa Catta-Preta, Priscila Zonzini Ramos, Opher Gileadi, Carina Gileadi, Rafael M Couñago, Brittany Stork, Christopher G Langendorf, Kevin Nay, Jonathan S Oakhill, Debarati Mukherjee, Luigi Racioppi, Anthony R Means, Brian York, Donald P Mcdonnell, John W Scott, Daniel E Frigo, David H Drewry

Faculty, Staff and Student Publications

The serine/threonine protein kinase calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) plays critical roles in a range of biological processes. Despite its importance, only a handful of inhibitors of CAMKK2 have been disclosed. Having a selective small molecule tool to interrogate this kinase will help demonstrate that CAMKK2 inhibition can be therapeutically beneficial. Herein, we disclose SGC-CAMKK2-1, a selective chemical probe that targets CAMKK2.

Disruption Of The Interaction Between Mutationally Activated Gαq And Gβγ Attenuates Aberrant Signaling, Jenna L Aumiller, Philip B Wedegaertner

Department of Biochemistry and Molecular Biology Faculty Papers

Heterotrimeric G protein stimulation via G protein-coupled receptors promotes downstream proliferative signaling. Mutations can occur in Gα proteins which prevent GTP hydrolysis; this allows the G proteins to signal independently of G protein-coupled receptors and can result in various cancers, such as uveal melanoma (UM). Most UM cases harbor Q209L, Q209P, or R183C mutations in Gαq/11 proteins, rendering the proteins constitutively active (CA). Although it is generally thought that active, GTP-bound Gα subunits are dissociated from and signal independently of Gβγ, accumulating evidence indicates that some CA Gα mutants, such as Gαq/11, retain binding to Gβγ, and this interaction is …

Differentiating Pc12 Cells To Evaluate Neurite Densities Through Live-Cell Imaging, Jordyn Karliner, Diane E Merry

Department of Biochemistry and Molecular Biology Faculty Papers

Although PC12 cells are a valuable tool in neuroscience research, previously published PC12 cell differentiation techniques fail to consider the variability in differentiation rates between different PC12 cell strains and clonal variants. Here, we present a comprehensive protocol to differentiate PC12 cells into equivalent neurite densities through live-cell imaging for morphological, immunocytochemical, and biochemical analyses. We detail steps on optimized substrate coating, plating techniques, culture media, validation steps, and quantification techniques.

Quantifying Metal Interactions With The Antimicrobial Peptide Calcitermin, Maria G. Aviles-Sandoval, Michael Stevenson

Featured Student Work

Antimicrobial Peptides (AMPs) are novel therapeutic agents that play important roles in the innate immune system with its ability to kill gram-positive and gram-negative bacteria. Antibiotics are losing their efficacy, thus requiring a larger dose of medicine for treatment resulting in the increase of antibiotic resistance. AMPs are an attractive approach for exploration due to their broad-spectrum activity and ease of synthesis. Furthermore, fewer bacteria have developed resistance to AMPs. Several AMPs have demonstrated increased antimicrobial activity with metal ions, like Zn(II) and Cu(II) binding to the peptide. In this study, we performed the purification of Calcitermin through high-performance liquid …

Observing Ceramide Pathway With Ferroptosis Via Mia Paca-2 Cell Treatment With Rsl3, Tazrin Rahman

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Composed of sphingosine and a fatty acid, ceramides are lipid molecules that serve as key metabolic signaling molecules of a sphingolipid pathway. While it acts as a precursor of complex sphingolipids, inducing ceramide generation can cause cell stress leading to subsequent cell death via apoptosis, necrosis, and even mitophagy. With regards to cell death specifically, a novel form of regulated cell death, ferroptosis, has recently been recognized of necrotic nature. Its unique morphological features and distinct properties have been observed over the last several decades; however, the molecular features were not identifiable as pure evidence of cell death, until recently …

Role Of The Ormdls In Keratinocytes, Souad Hatmi

Theses and Dissertations

The epidermis, the outermost layer of the skin, serves as a vital barrier protecting the body from environmental stressors, pathogens, and dehydration. Keratinocytes, the predominant cell type in the epidermis, play a central role in maintaining skin integrity and barrier function. In normal human skin, keratinocytes move from the basal layer to the stratum corneum, the top layer of the epidermis. In their travel, keratinocytes undergo a process of terminal differentiation, loss their ability to proliferate, secrete sphingolipids into the extracellular space, and gradually loss their nucleus and organelles. Sphingolipids, particularly ceramides, are key components of the intercellular lipid lamellae …

ความหลากหลายทางพันธุกรรมของโรคไขมันพอกตับที่สัมพันธ์กับการติดเชื้อเอชไอวีและโรคมะเร็งตับ, กมลชนก มูลลิสาร

