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Research articles / Review  

2023

Liu B#, Dong X#, Zheng C#, et al, Xue W*, Sontheimer E*. (2023) Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nature Biotechnology, https://doi.org/10.1038/s41587-023-01947-w

Zheng C#, Liu B#, et. al, Sontheimer E*, Xue W*. (2023) Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nature Comms, 14: 3369 

Shun-Qing Liang#, Pengpeng Liu#,*, et al, Sontheimer E, Xue W*, Wolfe S*. (2023) Genome-wide Profiling of Prime editor off-target sites in vitro and in vivo using PE-tag. Nature Methods. doi.org/10.1038/s41592-023-01859-2

Bowen Li#, Manan Singh#, Shunqing Liang#, et al, Gao G, Langer R, Xue W*, Anderson D*. (2023) Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing. Nature Biotechnology doi.org/10.1038/s41587-023-01679-x

2022

Rodriguez T*, Kwan SY*, Smith J*, et al, Sontheimer E#, Xue W#. (2022) Multi-omics characterization of mouse hepatoblastoma identifies novel Yap1 target genes. Hepatology, doi.org/10.1002/hep.32713

Liu B*, Dong X*, Cheng H, et al, Wen Xue#, Erik Sontheimer#. (2022) A split prime editor with untethered reverse transcriptase and circular RNA template. Nature Biotechnology, 40, 1388–1393 

Lee J, Kennedy Z, et al, Xue W, Brown R. (2022) Imaging Net Retrograde Axonal Transport In Vivo: A Physiological Biomarker. Annals of Neurology 91:716-729

Han Zhang, Nathan Bamidele, et al, Scot Wolfe, Wen Xue, and Erik Sontheimer. (2022) Single AAV delivered Nme2Cas9 adenine base editor corrects the disease mutation and phenotype in an adult mouse model of Tyrosinemia. GEN Biotechnology. 1:3

Liang S*, Liu P*, et al, Wolfe SA#, Wen Xue#. (2022) Genome-wide Detection of CRISPR editing in vivo using GUIDE-tag. Nature Comms. 13: 437

Zheng C, Liang S, Liu B, et al, Wolfe SA, Wen Xue#. (2022) A flexible split prime editor using truncated reverse transcriptase improves dual AAV delivery in mouse liver. Molecular Therapy, 30: 1343-1351

Shun-Qing Liang, Christopher Walkey, et al, William Lagor, Jason Heaney, Guangping Gao#, Wen Xue#. (2022) AAV5 delivery of CRISPR/Cas9 supports effective genome editing in mouse lung airway. Molecular Therapy. 30: 238-243

Jiang T, Zhang XO, Weng Z, Xue W#. (2022) Deletion and replacement of long genomic sequences using prime editing. Nature Biotechnology, 40, 227–234

2021

Raed Ibraheim, Phillip Tai, et al, Xue W, Gao G, Sontheimer EJ#. (2021) Self-inactivating, All-in-one AAV Vectors for Precision Cas9 Genome Editing via Homology-Directed Repair in vivo. Nature Comms. 12: 6267

Liu H, Pedros C, Kong K, et al, Xue W and Altman A. (2021) Leveraging the Treg-intrinsic CTLA4–PKCη signaling pathway for cancer immunotherapy. Journal for ImmunoTherapy of Cancer 9:e002792

Saha K, Sontheimer EJ, the SCGE Consortium. (2021) The NIH Somatic Cell Genome Editing program.  Nature 592: 195–204

Pengpeng Liu*, Shun-Qing Liang*, Chunwei Zheng, et al, Terence Flotte, Scot Wolfe#, Wen Xue#. (2021) Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat Comms.12: 2121 (PMID: 33837189)

Jiang T, Sánchez-Rivera F, et al, and Xue W#. (2021) Targeting de novo purine synthesis pathway via ADSL depletion impairs liver cancer growth by perturbing mitochondrial function. Hepatology, 74: 233-247. (PMID: 33336367)

2020

Smith J., Rodríguez T., Mou, H., Kwan, S-Y., Pratt, H., Zhang, X-O., Cao, Y., Liang, S., Ozata, D. M., Yu, T., Yin, Q., Hazeltine, M., Weng, Z., Sontheimer E. J., Xue, W#. (2020) YAP1 withdrawal in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte-like cells. Hepatology, 73: 1011-1027 (PMID: 32452550)

Jiang T., Henderson, J. M., Coote, K., Cheng, Y., Valley, H. C., Xhang, X-O., Wang, Q., Rhym, L. H., Cao, Y., Newby, G. A., Bihler, H., Mense, M., Weng, Z., Anderson, D. G., McCaffrey, A. P., Liu, D. R., Xue W#. (2020) Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. Nature Communications. 2020 11:1979 (PMID: 32332735)

