Robert A. Clark, M.D.

Research

The overarching integrated themes of our translational research program are inflammation, neurodegeneration, and diseases of aging. Specific project areas include the following:

• Neurodegeneration – mechanisms of injury and development of imaging technology:  I have been attracted in recent years to research on neurodegenerative disorders, in substantial part because of their close linkages to my long-standing interest in the areas of inflammation and oxidative stress.  The studies have focused primarily on Parkinson’s disease (PD), addressing both mechanisms of neuronal injury and the development of novel pharmacologic and cell-based therapeutic approaches.  These lines of investigation have been significantly informed by my previous work on mechanisms of inflammatory cellular injury and the cell biology of bone marrow-derived cells of the innate immune system.  Mechanistic work on neuronal injury uncovered a previously unsuspected pathway involving oxidative auto-activation of the non-receptor tyrosine kinase c-Abl, which in turn catalyzed the tyrosine phosphorylation of parkin, resulting in loss of its enzymatic activity as an E3 ubiquitin ligase.  In order to accelerate our mechanistic studies, we have developed new tools and resources for studying neurodegeneration in rodent models, focusing especially on high-end brain imaging.  Using MRI, we have characterized both genetic and toxin models of PD and, by fMRI, have mapped the mouse olfactory system, a major focus of our mechanistic studies and biomarker development work.  We also discovered that the α-synuclein transgenic mouse is a superb model of PD-associated reduced cerebral blood flow.
• Parkinson’s disease – novel cell-based and small-molecule therapeutics:  Our work on cell-based therapies for PD (in collaboration with Dr. Senlin Li, Professor Medicine) has capitalized on an innovative, non-cytoreductive system for hematopoietic stem cell transplantation.  A therapeutic gene (GDNF or neurturin) is expressed in a third-generation lentiviral vector under the regulation of our patented highly active, synthetic, macrophage-selective promoter.  Following non-toxic (mobilization-aided) engraftment in murine models of PD, macrophage progeny of the genetically engineered stem cells cross the blood-brain barrier and home selectively to areas of neurodegeneration, where they produce and deliver the therapeutic protein, resulting in mitigation of PD pathology and behavioral abnormalities.  We recently used a similar platform to achieve rejuvenation (e.g., 12% increase in lifespan) in older mice by mobilization-aided transplantation of hematopoietic stem cells from young mice.  We are also working with redox-active small molecules as neuroprotective agents, as demonstrated in our studies on the neuroprotective effects of methylene blue in a chronic PD mouse model.  Studies have recently been initiated in the lab to test the therapeutic potential of brain-penetrating small-molecule inhibitors of Nox family NADPH oxidases in α-synuclein transgenic mice. We are also developing expertise in single cell/single nucleus RNASeq and spatial assessment of gene expression, as well as chemogenetic and optogenetic tools for application to our PD models.

Awards & Accomplishments

Awards

• UTHSCSA Presidential Distinguished Senior Research Scholar Award
• University of Iowa Distinguished Achievement Award
• Society for Leukocyte Biology Legacy Keynote Lecture Award

Honorary elections

• American Society for Clinical Investigation
• Association of American Physicians
• Master, American College of Physicians
• Fellow, American Association for the Advancement of Science

Accomplishments

• National Institutes of Health, MERIT Award
• Veterans Health Administration, Medical Investigator Career Award
• Founding Director, Institute for Integration of Medicine & Science
• Clinical & Translational Science Award, NIH Contact Principal Investigator

Lab Members

	Biju K. Chandu, PhD (Neuroscience) Assistant Professor of Medicine
	Ada Felix-Ortiz, BA, MA (Neuroscience) Research Associate Senior
	Allison Stallings, BS (Neuroscience) Medical Student

Publications

Okulicz JF, Le TD, Agan BK, Camargo JF, Landrum ML, Wright E, Dolan ML, Ganesan A, Ferguson TM, Smith DM, Richman DD, Little SL, Clark RA, He W, Ahuja SK.  Influence of the timing of antiretroviral therapy on the potential for normalization of immune status in human immunodeficiency virus 1-infected individuals.  JAMA Intern Med 175(1):88-99, 2015 (PMCID4286496).

de Figueiredo ASP, Salmon AB, Bruno F, Jimenez F, Martinez HG, Halade GV, Ahuja SS, Clark RA, DeFronzo RA, Abboud HE, El Jamali A.  Nox2 mediates skeletal muscle insulin resistance induced by a high-fat diet.  J Biol Chem 290(21):13427-13439, 2015 (PMCID4505590).