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคไขมันพอกตับเป็นหนึ่งในสาเหตุหลักของโรคตับอักเสบเรื้อรังที่สามารถดำเนินโรคไปสู่โรคมะเร็งตับได้ ความชุกของโรคไขมันพอกตับในประเทศไทยพบประมาณร้อยละ 20-30 สาเหตุของการเกิดไขมันพอกตับที่พบบ่อยได้แก่โรคอ้วน เบาหวาน กลุ่มโรคเมตาบอลิกและปัจจัยทางพันธุกรรม การศึกษาที่ผ่านมาพบว่ามียีนหลายตำแหน่งที่มีบทบาทเกี่ยวข้องกับกลไกการเกิดโรค ที่สำคัญได้แก่ PNPLA3, TM6SF2 และ HSD17B13 งานวิจัยนี้มีจุดประสงค์เพื่อหาความสัมพันธ์ของความหลากหลายทางพันธุกรรมของยีนดังกล่าวกับการเกิดโรคไขมันพอกตับในคนไทย โดยศึกษาจีโนไทป์ของทั้งสามยีนด้วยเทคนิค TaqMan Real-time PCR จากตัวอย่างเลือด 900 ตัวอย่างของ 4 กลุ่มได้แก่ กลุ่มควบคุมที่มีสุขภาพดี ผู้ป่วยโรคไขมันพอกตับที่มีและไม่มีการติดเชื้อเอชไอวี และกลุ่มผู้ป่วยมะเร็งตับ ผลการศึกษาพบว่าจีโนไทป์ GG ของยีน PNPLA3 rs738409 เป็นปัจจัยเสี่ยงของการเกิดโรคไขมันพอกตับในทุกกลุ่มที่ศึกษาเมื่อเปรียบเทียบกับกลุ่มควบคุม ดังนี้ กลุ่มผู้ป่วยที่ไม่มีการติดเชื้อเอชไอวี [odds ratio (OR)=6.52, 95% confidence interval (CI) 2.64-16.08, P<0.001] กลุ่มผู้ป่วยที่มีการติดเชื้อเอชไอวี(OR=2.76, 95% CI 1.09-7.00, P=0.03) และกลุ่มผู้ป่วยมะเร็งตับ (OR=9.96, 95% CI 4.06-24.44, P<0.001) อย่างไรก็ตามไม่ พบความสัมพันธ์ของยีน TM6SF2 rs58542926 และ HSD17B13 rs6834314 กับการเกิดโรคของ กลุ่มตัวอย่างต่างๆ จากการวิเคราะห์หาปัจจัยเสี่ยงอิสระด้วยสมการถดถอยพบว่า ค่าดัชนีมวลกาย ที่สูง โรคเบาหวาน ระดับเอนไซม์ALT ที่สูงและการไม่ติดเชื้อเอชไอวีเป็นปัจจัยเสี่ยงในการทำให้ เกิดความรุนแรงในการสะสมไขมันในตับ โดยสรุปผลการวิจัยนี้พบว่าความหลากหลายทาง พันธุกรรมของ PNPLA3 มีความสัมพันธ์กับการเกิดโรคไขมันพอกตับและเพิ่มความเสี่ยงต่อการเกิด โรคมะเร็งตับในประชากรไทย แต่ไม่พบความสัมพันธ์ดังกล่าวสำหรับยีน TM6SF2 และ HSD17B13

การมีส่วนร่วมของปัจจัยทางพันธุกรรมต่อการสร้างซีซีซีดีเอ็นเอของไวรัสตับอักเสบบี, กัลยกร สิงห์สังข์

Chulalongkorn University Theses and Dissertations (Chula ETD)