Zhang, P., Zhang X-O., Jiang, T., Cai, L., Huang, X., Liu, Q., Li, D., Lu, A., Liu, Y., Xue, W., Zhang, P., Weng, Z. (2020) Comprehensive identification of alternative back-splicing in human tissue transcriptomes. Nucleic Acids Research. 2020 48(4):1779-1789.  (PMID: 31974555)

Song, C-Q.*, Jiang, T.*, Richter, M., Rhym, L. H., Koblan, L. W., Zafra, M. P., Schatoff, E. M., Doman, J. L., Cao, Y., Dow, L. E., Zhu, L. J., Anderson, D. G., Liu, D#, Yin, H#., Xue, W#. Adenine base editing in an adult mouse model of tyrosinemia. Nature Biomedical Engineering. 2020 4:125-130 (PMID: 31740768)

2019

Lee, J., Mou, H., Ibraheim, R., Liang, S-Q., Liu, P., Xue, W, Sontheimer, E.J. Tissue-specific Genome Editing in vivo by MicroRNA-repressible Anti-CRISPR Proteins. RNA. 2019. (PMID:31439808)

Elaimy, A. L., Wang, M., Sheel, A., Brown, C. W., Walker, M. R., Amante, J. J., Xue, W., Chan, A., Baer, C. E., Goel, H. L., Mercurio, A. M. Real-time imaging of integrin β4 dynamics using a reporter cell line generated by Crispr/Cas9 genome editing. Journal of Cell Science. 2019. (PMID: 31262785)

Kwan, S-Y.*, Sheel, A.*, Song, C-Q., Zhang, X-O., Jiang, T., Dang, H., Cao, Y., Ozata, D. M., Mou, H., Yin, H., Weng, Z., Wang, X. W., Xue, W#. Depletion of TRRAP induces p53-independent senescence in liver cancer by downregulating mitotic genes. Hepatology 2019. (PMID: 31188495)

Mou, H.*, Ozata*, D. M., Smith, J. L.*, Sheel, A.,  Kwan, S-Y., Hough, S., Kucukural, A., Kennedy, Z., Cao, Y., Xue, W#. CRISPR-SONIC: targeted somatic oncogene knock-in enables rapid in vivo cancer modeling. Genome Medicine 2019. (PMID: 30987660)

Wang, W., Yang, J., Edin, M. L., Wang, Y., Luo, Y., Wan, D., Yang, H., Song, C-Q., Xue, W., et al, Zeldin, D. C., Zhang, G. Targeted metabolomics identifies the cytochrome P450 monooxygenase eicosanoid pathway as a novel therapeutic target of colon tumorigenesis. Cancer Res. 2019. (PMID: 30803995)

Edraki, A., Mir, A., Ibraheim, R., Gainetdinov, I., Yoon, Y., Song, C-Q., Cao, Y., Gallant, J., Xue, W., Rivera-Pérez, J. A., Sontheimer, E. J. A Compact, High-Accuracy Cas9 with a Dinucleotide PAM for In Vivo Genome Editing. Molecular Cell. 2019 (PMID: 30581144)

Moon, S-H., Huang, C-H., Houlihan, S. L., Regunath, K., Freed-Pastor, W. A., Morris IV, J. P., Tschaharganeh, D. F., Kastenhuber, E. R., Barsotti, A. M., Culp-Hill, R., Xue, W., Ho, Y-J., Baslan, T., Li, X., Mayle, A., de Stanchina, E., Zender, L., Tong, D. R., D'Alessandro, A., Lowe, S. W., Prives, C. Represses the Mevalonate Pathway to Mediate Tumor Suppression. Cell. 2019 (PMID: 30580964)

2018

Ibraheim, R., Song, C-Q., Mir, A., Amrani, N., Xue, W., Sontheimer, E. J. All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo. Genome Biology 2018 (PMID: 30231914)

Zhang, X-O., Fu, Y., Mou, H., Xue, W., Weng, Z. The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. PLoS Genet. 2018 (PMID: 30148885)

Dan Wang, Jia Li, Chun-Qing Song, Karen Tran, et al, Phillip D. Zamore#, Wen Xue#, Guangping Gao#. Repairing Recessive Compound Heterozygous Mutations In Vivo Via Cas9-Mediated Allelic Exchange. Nat Biotechnology. 2018 36:839–842 Link

37. Song C-Q, Wang D, Jiang T, et al, Terence R#, Xue W#. in vivo genome editing partially restores alpha1-antitrypsin in a murine model of AAT deficiency. Human Gene Therapy. 2018 29(8):853-860 Link

