Philip Smaldino

Philip Smaldino

Associate Professor of Cell Biology


Room:CL 231E


University of Michigan - Postdoctoral Fellowship: 2013-2016
Wake Forest School of Medicine - PhD: 2008-2013
State University of New York at Buffalo - MS: 2006-2008
State University of New York at Fredonia - BS: 2002-2006

Co-investigator: Melissa A. Smaldino, PhD

Two figures of cellular activity.


The Smaldino laboratory is broadly interested in G-quadruplex nucleic acid structures and the cellular enzymes that unwind them. G-quadruplexes are stable, ‘knot-like’ structures that form within guanine (G)-rich regions of DNA or RNA. These structures provide an essential layer of transcriptional and translational regulation in a healthy cell. However, when in excess or aberrantly unwound, G-quadruplexes can become pathological. We apply our expertise in G-quadruplex biology to study normal neuronal development and G-quadruplex-linked diseases including, ALS (Lou Gehrig’s disease), dementia, and cancer. We leverage a combinatorial approach of biochemical assays, human cell culture models, and mouse models to study these topics.

Photos of students working in Dr. Smaldino's laboratory.

Project 1: ALS/Lou Gehrig’s Disease

Figure illustrating RNA processes

ALS is a deadly neurodegenerative disease with severely limited treatment option. Eighty percent of all ALS patients will succumb to the disease within 5 years of diagnoses. Thus, a greater mechanistic understanding of ALS is desperately needed. The most common ALS-linked mutation occurs in the gene C9ORF72 (C9) and consists of a GGGGCC-repeat (C9-repeat) expansion. Healthy individuals harbor ~2-30 repeats, while C9 ALS patients generally have >30, often hundreds to thousands of the C9-repeat. The guanine (G)-rich nature of the C9-repeat sequence allows it to fold into extensive G-quadruplex structures. When these structures become unwound, they are transcribed into toxic, G-quadruplex-forming RNA, which are then translated into toxic dipeptide repeat proteins that are major contributors to ALS pathogenesis (Figure 1). As such, C9 ALS is foundationally a ‘G-quadruplex disease’. The Smaldino laboratory studies the role of the major G-quadruplex helicase, G4 Resolvase1 (G4R1, aliases: DHX36 and RHAU) in C9 ALS using biochemical assays, patient cell culture, and mouse models. We are grateful for the ALS Association and their generous support of this work.

Project 2: Dementia

Frontal temporal dementia (FTD) is the second most common cause of young onset dementia, characterized by degeneration of the frontal and temporal lobes of the brain and accompanied by cognitive and behavioral declines. The average survival of FTD patients ranges from 3-12 years with limited effective treatment options. The most common mutation associated with FTD is the same repeat expansion mutation seen in C9ORF72 (C9) that causes C9 ALS (see above/Figure 1). Therefore, similar to C9 ALS, C9 FTD is foundationally a ‘G-quadruplex disease’. The Smaldino laboratory studies the role of the major G-quadruplex helicase, G4R1, in C9 FTD, primarily using mouse models.

Project 3: Development and Cancer

G-quadruplex DNA structures are present in the promoters of the majority of proto-oncogene/developmental genes where they impart an important layer of transcriptional regulation. Upon unwinding of these structures, transcription of that gene is generally elevated. Thus, enzymes that unwind G-quadruplex structures potentially represent important developmental/cancer gene regulators. G4R1 is the major G-quadruplex helicase enzyme in human cells, is essential for embryonic/early development in mammals, and is involved in several cancer types. We are exploring the role of G4R1 in development and cancer using biochemical assays, human cell line culture, and mouse models. 

Selected Publications

*  indicates authors contributed equally to the work
µ indicates student author

Chambers, A.E.*,µ, Richardson, A.E.* ,µ , Read, D.F.*, Waller, T.J.*, Bernstein, D.A., Smaldino, P.J. An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity (2018) J. Vis. Exp., Oct 8;(140)

McComb C., Otto, G. Garvey J. µ, Omans, D. µ, Smaldino, P.J. (2018) “Visualizing Cancer: A Transdisciplinary Art & Biology Collaborative”. Journal of Teaching and Learning 11 (2), 1-10.