การติดเชื้อไวรัสตับอักเสบบี (hepatitis B virus infection; HBV) เป็นปัญหาทางด้านสาธารณสุขที่สำคัญทั่วโลก เนื่องจากผู้ติดเชื้อไวรัสตับอักเสบบีสามารถพัฒนาความรุนแรงไปเป็นโรคตับแข็ง (cirrhosis) และมะเร็งตับ (hepatocellular carcinoma: HCC) ซึ่งนำไปสู่การเสียชีวิตได้ในที่สุด ถึงแม้ว่าในปัจจุบันโรคติดเชื้อไวรัสตับอักเสบบีสามารถรักษาได้ด้วยยาต้านไวรัส อย่างไรก็ตามยังไม่สามารถรักษาให้หายขาดได้ เนื่องจากการคงอยู่ของ covalently closed circular DNA (cccDNA) ซึ่งเป็น DNA สายคู่แบบวงปิดคล้ายโครโมโซมขนาดเล็กภายในนิวเคลียสของเซลล์ตับ ขบวนการสร้าง cccDNA จำเป็นต้องอาศัยการทำงานของปัจจัยทางพันธุกรรมของเซลล์เจ้าบ้าน (host factors) หลายชนิด โดยเฉพาะอย่างยิ่ง DNA damage binding protein 2 (DDB2) และ DNA polymerase δ (DNA pol δ) อย่างไรก็ตามการศึกษายังไม่พบการศึกษาการแสดงออกของ host factors ดังกล่าวต่อการสร้าง cccDNA ในเซลล์ตับของผู้ป่วยโรคไวรัสตับอักเสบบี โดยเฉพาะไวรัสตับอักเสบบีแบบแอบแฝง (occult HBV infection หรือ OBI) รวมทั้งยังไม่มีวิธีมาตรฐานในการตรวจวัดระดับของ cccDNA ในเซลล์ตับ ดังนั้นการศึกษานี้จึงมีวัตถุประสงค์ในการศึกษาความสัมพันธ์ของระดับของ cccDNA และ host factors ในเซลล์ตับของผู้ป่วยมะเร็งตับที่เกิดจากจากติดเชื้อไวรัสตับอักเสบบี (HBV-related HCC) และไวรัสตับอักเสบบีแบบแอบแฝง (occult HBV (OBI)-related HCC) ด้วยการทำdroplet digital PCR (ddPCR) และ Western blot ตามลำดับ จากเนื้อเยื่อบริเวณ non-tumor หรือ adjacent tissues ผลการศึกษาระดับการแสดงออกของ intrahepatic HBV DNA และ cccDNA ในเซลล์ตับ ของผู้ป่วย พบว่าผู้ป่วยกลุ่ม HBV-related HCC มีการแสดงออกของ intrahepatic HBV …

Hif-1 Activation And Inflammatory Responses To Hypoxia, Shazreen Shaharuddin, Nik Mohd Afizan Nik Abd Rahman, Mas Jaffri Masarudin, Mohammedarfat N Alamassi

International Journal of Aviation, Aeronautics, and Aerospace

Acute hypoxia is a significant physiological danger during high-altitude flying and military aircraft missions. The human brain requires a constant supply of oxygen to function properly, and is susceptible to settings with low availability of air oxygen. Hypoxia can influence inflammatory signalling, and both central and systemic responses can activate HIF pathway genes. HIFs are critical molecules that regulate inflammation andhypoxia, ensuring appropriate cell function and survival. Hypoxia is the condition in which insufficient oxygen reaches the body's tissues. It can be caused by a decrease in partial oxygen pressure (PO2) in the environment, problems with breathing and/or oxygen transport, …

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 …

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 …

Microrna-1 Attenuates The Growth And Metastasis Of Small Cell Lung Cancer Through Cxcr4/Foxm1/Rrm2 Axis, Parvez Khan, Jawed A. Siddiqui, Prakash Kshirsagar Dr., Ramakanth Chirravuri Venkata, Shailendra K. Maurya, Tamara Mirzapoiazova, Naveenkumar Perumal, Sanjib Chaudhary, Ranjana K. Kanchan, Mahek Fatima, Md Arafat Khan, Asad Ur Rehman, Imayavaramban Lakshmanan, Sidharth Mahapatra, Geoffrey A. Talmon, Prakash Kulkarni, Apar Kishor Ganti, Maneesh Jain, Ravi Salgia, Surinder K. Batra, Mohd W. Nasser

Journal Articles: Biochemistry & Molecular Biology

BACKGROUND: Small cell lung cancer (SCLC) is an aggressive lung cancer subtype that is associated with high recurrence and poor prognosis. Due to lack of potential drug targets, SCLC patients have few therapeutic options. MicroRNAs (miRNAs) provide an interesting repertoire of therapeutic molecules; however, the identification of miRNAs regulating SCLC growth and metastasis and their precise regulatory mechanisms are not well understood.

