Andrei Thomas-Tikhonenko, Ph.D.

faculty photo
Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations

Contact information
4056 Colket Translational Research Bldg
3501 Civic Center Blvd
Philadelphia, PA 19104
Office: 267-426-9699
Fax: 267-426-8125
BSc (Biochemistry/Virology)
Moscow State University, 1984.
PhD (Oncology/Virology)
Russian Academy of Medical Sciences, 1988.
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Description of Research Expertise

My laboratory has a long-standing interest in pathobiology of solid and hematopoietic malignancies, in particular lymphomas and leukemias and other adult and pediatric cancers driven by MYC overexpression. The current research focuses on the role of non-coding RNAs (including microRNAs) and mRNA processing in cancer pathogenesis and therapeutic resistance.

Description of Research & Rotation Projects

1. Aberrant splicing in lymphoid malignancies and its implications for immunotherapy
CD19 is expressed on the surface of most B-cell neoplasms, including acute lymphoblastic leukemias (B-ALL). There it can be targeted by a variety of effective immunotherapeutic agents, such as CART-19. However, relapses with epitope loss occur in up to 20% of B-ALL treated with CD19-directed immunotherapy. Using whole exome and RNA sequencing and copy number alteration analysis, we detected acquired hemizygous deletions spanning the CD19 locus and de novo frameshift and missense mutations in exon 2 of CD19 in some - but not all - relapse samples. We also identified two alternatively spliced CD19 mRNA species: one lacking exons 5-6 (Δex5-6), which encode the transmembrane domain, and another lacking exon 2 (Δex2), compromising surface localization of CD19 (Bagashev et al, Blood 2015). Pull-down and siRNA experiments identified SRSF3 as a key splicing factor involved in exon 2 retention and differentially expressed in primary vs. relapsed B-ALL (Black et al, Blood 2015). Using CRISPR/Cas9-mediated gene editing, we demonstrated that exon 2 skipping can effectively bypass deleterious exon 2 mutations in B-ALL cells and yield truncated CD19 protein variants, which fail to trigger killing by CART-19 but partly rescue defects in cell proliferation and pre-BCR signaling associated with CD19 loss. Thus, there exists a novel mechanism of resistance to immunotherapy, based on a combination of deleterious mutations and selection for alternatively spliced RNA isoforms (Sotillo et al, Cancer Discovery 2015).

2. The key role of the B-cell receptor (BCR) pathway in lymphoid malignancies
Using novel murine models based on retroviral transduction of bone marrow progenitors, we made a surprising discovery that the resultant neoplasms are prone to losing their B-cell identity and converting into myeloid cancers by virtue of extinguishing the key lineage fidelity transcriptions factor PAX5 (Yu et al, Blood, 2003). Since PAX5 loss entails silencing of key BCR components (e.g., CD19), we were able to address the role of the Pax5-BCR axis in hematological malignancies. We were the first to formally prove that PAX5 promotes neoplastic growth through stimulation of BCR signaling (Cozma et al, J Clin Invest 2007). Subsequently, we made an unexpected discovery that CD19 can drive drives neoplastic growth in the absence of the BCR, by virtue of recruiting PI3 kinase and stabilizing the MYC protein (Chung et al, J Clin Invest 2012). This finding has particular relevance for acute lymphoblastic leukemias derived from immature pro-B-cells. On the other hand, in post-germinal center neoplasms (e.g., diffuse large B-cell lymphoma), activation of MYC by the CD19-BCR complex starts a positive feed-forward loop, whereby MYC boosts BCR signaling by down-modulating its antagonists known as ITIM proteins (Psathas et al, Blood 2013).

3. microRNAs as key downstream effectors of MYC
Our interest in non-canonical functions of MYC was spurred by the early discovery that some of well-known MYC-repressed genes (e.g., the angiogenesis inhibitor thrombospondin-1) are regulated by MYC at the level of mRNA turnover, not promoter silencing (Janz et al, Nucl Acids Res 2000). At the time, we didn’t know what the underlying mechanism was, but the discovery of the first MYC-activated microRNA cluster, miR-17-92 (a.k.a. oncomir-1) provided us with an intriguing clue. We indeed discovered that thrombospondin-1 is an essential target of the MYC - miR-17-92 axis, and that this targeting drives tumor angiogenesis (Dews et al, Nat Genet 2006). This was the first demonstration of microRNAs affecting tumor microenvironment – and the second report of microRNAs playing a role in gene repression by MYC. Subsequently, we showed, in collaboration with the Mendell and Dang labs, that MYC also down-regulates select microRNA leading to a broad gene activation program (Chang et al, Nat Genet 2008). The mechanisms of microRNA deregulation by MYC range from promoter-based to biogenesis-mediated. For example, we found that MYC regulates Lin28b, which is a key negative regulator of the let-7 family of tumor suppressive microRNAs (Chang et al, Proc Natl Acad Sci USA 2009).