36. Yin H*, Song C-Q*, et al, Xue W#, Langer R#, Anderson DG#. Partial DNA-guided Cas9 enables efficient genome editing with reduced off-target activity. Nature Chemical Biology 2018 14: 311–316 Link

2017

35. Yin H, Song C-Q, et al, Xue W, Langer R, Anderson DG. Structure-guided chemical modification of guide RNA enables potent non-viral Cas9-mediated genome editing in vivo. Nat Biotechnology. 2017. 35:1179-1187 Link

34. Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW. Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma. Cancer Cell 2017 32:101-114. Link 

33. Mou H*, Smith J*, et al, Moore M#, Weng Z#, Xue W#. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biology 2017. 18:108 

32. Tammela T, Sanchez-Rivera, et al., Xue W, Katajisto P, Bhutkar A, & Jacks T. (2017). A Wnt-producing niche drives proliferative potential and progression in lung adenocarcinoma. Nature 2017. 545:355-359 

31. Mou H*, Moore J*, Malonia SK*, Li Y, Ozata DM, Hough S, Song CQ, Smith JL, Fischer A, Weng Z, Green MR#, Xue W#. Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis. PNAS 2017. 114(14):3648-3653 

30. Song C-Q*, Li Y*, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte Jr D, Zender L, Wang XW, Thorgeirsson S, Weng Z#, Xue W#. Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice. Gastroenterology. 2017. 152(5):1161-1173.e1  

2016

29. Akama-Garren E, Joshi N, Tammela T, Chang G, Wagner B, Lee D, Rideout W, Papagiannakopoulos T, Xue W, and Jacks T. "A Modular Assembly Platform for Rapid Generation of DNA Constructs". Scientific Reports. 2016. 6:16836 Link

28. Yin H, Song C, Dorkin JR,..., Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, Xue W#, Anderson DG#. "Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components to the mouse liver". Nat Biotechnology. 2016. 34: 328-333 Link   PDF 

27. Yin H, Bogorad RL, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, et al, Anderson DG. "Control of liver size by RNAi-mediated multiplex knockdown and its application for discovery of regulatory mechanisms". J Hepatology, 2016 64:899-907. Link

2015

26. Wang D*, Mou H*, Li SY*, Li Y, Hough S, Tran K, Li J, Yin H, Anderson DG, Sontheimer EJ, Weng Z#, Gao G#, Xue W#. "Adenovirus-mediated somatic genome editing of Pten by CRISPR/Cas9 in mouse liver in spite of Cas9-specific immune responses". Human Gene Therapy. 26:432-42. (2015) (# co-corresponding) Link

25. Li Y*, Park A*, Mou H*, Colpan C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng Z#, Xue W#. "A versatile reporter system for CRISPR-mediated chromosomal rearrangements". Genome Biology. 16(1):111. (2015) Link

24. Khan OF, Zaia EW, Jhunjhunwala S, Xue W, Cai W, Yun DS, Barnes C, Dahlman JE, Dong Y, Pelet JM, Webber MJ, Tsosie J, Jacks T, Langer R, Anderson DG. Dendrimer-inspired nanomaterials for the in vivo delivery of siRNA to lung vasculature. Nano Lett. 2015 Mar 19. Link

  • 23. Li J, Chanrion M, Sawey E, Wang T, Chow E, Tward A, Su Y, Xue W, Lucito R, Zender L, Lowe SW, Bishop JM, Powers S. Reciprocal Interaction of Wnt and RXR-α Pathways in Hepatocyte Development and Hepatocellular Carcinoma. PLoS One. 10(3):e0118480. (2015)

2014

  1. Sánchez-Rivera FJ, Papagiannakopoulos T, Romero R, Tammela T, Bauer MR, Bhutkar A, Joshi NS, Subbaraj L, Bronson RT, Xue W, Jacks T. Rapid modelling of cooperating   genetic events in cancer through somatic genome editing. Nature. 2014 doi: 10.1038/nature13906. Link

  2. Xue W*, Chen S*, Yin H*, Anderson D, Sharp PA, Jacks T, et al. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature. 2014 514:380-4.  Link

  3. Tschaharganeh D, Xue W, Lowe SW, et al. p53-dependent Nestin regulation couples tumor suppressive functions and cell fate decisions in liver cancer. Cell. 2014. 158(3):579-92. Link

  4. Xue W*, Dahlman J*, Anderson D, Jacks T, et al. Small RNA combination therapy for lung cancer. Proc Natl Acad Sci U S A. 2014 111(34):E3553-61. Link

  5. Shao D*, Xue W*, Jacks T, Hahn W, et al. KRAS and YAP1 converge to regulate EMT and tumor survival. Cell. 2014 158(1):171-84. Link

  6. Yin H*, Xue W*, Sharp PA, Jacks T, Anderson D, et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014 32(6):551-3. Link

