Document Type



Doctor of Philosophy (PhD)


Biomedical Sciences

First Advisor's Name

Hoshang Unwalla

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Madhavan Nair

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Marisela Agudelo

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Yuan Liu

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Sabita Roy

Fifth Advisor's Committee Title

Committee member


microRNA, COPD, HIV, CRISPR, TGF-β, Aptamer, MCC

Date of Defense



Chronic Respiratory diseases like chronic obstructive pulmonary disease (COPD), pulmonary hypertension, asthma, and pneumonia are emerging as significant comorbidities in people living with HIV in the combination antiretroviral therapy (cART) era. HIV is an independent risk factor for these diseases independent of tobacco smoke, and cigarette smoking exacerbates outcomes in HIV patients. Both tobacco smoke and HIV infection suppress nasal mucociliary clearance (MCC) as well as bronchial MCC, a primary innate defense mechanism in the airway. Optimal MCC depends on airway surface liquid (ASL) lining the airway epithelium that facilitates ciliary beating to clear the mucus. Attenuation of any component of the MCC leads to mucus impaction and microbial colonization leading to lung infections. Cystic fibrosis transmembrane conductance regulator (CFTR) plays a pivotal role in airway MCC by virtue of its ability to regulate ASL levels, ASL pH, and consequently mucus viscosity.

Our studies showed that TGF-β signaling is induced by HIV Tat protein and cigarette smoke. We found that HIV Tat protein and cigarette smoke individually and additively inhibit CFTR biogenesis and function in normal human bronchial epithelial cells via a common TGF-β signaling pathway. Inhibiting miRNA processing using Aurin-tricarboxylic acid (ATA), a small molecule inhibitor of the pri-miRNA processing enzyme Drosha completely rescues TGF-β -mediated CFTR suppression suggesting an important role for miRNA mediated post-transcriptional gene silencing. We show that TGF-β signaling alters the bronchial epithelial microRNAome. Specifically, TGF-β upregulates miR-145-5p to suppress CFTR and a CFTR modifying gene SLC26A9. We demonstrate that like TGF-β, HIV Tat also alters the bronchial epithelial microRNAome to upregulate miR-145-5p that functions co-operatively with miR-509 to suppress CFTR. A neutralizing aptamer to TGFBR2 and miR-145-5p antagonism rescues TGF-β mediated CFTR suppression. However, given the important role of miR-145-5p as a tumor suppressor, we attempt a novel approach called gene-specific microRNA antagonism to preserve CFTR function in the context of HIV and cigarette smoke without blocking the entire TGF-β signaling pathway or interfering with the broader miRNA-mediated regulation of other genes.




Previously Published In

Dutta RK, Chinnapaiyan S, Rasmussen L, Raju SV, Unwalla HJ. A Neutralizing Aptamer to TGFBR2 and miR-145 Antagonism Rescue Cigarette Smoke- and TGF-beta-Mediated CFTR Expression. Mol Ther. 2019; 27(2):442-55. doi: 10.1016/j.ymthe.2018.11.017. PubMed PMID: 30595527.

Ahmed MS, Dutta RK (Equal Contribution), Manandhar P, Li X, Torabi H, Barrios A, Wang P, Chinnapaiyan S, Unwalla HJ, Moon JH. A guanylurea-functionalized conjugated polymer enables RNA interference in ex vivo human airway epithelium. Chemical Communications. 2019; 55(54):7804-7. doi: 10.1039/C9CC02856K.

Dutta RK, Chinnapaiyan S, Unwalla HJ. Aberrant MicroRNAomics in pulmonary complications: Implications in Lung health, and diseases. Molecular Therapy Nucleic Acids, 2019. 18: p. 413-431. doi: (2019).

Chinnapaiyan S, Dutta RK, Devadoss D, Chand H, Rahman I, Unwalla H. Role of Non-coding RNAs in Lung Circadian Clock Related Diseases. International Journal of Molecular Sciences.2020, 21(8), 3013;

Caobi A, Dutta RK, Garbinsky L, Lopez ME, Ceyhan Y, Mickasone A, Manevski M, Ojha CR, Lapierre J, Tiwari S, Parira T, El-Hage N. The impact of CRISPR-Cas9 on age-related disorders: From pathology to therapy. Aging and Disease, 2019. doi: 10.14336/ad.2019.0927.

Chinnapaiyan S, Dutta RK, Nair M, Chand HS, Rahman I, Unwalla HJ. TGF-β1 increases viral burden and promotes HIV-1 latency in primary differentiated human bronchial epithelial cells. Scientific Reports. 2019;9(1):12552. doi: 10.1038/s41598-019-49056-6.

Chinnapaiyan S, Dutta RK, Bala J, Parira T, Agudelo M, Nair M, Unwalla HJ. Cigarette smoke promotes HIV infection of primary bronchial epithelium and additively suppresses CFTR function. Scientific Reports. 2018; 8(1):7984. doi: 10.1038/s41598-018-26095-z.

Chinnapaiyan S, Parira T, Dutta RK, Agudelo M, Morris A, Nair M, Unwalla HJ. HIV Infects Bronchial Epithelium and Suppresses Components of the Mucociliary Clearance Apparatus. PLOS ONE. 2017; 12(1):e0169161. doi: 10.1371/journal.pone.0169161.

Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biology. 2018; 15(3):327-37. doi: 10.1080/15476286.2017.1414131.

Pawitwar SS, Dhar S, Tiwari S, Ojha CR, Lapierre J, Martins K, Rodzinski A, Parira T, Paudel I, Li J, Dutta RK, Silva MR, Kaushik A, El-Hage N. Overview on the Current Status of Zika Virus Pathogenesis and Animal-Related Research. Journal of Neuroimmune Pharmacology. 2017; 12(3):371-88. doi: 10.1007/s11481-017-9743-8.

Tiwari S, Lapierre J, Ojha CR, Parira T, Dutta RK, Caobi A, Garbinsky L, Ceyhan Y, Lopez ME, El-Hage N. Signaling pathways and therapeutic perspectives related to environmental factors associated with multiple sclerosis. Journal of Neuroscience Research. 2018; 96(12):1831-46. doi:10.1002/jnr.24322



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