4. Harnessing the pro-apoptotic acitivity of Myc for therapeutic purposes
While Myc is a gene known to drive tumor cell proliferation, it also accounts for high levels of cell death, and in certain types of B-lymphomas the so-called MYC signature correlates with improved survival. The unmet challenge is to boost the pro-apoptotic effects of Myc without promoting growth of neoplastic cells. We had begun to address this challenge by refining our murine B-cell neoplasm models to include conditional activation of MYC (Yu et al, Cancer Res 2005) or transient reactivation of the p53 tumor suppressor (Yu et al, Blood 2007; Amaravadi et al, J Clin Invest 2007). Subsequently, we demonstrated that the increase in therapeutic apoptosis could be achieved by inhibiting microRNAs that target endogenous MYC such as miR-34a (Sotillo et al, Oncogene 2011). We are currently pursuing the idea that chemosensitization could be achieved pharmacologically by transiently elevating MYC levels with small-molecules inhibitors of GSK3.

5. Understanding and targeting tumor angiogenesis
This work had begun in earnest with the discovery that Myc overexpression is necessary for the hyper-vascular phenotype in simple xenograft models (Ngo et al, Cell Growth Diff, 2000) as well as in genetically complex cancers. This frequently occurs by a microRNA-dependent mechanism, through activation of the miR-17-92 cluster (see above). Subsequently, we demonstrated that in solid tumors, such as pediatric neuroblastoma and colon adenocarcinoma, deregulation of miR-17-92 leads to profound suppression of TGFβ signaling and diminished production of many anti-angiogenic TGFβ-inducible factors such as thrombospondin-1, CTGF, and clusterin (Dews et al, Cancer Res 2010). In fact, the MYC | miR-1792 and TGFβ pathways exhibit an epistatic relationship, where mutations in one pathway make mutations in the other redundant (Dews et al, J Natl Cancer Inst 2014). However, miR-17-92 is not the only pro-angiogenic microRNA. For example, colon cancer neovascularization also requires p53-regulated miR-194 (Sundaram et al, Cancer Res 2011). Thus, targeting microRNAs might be a viable anti-angiogenic strategy, especially in tumors without VEGF overexpression.

Lab personnel:
Priyanka Sehgal, PhD, Postdoctoral Fellow
Manuel Torres Diz, PhD, Postdoctoral Fellow
Zhiwei Ang, PhD, Postdoctoral Fellow
Scarlett Yang, Immunology (IGG) Graduate Student
Carolin Schmidt, Research Technician II
Katharina Hayer, Bioinformatics Scientist III
Rawan Shraim, Bioinformatics Scientist I
Jacob Stanger, Penn Undergraduate Student
Ryan Sathianathen, Penn Undergraduate Student
Kathryn Wurges, MHA/MHE, Office Manager

Affiliated personnel:
Mathieu Quesnel-Vallières, PhD (Postdoctoral Fellow in the Barash/Lynch labs @Penn)
David Wang (GCB Graduate Student in the Barash lab @Penn)

Recent alumni:
Sisi Zheng, MD, Pediatric Hem-Onc Fellow
Ammar Naqvi, PhD, Postdoctoral Fellow
Mukta Asnani, PhD, Postdoctoral Fellow
Colleen Harrington, CAMB Graduate Student
Claudia Lanauze, CAMB Graduate Student

Description of Other Expertise

In 2008, I moved my lab across campus to The Children's Hospital of Philadelphia, where it became an integral part of the Center for Childhood Cancer Research. This integration allowed me to foster new collaborations with key physician-scientists and pursue several translational projects. Because of my contributions to the field of immunobiology, in 2013 I became Investigator of the multi-institutional Stand Up to Cancer-St. Baldrick's Pediatric Cancer Dream Team and as a key member of that group received the 2021 AACR Team Science Award.

Selected Publications

L.Schulz, M.Torres-Diz, M.Cortés-López, K.E.Hayer, M.Asnani, S.K.Tasian, Y.Barash, E.Sotillo, K.Zarnack, J.König, and A.Thomas-Tikhonenko: Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 22(1): 190, June 2021.

C.Radens, B.Slaff, P.Jewell, A.Jha, N.Lahens, G.Grant, A.Thomas-Tikhonenko, K.W.Lynch, and Y.Barash: MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis. Nat Commun 12(1): 3353, June 2021.

