Andrei Thomas-Tikhonenko, PhD

Professor of Pathology and Laboratory Medicine
Professor of Pediatrics
University of Pennsylvania Perelman School of Medicine

Mildred L. Roeckle Endowed Chair in Pathology
Chief, Division of Cancer Pathobiology
Director, Experimental Pathology Branch
Children's Hospital of Philadelphia

Contact Information4056 Colket Translational Research Bldg
3501 Civic Center Blvd
Philadelphia, PA, 19104
Office: 267-426-9699
Fax: 267-426-8125


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, Research Associate
Manuel Torres Diz, PhD, Research Associate
Zhiwei Ang, PhD, Research Associate
Charles Drummer IV, PhD, Postdoctoral Fellow (starting Spring '22 )
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
Hayden Siesel, Penn Undergraduate Student
Kathryn Wurges, MHA/MHE, Project 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

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. 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. Also, since 2018, my lab has been part of the Pediatric Immunotherapy Discovery and Development Network (PI-DDN) funded through Beau Biden Cancer Moonshot Initiative.

Graduate Groups

Cell and Molecular Biology


BSc (Biochemistry/Virology), Moscow State University, 1984
PhD (Oncology/Virology), Russian Academy of Medical Sciences, 1988

Specialty Certification

Postgraduate Training

Visiting Scientist, Université Libre de Bruxelles, Brussels, Belgium, 1989-1989
Junior Researcher, Researcher, All-Russia Cancer Research Center, Moscow, Russia, 1989-1990
Postdoctoral Research Associate, Fred Hutchinson Cancer Research Center, Seattle, WA, 1990-1992
Staff Scientist, Fred Hutchinson Cancer Research Center, Seattle, WA, 1992-1997

Awards and Honors

ICRETT Award (short-term exchange), International Union Against Cancer, 1990
Special Fellow, Leukemia Society of America, 1994-1997
Travel Award, Fundación Juan March, 1995
Travel Award, American Society for Microbiology, 1996
NIH FIRST Award, 1997-2002
Elizabeth & William Whitney Clark Developmental Chair in Oncology, University of Pennsylvania, 1999-2005
Honorary Member of the Phi Zeta Honor Society of Veterinary Medicine (Beta Chapter), 2000-present
Pfizer Award for Research Excellence, Pfizer Animal Health, 2005
Innovation Award, Alex's Lemonade Stand Foundation, 2010-2013
Mildred L. Roeckle Endowed Chair in Pathology at The Children's Hospital of Philadelphia, 2011-present
Department of Cancer Biology 4th Annual Award for Excellence in Teaching, Perelman School of Medicine at the University of Pennsylvania, 2012
Ethel Brown Foerderer Fund for Excellence Award, 2013
Immunogenomics Pediatric Dream Team Investigator, Stand Up To Cancer - St. Baldrick's Foundation, 2013-2022
Keynote Speaker, The Tumor Biology Program Mini-Symposium, Sylvester Comprehensive Cancer Center, Miami, FL, 2018
Richard 'Buz' Cooper Scholar Award, University of Pennsylvania Abramson Cancer Center, 2019-2021
Team Science Award, American Association for Cancer Research (AACR), 2021