2012

  1. Xue W*, Kitzing T*, Roessler S, Zuber J, Lowe SW, et al.A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions.Proc Natl Acad Sci U S A . 2012 109(21):8212-7. Link

2011

  1. Xue W, Meylan E, Oliver TG, Feldser DM, Winslow MM, Bronson R, Jacks T. Response and resistance to NF-κB inhibitors in mouse models of lung adenocarcinoma. Cancer Discovery. 2011 1(3):236-247. Link

  2. Oliver TG, Meylan E, Chang GP, Xue W, Burke JR, Humpton TJ, Hubbard D, Bhutkar A, Jacks T. Caspase-2-Mediated Cleavage of Mdm2 Creates a p53-Induced Positive Feedback Loop. Mol Cell. 2011 43(1):57-71. Link

2002-2009

  1. Liu LX, Lee NP, Chan VW, Xue W, et al. Targeting cadherin-17 inactivates Wnt signaling and inhibits tumor growth in liver carcinoma. Hepatology. 2009 50(5):1453-63. Link

  2. Krizhanovsky V, Xue W, Zender L, Yon M, Hernando E, AND Lowe S.W. Implications of Cellular Senescence in Tissue Damage Response, Tumor uppression, and Stem Cell Biology. Cold Spring Harb Symp Quant Biol. 2008 73:513-22. Link

  3. Gyrd-Hansen M, Darding M, Miasari M, Santoro MM, Zender L, Xue W, Tenev T, et al. IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis. Nat Cell Biol. 2008 10:1309-17. Link

  4. Burgess DJ, Doles J, Zender L, Xue W, Ma B, Lowe SW, et al. Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A. 2008 105:9053-8. Link

  5. Zender L*, Xue W*, Zuber J, Semighini C, Lowe SW, et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell, 2008 135:852-64. Link

  6. Xue W, Krasnitz A, Lucito R, Sordella R, Vanaelst L, Cordon-Cardo C, Singer S, Kuehnel F, Wigler M, Powers S, Zender L, Lowe SW. DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma. Genes Dev. 2008 22:1439-44. Link

  7. He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, et al. A microRNA component of the p53 tumour suppressor network. Nature. 2007 447:1130-4. Link

  8. Xue W*, Zender L*, Miething C, Dickins RA, Hernando E, Krizhanovsky V, Cordon-Cardo C, Lowe SW. Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas. Nature. 2007 445:656-60. Link

  9. Lakshmi B, Hall IM, Egan C, Alexander J, Leotta A, Healy J, Zender L, Spector MS, Xue W, Lowe SW, Wigler M, Lucito R. Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A. 2006 103:11234-9. Link

  10. Zender L, Spector MS, Xue W, Lowe SW, et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell. 2006 125:1253-67. Link

  11. Zender L, Xue W, Lowe SW, et al. Generation and analysis of genetically defined liver carcinomas derived from bipotential liver progenitors. Cold Spring Harb Symp Quant Biol. 2005 70:251-61 Link

  12. Xue W, Wang J, et al. Enrichment of Transcriptional Regulatory Sites in the non-coding genomic region. Bioinformatics, 2004, 20: 569-575. Link

  13. Xue W, Wang J, et al. Synergistic Activation of Eukaryotic Gene Transcription by Multiple Upstream Sites. Prog Biochem Biophys, 2002, 29: 510-513. Link

Reviews and editorial (# corresponding)

7. Wu S*, Li Q*, Yin C, Xue W#, Song CQ#. Advances in CRISPR/Cas-based Gene Therapy in Human Genetic Diseases. Theranostics, 2020 10:4374-4382 Link

6. Yin H#, Xue W#, and Anderson DG#. CRISPR–Cas: a tool for cancer research and therapeutics. Nature Reviews Clinical Oncology  2019 16:281-295 Link

5. Smith JL, Mou H and Xue W#. Understanding and repurposing CRISPR-mediated alternative splicing. Genome Biology 2018 19:184 Link

4. Song C-Q, Xue W#. CRISPR–Cas-related technologies in basic and translational liver research. Nature Reviews Gastroenterology & Hepatology. 2018 15:251-252 Link

3. Ankur Sheel and Xue W#. Genomic amplifications cause false positives in CRISPR screens. Cancer Discovery. 2016 6; 824 ("in the spotlight" article).

2. Xue W#, Wang XW#. The search for precision models clinically relevant to human liver cancer. Hepatic Oncology. 2015 2: 315-319 (Editorial). Link

1. Mou H, Kennedy Z, Anderson DG, Yin H#, and Xue W#. Precision cancer mouse models through genome editing with CRISPR-Cas9. Genome Medicine, 7(1):53 (2015) Link