C.B.Lanauze, P.Sehgal, K.Hayer, M.Torres-Diz, J.A.Pippin, S.F.A.Grant, and A.Thomas-Tikhonenko: Colorectal cancer-associated Smad4 R361 hotspot mutations boost Wnt/β-catenin signaling through enhanced Smad4-LEF1 binding. Mol Cancer Res 0.1158/1541-7786.MCR-20-0721, Feb 2021.

Lee J, Robinson ME, Ma N, Artadji D, Ahmed MA, Xiao G, Sadras T, Deb G, Winchester J, Cosgun KN, Geng H, Chan LN, Kume K, Miettinen TP, Zhang Y, Nix MA, Klemm L, Chen CW, Chen J, Khairnar V, Wiita AP, Thomas-Tikhonenko A, Farzan M, Jung JU, Weinstock DM, Manalis SR, Diamond MS, Vaidehi N, Müschen M.: IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells. Nature 588: 491-497, Dec 2020.

M.Asnani, K.E.Hayer, A.S.Naqvi, S.Zheng, S.Y.Yang, D.Oldridge, F.Ibrahim, M.Maragkakis, M.R.Gazzara, K.L.Black, A.Bagashev, D.Taylor, Z.Mourelatos, S.A.Grupp, D.Barrett, J.M.Maris, E.Sotillo, Y.Barash, and A.Thomas-Tikhonenko: Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19. Leukemia 34(4): 1202–1207, Apr 2020.

V.Pillai, K.Muralidharan, W.Meng, A.Bagashev, D.A.Oldridge, J.Rosenthal,J.Van Arnam, J.J.Melenhorst, D.Mohan, A.M.DiNofia, M.Luo, S.Cherian, J.R.Fromm, G.Wertheim, A.Thomas-Tikhonenko, M.Paessler, C.H.June, E.T.Luning Prak, V.G.Bhoj, S.A.Grupp, S.L.Maude, and S.R.Rheingold: CAR T-cell therapy is effective for CD19-dim B-lymphoblastic leukemia but is impacted by prior blinatumomab therapy. Blood Adv 3(22): 3539-3549, Nov 2019.

C.T.Harrington, E.Sotillo, A.Robert, K.E.Hayer, A.M.Bogusz, J.Psathas, D.Yu, D.Taylor, C.V.Dang, P.Klein, M.D.Hogarty, B.Geoerger, W.S.El-Deiry, J.Wiels, and A.Thomas-Tikhonenko : Transient stabilization, rather than inhibition of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma. Leukemia 33(10): 2429–2441, Oct 2019.

S.Zheng, M.Asnani, and A.Thomas-Tikhonenko: Escape from ALL-CARTaz: Leukemia immunoediting in the age of chimeric antigen receptors. Cancer J 25(3): 217-222, May 2019.

K.L.Black, A.S.Naqvi, M.Asnani, K.E.Hayer, S.Y.Yang, E.Gillespie, A.Bagashev, V.Pillai, S.K.Tasian, M.R.Gazzara, M.Carroll, D.M.Taylor, K.W.Lynch, Y.Barash, and A.Thomas-Tikhonenko: Aberrant splicing in B-cell acute lymphoblastic leukemia. Nucleic Acids Res 46(21): 11357–11369, Nov 2018.

E.Sotillo, D.M.Barrett, K.L.Black, A.Bagashev, D.Oldridge, G.Wu, R.Sussman, C.Lanauze, M.Ruella, M.R.Gazzara, N.M.Martinez, C.T.Harrington, E.Y.Chung, J.Perazzelli, T.J.Hofmann, S.L.Maude, P.Raman, A.Barrera, S.Gill, S.F.Lacey, J.J.Melenhorst, D.Allman, E.Jacoby, T.Fry, C.Mackall, Y.Barash, K.W.Lynch, J.M.Maris, S.A.Grupp, and A.Thomas-Tikhonenko: Convergence of acquired mutations and alternative splicing of CD19 enables resistance to CART-19 immunotherapy. Cancer Discov 5(12): 1282-1295, Dec 2015 Notes: HIGHLIGHTED IN: S.Behjati "Hiding from the enemy", Sci Transl Med, 7:313ec193 (2015) | G.K.Alderton "Skipping out epitopes", Nat Rev Cancer, 15, 699 (2015) | H.J.Jackson & R.J.Brentjens "Overcoming Antigen Escape with CAR T-cell Therapy", Cancer Discov, 5:1238 (2015).

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Last updated: 09/16/2021
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