METHODS: To identify novel miRNAs regulating SCLC, we performed miRNA-sequencing from donor/patient serum samples and analyzed the bulk RNA-sequencing data from the tumors of SCLC patients. Further, we developed a nanotechnology-based, highly sensitive method to detect microRNA-1 (miR-1, …

The Mucin Family Of Proteins: Candidates As Potential Biomarkers For Colon Cancer, Kristin E. Cox, Shanglei Liu, Thinzar M. Lwin, Robert M. Hoffman, Surinder K. Batra, Michael Bouvet

Journal Articles: Biochemistry & Molecular Biology

Mucins (MUC1-MUC24) are a family of glycoproteins involved in cell signaling and barrier protection. They have been implicated in the progression of numerous malignancies including gastric, pancreatic, ovarian, breast, and lung cancer. Mucins have also been extensively studied with respect to colorectal cancer. They have been found to have diverse expression profiles amongst the normal colon, benign hyperplastic polyps, pre-malignant polyps, and colon cancers. Those expressed in the normal colon include MUC2, MUC3, MUC4, MUC11, MUC12, MUC13, MUC15 (at low levels), and MUC21. Whereas MUC5, MUC6, MUC16, and MUC20 are absent from the normal colon and are expressed in colorectal …

Specific Targeting And Labeling Of Colonic Polyps In Cpc-Apc Mice With Mucin 5ac Fluorescent Antibodies: A Model For Detection Of Early Colon Cancer, Michael A. Turner, Kristin E. Cox, Shanglei Liu, Nicholas Neel, Siamak Amirfakhri, Hiroto Nishino, Mojgan Hosseini, Joshua A. Alcantara, Amer Ali Abd El-Hafeez, Thinzar M. Lwin, Kavita Mallya, Joseph R. Pisegna, Satish K. Singh, Pradipta Ghosh, Robert M. Hoffman, Surinder K. Batra, Michael Bouvet

Journal Articles: Biochemistry & Molecular Biology

Poor visualization of polyps can limit colorectal cancer screening. Fluorescent antibodies to mucin5AC (MUC5AC), a glycoprotein upregulated in adenomas and colorectal cancer, could improve screening colonoscopy polyp detection rate. Adenomatous polyposis coli flox mice with a Cdx2-Cre transgene (CPC-APC) develop colonic polyps that contain both dysplastic and malignant tissue. Mice received MUC5AC-IR800 or IRdye800 as a control IV and were sacrificed after 48 h for near-infrared imaging of their colons. A polyp-to-background ratio (PBR) was calculated for each polyp by dividing the mean fluorescence intensity of the polyp by the mean fluorescence intensity of the background tissue. The mean 25 …

Gpcrs And Fibroblast Heterogeneity In Fibroblast-Associated Diseases, Nidhi V. Dwivedi, Souvik Datta, Karim El-Kersh, Ruxana Sadikot Md, Mrcp, Apar Kishor Ganti, Surinder K. Batra, Maneesh Jain

Journal Articles: Biochemistry & Molecular Biology

G protein-coupled receptors (GPCRs) are the largest and most diverse class of signaling receptors. GPCRs regulate many functions in the human body and have earned the title of "most targeted receptors". About one-third of the commercially available drugs for various diseases target the GPCRs. Fibroblasts lay the architectural skeleton of the body, and play a key role in supporting the growth, maintenance, and repair of almost all tissues by responding to the cellular cues via diverse and intricate GPCR signaling pathways. This review discusses the dynamic architecture of the GPCRs and their intertwined signaling in pathological conditions such as idiopathic …

Immunotherapy: An Emerging Modality To Checkmate Brain Metastasis, Aatiya Ahmad, Parvez Khan, Asad Ur Rehman, Surinder K. Batra, Mohd W. Nasser

Journal Articles: Biochemistry & Molecular Biology

The diagnosis of brain metastasis (BrM) has historically been a dooming diagnosis that is nothing less than a death sentence, with few treatment options for palliation or prolonging life. Among the few treatment options available, brain radiotherapy (RT) and surgical resection have been the backbone of therapy. Within the past couple of years, immunotherapy (IT), alone and in combination with traditional treatments, has emerged as a reckoning force to combat the spread of BrM and shrink tumor burden. This review compiles recent reports describing the potential role of IT in the treatment of BrM in various cancers. It also examines …

Roles Unveiled For Membrane-Associated Mucins At The Ocular Surface Using A Muc4 Knockout Mouse Model, Rafael Martinez-Carrasco, Satyanarayan Rachagani, Surinder K. Batra, Pablo Argüeso, M Elizabeth Fini

Journal Articles: Biochemistry & Molecular Biology

Membrane-associated mucins (MAMs) are proposed to play critical roles at the ocular surface; however, in vivo evidence has been lacking. Here we investigate these roles by phenotyping of a Muc4 KO mouse. Histochemical analysis for expression of the beta-galactosidase transgene replacing Muc4 revealed a spiraling ribbon pattern across the corneal epithelium, consistent with centripetal cell migration from the limbus. Depletion of Muc4 compromised transcellular barrier function, as evidenced by an increase in rose bengal staining. In addition, the corneal surface was less smooth, consistent with disruption of tear film stability. While surface cells presented with well-developed microprojections, an increase in …

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 …

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, …

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