Publications

Key Publications

bioRxiv 2023
Coordinated inheritance of extrachromosomal DNA species in human cancer cells
Hung KL*, Jones MG*, Wong ITL*, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY (*co-first authorship)

Nature Genetics 2022
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong ITL, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, Chamorro R, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law J, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY

Nature Structural & Molecular Biology 2022
Gene regulation on extrachromosomal DNA
Hung KL, Mischel PS, Chang HY

Nature 2021
ecDNA hubs drive cooperative intermolecular oncogene expression
Hung KL*, Yost KE*, Xie L*, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY (*co-first authorship)

Molecular Therapy 2018
Engineering protein-secreting plasma cells by homology-directed repair in primary human B cells
Hung KL, Meitlis I, Hale M, Chen C, Singh S, Jackson SW, Miao CH, Khan IF, Rawlings DJ, James RG

Cover Features

All Publications

2024:

bioRxiv 2024
CoRAL accurately resolves extra-chromosomal DNA genome structures with long-read sequencing
Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong ITL, Zhang S, Mischel PS, Chang HY, Bafna V

2023:

bioRxiv 2023
Coordinated inheritance of extrachromosomal DNA species in human cancer cells
Hung KL*, Jones MG*, Wong ITL*, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY (*co-first authorship)

bioRxiv 2023
Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair
Rose JC, Wong ITL, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY

Nature Genetics 2023
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
Chapman OS, Luebeck J, Sridhar S, Wong ITL, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala M, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JEA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L

Nature Genetics 2023
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
González RC, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Garcia HD, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG

Nature Communications 2023
The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner
Gonzalez-Sandoval A, Pekrun K, Tsuji S, Zhang F, Hung KL, Chang HY, Kay MA

2022:

Nature Genetics 2022
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong ITL, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, Chamorro R, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law J, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY

Nature Structural & Molecular Biology 2022
Gene regulation on extrachromosomal DNA
Hung KL, Mischel PS, Chang HY

Nature Communications 2022
Ex vivo engineered human plasma cells exhibit robust protein secretion and long-term engraftment in vivo
Cheng RYH, Hung KL, Zhang T, Stoffers CM, Ott AR, Suchland ER, Camp ND, Khan IF, Singh S, Yang YJ, Rawlings DJ, James RG

Nature Genetics 2022
The evolutionary dynamics of extrachromosomal DNA in human cancers
Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS

Cancer Discovery 2022
Oncogene convergence in extrachromosomal DNA hubs
Weiser NE, Hung KL, Chang HY

2021:

Nature 2021
ecDNA hubs drive cooperative intermolecular oncogene expression
Hung KL*, Yost KE*, Xie L*, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY (*co-first authorship)

Cell 2021
Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing
Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS

Cancer Discovery 2021
A functional taxonomy of tumor suppression in oncogenic KRAS-driven lung cancer
Cai H, Chew SK, Li C, Tsai MK, Andrejka L, Murray CW, Hughes NW, Shuldiner EG, Ashkin EL, Tang R, Hung KL, Chen LC, Lee SYC, Yousefi M, Lin WY, Kunder CA, Cong L, McFarland CD, Petrov DA, Swanton C, Winslow MM

2018 and earlier:

Molecular Therapy 2018
Engineering protein-secreting plasma cells by homology-directed repair in primary human B cells
Hung KL, Meitlis I, Hale M, Chen C, Singh S, Jackson SW, Miao CH, Khan IF, Rawlings DJ, James RG

Development 2015
Wnt signaling and tbx16 form a bistable switch to commit bipotential progenitors to mesoderm
Bouldin CM, Manning AJ, Peng YH, Farr GH III, Hung KL, Dong A, Kimelman D