Routh E.D.*,  Creacy S.D.*, Beerbower, P.E.µ, Akman S.A., Vaughn J.P.C, Smaldino P.J. (2017)  “G-quadruplex DNA affinity purification of catalytically active G4 Resolvase1” J Vis Exp. Mar 18;(121). doi: 10.3791/55496

*Read D.F.µ, *Waller T.J.µ, Tse E, Southworth D.R., Engelke D.R.C , Smaldino P.J. (2017) “Aggregation of Mod5 is affected by tRNA binding with implications for tRNA gene-mediated silencing” FEBS Lett. Jun;591(11):1601-1610. doi: 10.1002/1873-3468.12627.

*Waller, T.J.µ, *Read, D.F.µ, Engelke, D.R. C, Smaldino P.J. (2017) “The human tRNA-modifying protein, TRIT1, forms amyloid fibers in vitro”  Gene. 612:19-24. doi: 10.1016/j.gene.2016.10.041.

Kharytonchyk, S., Monti, S., Smaldino, P.J., Van, V., Bolden, N.C., Brown, J.D., Russo, E., Swanson, C., Shuey, A., Telesnitsky, A., Summers, M.F. (2016)  “Transcriptional start site heterogeneity modulates the structure and function of the HIV-1 genome” Proceedings of the National Academey of Sciences U S A  2016 Nov 22;113(47):13378-13383. 

Carrick B.H. µ, Hao L., Smaldino P.J., and Engelke D.R. A novel recombinant DNA system for high efficiency affinity purification of proteins in Saccharomyces cerevisiae (2015). Gene Genomes Genetics, 6(3):573-8.

Smaldino P.J., Routh E.D., Kim J.H. µ, Giri B., Creacy S.D., Hantgan R.R., Akman S.A., Vaughn J.P. (2015)  Mutational Dissection of Telomeric DNA Binding Requirements of G4 Resolvase 1 Shows that G4-Structure and Certain 3’-Tail Sequences Are Sufficient for Tight and Complete Binding. PLOS ONE. 10(7) 

Smaldino P.J., Read D.F. µ, Pratt-Hyatt M., Hopper A.K., Engelke D.R. (2015) The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer. Gene. 556(1):13-8. 

Stoler D.L., Smaldino P.J., Darbary H.K., Sullivan M.A., Rigual N.R., Popat S.R., Hicks W.L., Merzianu M., Gaile D.P., Anderson G.A., Loree T.R. (2013) Human Papillomavirus and Tobacco Usage in Base of Tongue Cancers. Ears, Nose and Throat Ear Nose Throat J. 92(8):372-80. 

*Huang W.,  *Smaldino, P.J.*Zhang Q., Miller L.D., Cao P., Stadelman K., Wan M., Giri B., Lei M., Nagamine Y., Vaughn J.P., Akman S.A., Sui G. (2012) Yin Yang 1 contains G-quadruplex structures in its promoter and 5'-UTR and its expression is modulated by G4 resolvase 1. Nucleic Acids Res. 40(3) 1033-49  *Authors contributed equally.

*Giri, B., *Smaldino, P.J., Thys, R.G., Creacy, S.D., Routh, E.D., Hantgan, R.R., Lattmann, S., Nagamine, Y., Akman, S.A., Vaughn, J.P. (2011) G4 Resolvase 1 tightly binds and unwinds unimolecular G4-DNA. Nucleic Acids Res. 39 (16) 7161-78. *Authors contributed equally.

Tezal, M., Sullivan Nasca, M., Stoler, D.L., Melendy, T., Hyland, A., Smaldino, P.J., Rigual, N.R., Loree, T.R. (2009). Chronic Periodontitis–Human Papillomavirus Synergy in Base of Tongue Cancers. Archives of Otolaryngology and Head and Neck Surgery, 135(4), 391-6.

Course Schedule
Course No. Section Times Days Location
Methods in Cell Biol 315 2 1200 - 1440 W FB, room 352
Methods in Cell Biol 315 3 1200 - 1440 M FB, room 352
Undergraduate Resear 498 125 0000 - 0000 TBD, room TBD
Readings in Biology 628 225 0000 - 0000