Recent Publications
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Lymphoma immunotherapy: the garden of forking paths
Z.Ang and A.Thomas-Tikhonenko, Blood, 143(8):655–657, 2024
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer
M.Quesnel-Vallières, S.Jewell, K.W.Lynch, A.Thomas-Tikhonenko, and Y.Barash, Nucleic Acids Res, 52(D1):D213-D221, 2024
Alternative splicing of its 5’ untranslated region controls CD20 mRNA translation and enables resistance to CD20-directed immunotherapies
Z.Ang, L.Paruzzo, K.E.Hayer, C.Schmidt, M.Torres-Diz, S.Zheng, F.Xu, U.Zankharia, Y.Zhang, S.S.Soldan, S.Zheng, C.D.Falkenstein, J.P.Loftus, S.Y.Yang, M.Asnani, P.King Sainos, V.Pillai, E.Chong, M.M.Li, S.K.Tasian, Y.Barash, P.M.Lieberman, M.Ruella,S.J.Schuster, and A.Thomas-Tikhonenko, Blood, 142(20):1724-1739, 2023
Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment
N.Li, Q.Zhu, Y.Tian, K.J.Ahn, X.Wang, Z.Cramer, I.W.Folkert, P.Yu, J.Jou, S.Adams-Tzivelekidis, P.Sehgal, N.N.Mahmoud, C.B.Aarons, R.E.Roses, A.Thomas-Tikhonenko, E.E.Furth, B.Z.Stanger, A.Rustgi, M.Haldar, B.W.Katona, K.Tan, and C.J.Lengner, Nat Commun, 14(120):7915, 2023
FBXW7ß isoform drives transcriptional activation of the proinflammatory TNF cluster in human pro-B cells
S.Y.Yang, K.E.Hayer, H.Fazelinia, L.A.Spruce, M.Asnani, K.L.Black, A.S.Naqvi, V.Pillai, Y.Barash, K.S.J.Elenitoba-Johnson, and A.Thomas-Tikhonenko, Blood Adv, 7(7):1077-1091, 2023
Discovery of antibodies targeting multipass transmembrane proteins using a suspension cell-based evolutionary approach
P.J.Krohl, J.Fine, H.Yang, D.VanDyke, Z.Ang, K.B.Kim, A.Thomas-Tikhonenko, and J.B.Spangler, Cell Rep Methods, 3(3):100429, 2023
A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers
D.Wang, M.Quesnel-Vallieres, S.Jewell, M.Elzubeir, K.Lynch, A.Thomas-Tikhonenko, and Y.Barash, Nat Commun 14(1):63, 2023
A convergent malignant phenotype in B-cell acute lymphoblastic leukemia involving the splicing factor SRRM1
A.Closa, M.Reixachs-Sole, A.C.Fuentes-Fayos, K.E.Hayer, J.L.Melero, F.R.S.Adriaanse, R.S.Bos, M.Torres-Diz, S.P.Hunger, K.G.Roberts, C.Mullighan, R.W.Stam, A.Thomas-Tikhonenko, J.P.Castano, R.M.Luque, and E.Eyras, NAR Cancer 4(4):zcac041, 2022
High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance
M.Cortés-López, L.Schulz, M.Enculescu, C.Paret, B.Spiekermann, M.Quesnel-Vallières, M.Torres-Diz, S.Unic, A.Busch, A.Orekhova, M Kuban, M.Mesitov, M.Mulorz, R.Shraim, F.Kielisch, J.Faber, Y.Barash, A.Thomas-Tikhonenko, K.Zarnack, S.Legewie, and J.König, Nat Commun 13(1):5570, 2022
Loss of AID exacerbates the malignant progression of CLL
A.C.Lee, S.R.Pingali, J.A.Pinilla-Ibarz, M.L.Atchison, C.Koumenis, Y.Argon, A.Thomas-Tikhonenko, C.De Trez, C.A.Hu, and C.A.Tang, Leukemia 36(10):2430–2442, 2022
Identifying common transcriptome signatures of cancer by interpreting deep learning modelsA.Jha, M.Quesnel-Vallières, D.Wang, A.Thomas-Tikhonenko, K.W.Lynch, and Y.Barash, Genome Biol 23(1):117, 2022
Targeting CD123 in blastic plasmacytoid dendritic cell neoplasm using allogeneic anti-CD123 CAR T cells
T.Cai, A.Gouble, K.L.Black, A.S.Naqvi, D.Taylor, M.Zhao, Q.Yuan, M.Sugita, R.Galetto, S.Filipe, A.Cavazos, L.Han, Q.Zhang, V.Kuruvilla, H.Ma, C.G.Liu, X.Liu, S.Konoplev, J.Gu, G.Tang, X.Su, G.Al-Atrash, S.Ciurea, S.S.Neelapu, A.A.Lane, H.Kantarjian, M.L.Guzman, N.Pemmaraju, J.Smith, A.Thomas-Tikhonenko, and M.Konopleva, Nat Commun 13(1):2228, 2022
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
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
B.Slaff, C.M.Radens, P.Jewell, A.Jha, N.F.Lahens, G.R.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
IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells
J.Lee, M.E.Robinson, N.Ma, D.Artadji, M.A.Ahmed, G.Xiao, T.Sadras, G.Deb, J.Winchester, K.N.Cosgun, H.Geng, L.N.Chan, K.Kume, T.P.Miettinen, Y.Zhang, M.A.Nix, L.Klemm, C.W.Chen, J.Chen, V.Khairnar, A.P.Wiita, A.Thomas-Tikhonenko, M.Farzan, J.U.Jung, D.M.Weinstock, S.R.Manalis, M.S.Diamond, N.Vaidehi, and M.Müschen, Nature 588(4):491–497, 2020
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