Memberships and Professional Organizations

American Association for Cancer Research, 1999 - present
Ohio Cancer Research Associates, 2002 - 2002
National Library of Medicine-sponsored "Myc Cancer Gene" bioinformatics hubsite (5G13LM007515), 2003 - 2004
Italian Association for Cancer Research, 2005 - 2017
SPARKS Foundation (United Kingdom), 2005 - 2005
Tumor Progression and Metastasis Study Section, NIH, 2006 - 2011
National Canine Cancer Foundation, 2006 - 2008
Intramural Laboratory Review Panel, National Cancer Institute, NIH, 2006 - 2006
Oncological Sciences Fellowship Study Section, NIH, 2006 - 2006
L'Institut National du Cancer, France, 2007 - 2007
International Cancer Microenvironment Society, 2007 - present
Joint Research Projects in Cancer, National Cancer Institute - Health Research Board Ireland Consortium, 2007 - 2007
Basic Mechanisms of Cancer Therapeutics Study Section, NIH, 2007 - 2007
Cancer Research UK, 2007 - 2015
Estonian Science Foundation, 2007 - 2007
CCNY/MSKCC Partnership U54 grant, National Cancer Institute, 2008 - 2008
The Neuroblastoma Society (United Kingdom), 2008 - 2012
American Society of Hematology, 2008 - present
Alex's Lemonade Stand Foundation, 2009 - present
NIH Review Panel: ARRA 2009 Challenge Grants, 2009 - 2009
Erwin Schroedinger Program-Austrian Science Fund, 2010 - 2010
American Society for Clinical Investigation, 2010 - 2012
NCI Special Emphasis Panels: Program Project Grants (P01), 2010 - 2014
International CCN Society, 2010 - 2013
l’Agence Nationale de la Recherche (France), 2011 - 2011
NCI Special Emphasis Panels: Omnibus R03/R21, 2012 - 2015
Swiss National Science Foundation, 2012 - 2014
NCI Special Emphasis Panel: Collaborative Research in Integrative Cancer Biology and the Tumor Microenvironment (U01), 2012 - 2012
Lymphoma Research Foundation, 2012 - 2013
Regulatory Genomics Special Interest Group (RegGenSIG) Advisory Committee, 2013 - 2014
St. Baldrick’s Foundation, 2014 - 2015
Austrian Science Fund (FWF), 2014 - 2014
NCI Subcommittee I - Transition to Independence, 2014 - 2014
Qatar National Research Fund (QNRF), 2014 - 2021
NCI Outstanding Investigator Award (R35) Special Emphasis Panel, 2015 - 2017
Pediatric Immunotherapy Discovery and Development Network (PI-DDN)/Beau Biden Cancer Moonshot Initiative, 2018 - 2023
Mechanisms of Cancer Therapeutics - 2 Study Section, NIH, 2019 - 2021
Breakthrough Cancer Research Ireland, 2020 - 2020

Web Links

Selected Publications

Modulation of CD22 protein expression in childhood leukemia by pervasive splicing aberrations: implications for CD22-directed immunotherapy

S.Zheng, E.Gillespie, Ammar S. Naqvi, K.E.Hayer, Z.Ang, M.Torres-Diz, M.Quesnel-Vallières, D.A.Hottman, A.Bagashev, J.Chukinas, C.Schmidt, M.Asnani, R.Shraim, D.M.Taylor, S.R.Rheingold, M.M.O’Brien, N.Singh, K.W.Lynch, M.Ruella, Y.Barash, S.K.Tasian, and A.Thomas-Tikhonenko, Blood Cancer Discov 3(2): 103–115, 2022, PMID:35015683

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MYC hyperactivates WNT signaling in APC/CTNNB1-mutated colorectal cancer cells through miR-92a-dependent repression of DKK3

P.Sehgal, C.Lanauze, X.Wang, K.E.Hayer, M.Torres-Diz, N.A.Leu, Y.Sela, B.Z.Stanger, C.J. Lengner, and A.Thomas-Tikhonenko, Mol Cancer Res 19(12): 2003-2014, 2021

Tilting MYC toward cancer cell death

C.T.Harrington, E.Sotillo, C.V.Dang, and A.Thomas-Tikhonenko, Trends Cancer 7(11): 982-994, 2021

RNA-binding proteins of COSMIC significance in cancer

P.S.Choi and A.Thomas-Tikhonenko, J Clin Invest 131(18): e151627, 2021

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts

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, Genome Biol 22(1): 190, 2021

MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

C.Radens, B.Slaff, P.Jewell, A.Jha, N.Lahens, G.Grant, A.Thomas-Tikhonenko, K.W.Lynch, and Y.Barash, Nat Commun 12(1): 3353, 2021

Colorectal cancer-associated Smad4 R361 hotspot mutations boost Wnt/β-catenin signaling through enhanced Smad4-LEF1 binding

C.B.Lanauze, P.Sehgal, K.Hayer, M.Torres-Diz, J.A.Pippin, S.F.A.Grant, and A.Thomas-Tikhonenko, Mol Cancer Res 19(5): 823-833, 2021, PMID:33608451

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Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

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, Leukemia 34(4): 1202–1207, 2020

IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells

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., Nature 588(): 491-497, 2020, PMID:33149299

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Transient stabilization, rather than inhibition of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma

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, Leukemia 33(10): 2429–2441, 2019

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