He W, Jimenez F, Martinez H, Harper NL, Manoharan MS, Carrillo A, Ingale P, Liu YG, Ahuja SS, Clark RA, Rather CG, Ramirez DA, Andrews CP, Jacobs RL, Ahuja SK.  Cockroach sensitization mitigates allergic rhinoconjunctivitis symptom severity in patients allergic to house dust mites and pollen. J Allergy Clin Immunol 136:658-666, 2015 (PMID26026342).

Gornalusse G, Mummidi S, Gaitan AA, Jimenez F, Ramsuran V, Picton A, Rogers K, Manoharan M, Avadhanam N, Murthy KK, Martinez H, Molano Murillo AM, Chykarenko ZA, Hutt R, Daskalakis D, Shostakovich-Koretskaya L, Karim SA, Martin JN, Deeks SG, Hecht F, Sinclair E, Clark RA, Okulicz J, Valentine FT, Martinson N, Tiemessen CT, Ndung’u T, Hunt PW, He W, Ahuja SK.  Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor.  Proc Natl Acad Sci USA 112:E4762-E4771, 2015 (PMCID4553789).

Clark RA.  Proton pathway paradox:  Hv1 H+ channel sustains neutrophil Nox2 activity, yet suppresses HOCl formation (peer-reviewed editorial).  J Leukocyte Biol 99(1):1-4, 2016.

Li G, Chen C, Laing S, Ballard C, Biju KC, Reddick R, Clark RA, Li S.  Hematopoietic knockdown of PPARδ reduces atherosclerosis in LDLR-/- mice.  Gene Therapy 23(1):78-85, 2016 (PMCID4939901).

Cong L., Muir ER, Chen C, Qian Y, Liu J, Biju KC, Clark RA, Li S, Duong TQ.  Multimodal MRI evaluation of the MitoPark mouse model of Parkinson’s disease.  PLoS ONE 11(3), e0151884. doi:10.1371, 2016 (PMID27003179).

Ahuja SK, Manoharan MS, Harper NL, Jimenez F, Hobson, BD, Martinez H, Ingale P, Liu Y-G, Carrillo A, Lou Z, Kellogg DL, Ahuja SS, Rather CG, Esch RE, Ramirez DA, Clark RA, Nadeau K, Andrews CP, Jacobs RL, He W. Preservation of epithelial cell barrier function and muted inflammation in resistance to allergic rhinoconjunctivitis from house dust mite challenge. J Allergy Clin Immunol 139:844-854, 2017 (PMID27658763).

Chen C, Li X, Ge G, Liu J, Biju KC, Laing SD, Qian Y, Ballard C, He Z, Masliah E, Clark RA, O’Connor JC, Li S. GDNF-expressing macrophages mitigate loss of dopamine neurons and improve Parkinsonian symptoms in MitoPark mice.  Scientific Reports 8:5460, 2018.  doi:10.1038/s41598-018-23795-4.

Biju KC, Evans RC, Shrestha K, Carlisle DC, Gelfond J, Clark RA. Methylene blue ameliorates olfactory dysfunction and motor deficits in a chronic MPTP/probenecid mouse model of Parkinson’s disease.  Neuroscience 380:111-122, 2018.  doi: 10.1016/j.neuroscience.2018.04.008 (PMID29684508).

Ge G, Chen C, Guderyon MJ, Liu J, He Z, Yu Y, Clark RA, Li S. Regulatable lentiviral hematopoietic stem cell gene therapy in a mouse model of Parkinson’s disease.  Stem Cells & Development 27:995-1005, 2018.  doi: 10.1089/scd.2018.0030 (PMID29562865).

Schmidt S, Shay LA, Saygin C, Wan H, Schulz K, Clark, RA, Shireman PK. Improving pilot project application and review processes: A novel application of lean six sigma in translational science.  J Clin Trans Sci 2(3):135-138, 2018. doi.org/10.1017/cts.2018.30 (PMCID6199542).

Chen C, Guderyon MJ, Guo G, Clark RA, Li S.  Lentiviral Infection of Mouse Bone Marrow Cells for Hematopoietic Stem Cell Transplantation.  IN:  Daadi, MM, ed, Neural Stem Cells:  Methods and Protocols.  Methods in Molecular Biology, vol. 1919, Springer Science+Business Media, LLC, part of Springer Nature, 2019, pp. 205-213.

Nauseef WM, Clark RA.  Intersecting Stories of the Phagocyte NADPH Oxidase and Chronic Granulomatous Disease. IN:  Knaus, U and Leto, TL, ed, NADPH Oxidases:  Methods in Molecular Biology, vol. 1982, Springer Nature, 2019, 978-1-4939-9423-6, 450250_1_En, (1).

Muir ER, Biju KC, Cong L, Rogers WE, Torres Hernandez E, Duong TQ, Clark RA. Functional MRI of the mouse olfactory system. Neurosci Lett 704:57-61, 2019. doi.org/10.1016/j.neulet.2019.03.055 (PMID30951799).

Biju KC, Shen Q, Torres Hernandez E, Mader, MJ, Clark RA. Reduced cerebral blood flow in an α-synuclein transgenic mouse model of Parkinson’s disease.  J Cereb Blood Flow Metab 2019. doi.org/10.1177/0271678X19895432 (PMID31856640).

Chen C, Guderyon MJ, Li Y, Ge G, Bhattacharjee A, Ballard C, He Z, Masliah E, Clark RA, O’Connor JC, Li S. Nontoxic hematopoietic stem cell transplantation-based macrophage/microglia-mediated GDNF delivery for Parkinson’s disease.  Molecular Therapy: Methods & Clinical Development.  17: 2020. doi.org/10.1016/j.omtm.2019.11.013 (PMID31890743).

Guderyon MJ, Chen C, Bhattacharjee A, Ge G, Fernandez RA, Gelfond JAL, Gorena, KM, Cheng CJ, Li Y, Nelson JF, Strong RJ, Hornsby PJ, Clark RA, Li S. Mobilization-based transplantation of young-donor hematopoietic stem cells extends lifespan in mice.  Aging Cell 2020: 00:e13110. doi.org/10.1111/acel.13110 (PMID:32012439).

Smith AM, Harper N, Meunier JA, Branum AP, Jimenez F, Pandranki L, Carrillo A, Dela Cruz CS, Restrepo MI, Maselli DJ, Rather CG, Heisser AH, Ramirez DA, He W, Clark RA, Andrews CP, Evans SE, Pugh JA, Zhang N, Lee GC, Moreira AG, Segal LN, Ramirez RM, Jacobs RL, Manoharan MS, Okulicz JF, Ahuja SK. Repetitive aeroallergen challenges elucidate maladaptive epithelial and inflammatory traits that underpin allergic airway diseases.  J Allergy Clin Immunol 148(2):533-549, 2021; doi.org/10.1016/j.jaci.2021.01.008.

Lee GC, Restrepo MI, Harper N, Manoharan MS, Smith AM, Meunier JA, Sanchez-Reilly S, Ehsan A, Branum AP, Winter C, Winter L, Jimenez F, Pandranki L, Carrillo A, Perez GL, Anzueto A, Trinh H, Lee M, Hecht JM, Martinez C, Sehgal RT, Cadena J, Walter EA, Oakman K, Benavides R, Pugh JA, South Texas Veterans Health Care System COVID-19 team, Letendre S, Steri M, Orrù V, Fiorillo E, Cucca F, Moreira AG, Zhang N, Leadbetter E, Agan BK, Richman DR, He W, Clark RA, Okulicz JF, Ahuja SK. Immunologic resilience and COVID-19 survival advantage.  J Allergy Clin Immunol 2021; doi.org/10.1016/j.jaci.2021.08.021 (PMCID8425719).

Smith AM, Ramirez RM, Harper N, Jimenez F, Branum AP, Meunier JA, Pandranki L, Carrillo A, Winter C, Winter L, Rather CG, Ramirez DA, Andrews CP, Restrepo MI, Maselli DJ, Pugh JA, Clark RA, Lee GC, Moreira AG, Manoharan MS, Okulicz JF, Jacobs RL, Ahuja SK. Large-scale provocation studies identify maladaptive responses to ubiquitous aeroallergens as a correlate of severe allergic rhinoconjunctivitis and asthma.  Allergy 2021; doi.org/10.1111/all.15124.

Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King C, Zheng Y-T, Zheng H-Y, Kimani J, Ball TB, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA, South Texas Veterans Health Care System COVID-19 team, Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W. Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection.  Nature Communications 2023. Designated among the Top 25 COVID-19 articles for 2023. https://doi.org/10.1038/s41467-023-38238-6; https://www.nature.com/articles/s41467-023-38238-6

Ge Guo, Sivasubramanian B, Geng B, Zhao S, Zhou Q, Huang, O’Connor J, Clark RA, Li S. Long-term benefits of hematopoietic stem cell-based macrophage/microglia delivery of GDNF to the CNS in a mouse model of Parkinson’s disease. Gene Therapy 2024; https://doi.org/10.1038/s41434-024-00451-3.