Peter Ly Lab | Papers

PUBLICATIONS

Featured Publications:

The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance
Engel JL, Zhang X, Wu M, Wang Y, Espejo Valle-Inclán J, Hu Q, Woldehawariat K, Sanders MA, Smorgorzewska A, Chen J, Cortés-Ciriano I, Lo RS, and Ly P

Cell 187:6055-6070 (2024)

Nature Reviews Cancer Research Highlight: Fanconi anaemia pathway induces chromosome shattering
Cancer Discovery Research Watch: The Fanconi anemia pathway mediates chromothripsis and resistance to therapy

Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors

Hu Q, Espejo Valle-Inclán J, Dahiya R, Guyer A, Mazzagatti A, Maurais EG, Engel JL, Lu H, Davis AJ, Cortés-Ciriano I, and Ly P

Nature Communications 15:5611 (2024)

Boveri and beyond: Chromothripsis and genomic instability from mitotic errors

Mazzagatti A, Engel JL, and Ly P

Molecular Cell 84:55-69 (2024)

Mitotic clustering of pulverized chromosomes from micronuclei

Lin YF, Hu Q, Mazzagatti A, Espejo Valle-Inclán J, Maurais EG, Guyer A, Sanders JT, Engel JL, Nguyen GC, Bronder D, Bakhoum SF, Cortés-Ciriano I, and Ly P

Nature 618:1041-1048 (2023)

Nature News and Views: A mitotic glue for shattered chromosomes
Molecular Cell Spotlight: CIP2A and TOPBP1: Molecular lassos that herd pulverized micronuclear chromosomes

Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements

Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, and Cleveland DW

Nature Genetics 51:705-715 (2019)

Rebuilding chromosomes after catastrophe: emerging mechanisms of chromothripsis

Ly P and Cleveland DW

Trends in Cell Biology 27:917-930 (2017)

Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining

Ly P, Teitz LS, Kim DH, Shoshani O, Skaletsky H, Fachinetti D, Page DC, and Cleveland DW

Nature Cell Biology 19:68-75 (2017)

Nature Cell Biology News and Views: Y chromothripsis?

All Publications:

TASOR expression in naive embryonic stem cells safeguards their developmental potential

Pinzon-Arteaga CA, O’Hara R, Mazzagatti A, Ballard E, Hu Y, Pan A, Schmitz DA, Wei Y, Sakurai M, Ly P, Banaszynski LA, and Wu J

Cell Reports 43:114887 (2024)

A p62-dependent rheostat dictates micronuclei catastrophe and chromosome rearrangements

Martin S, Scorzoni S, Cordone S, Mazzagatti A, Beznoussenko GV, Gunn AL, Di Bona M, Eliezer Y, Leor G, Ben-Yishay T, Loffreda A, Cancila V, Chiara Rainone M, Rosaria Ippolito M, Martis V, Bedin F, Garre M, Vaites Pontano L, Vasapolli P, Polo S, Parazzoli D, Tripodo C, Mironov AA, Cuomo A, Ben-David U, Bakhoum SF, Hatch EM, Ly P, and Santaguida S

Science 385:eadj7446 (2024)

Micronuclear collapse from oxidative damage

Di Bona M, Chen Y, Agustinus AS, Mazzagatti A, Duran MA, Deyell M, Bronder D, Hickling J, Hong C, Scipioni L, Tedeschi G, Martin S, Li J, Ruzgaite A, Riaz N, Shah P, D’Souza EK, Zack Brodtman D, Sidoli S, Diplas B, Jalan M, Lee NY, Ordureau A, Izar B, Laughney AM, Powell S, Gratton E, Santaguida S, Maciejowski J, Ly P, Jeitner TM, and Bakhoum SF

Science 385:eadj8691 (2024)

Induction of chromosome-specific micronuclei and chromothripsis by centromere inactivation

Lin YF, Hu Q, Guyer A, Fachinetti D, and Ly P

Methods in Cell Biology 182:1-20 (2024)

SETD2 safeguards the genome against isochromosome formation

Mason FM, Kounlavong ES, Tebeje AT, Dahiya R, Vlach L, Guess T, Khan A, Vlach L, Norris SR, Lovejoy CA, Dere R, Strahl BD, Ohi R, Ly P, Walker CL, and Rathmell WK

PNAS 120:e2303752120 (2023)

Epigenetic dysregulation from chromosomal transit in micronuclei

Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, and Bakhoum SF

Nature 619:176-183 (2023)

Light-activated macromolecular phase separation modulates transcription by reconfiguring chromatin interactions

Kim YJ, Jing J, Lee M, Lee YT, Sanders JT, Botten GA, He L, Lyu J, Zhang Y, Mettlen M, Ly P, Zhou Y, and Xu J

Science Advances 9:eadg1123 (2023)

Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription

Botten GA, Zhang Y, Dudnyk K, Kim YJ, Liu X, Sanders JT, Imanci A, Droin NM, Cao H, Kaphle P, Dickerson KE, Chen M, Kumar KR, Chen M, Chen W, Solary E, Ly P, Zhou J, and Xu J

Blood 142:336-351 (2023)

Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cell types

Mahlke MA, Lumerman L, Ly P, and Nechemia-Arbely Y

Life Science Alliance 6:e202201801 (2023)

De novo pyrimidine synthesis is a targetable vulnerability in IDH-mutant gliomas

Shi DD, Savani MR, Levitt MM, Wang AC, Endress JE, Bird CE, Buehler J, Stopka S, Regan MS, Lin YF, Puliyappadamba VT, Gao W, Khanal J, Evans L, Lee JH, Guo L, Xiao Y, Xu M, Huang B, Jennings RB, Bonal DM, Martin-Sandoval MS, Dang T, Gattie LC, Cameron AB, Lee S, Asara JM, Kornblum HI, Mak TW, Looper RE, Nguyen Q-D, Signoretti S, Gradl S, Sutter A, Jeffers M, Janzer A, Lehrman MA, Zacharias LG, Mathews TP, Losman JA, Richardson TE, Cahill DP, DeBerardinis RJ, Ligon KL, Xu L, Ly P, Agar NYR, Abdullah KG, Harris IS, Kaelin WGJ, and McBrayer SK

Cancer Cell 40:939-956 (2022)

Restoration of DNA repair mitigates genome instability and increases productivity of Chinese hamster ovary cells

Spahn PN, Zhang X, Hu Q, Lu H, Hamaker NK, Hefzi H, Li S, Kuo CC, Huang H, Lee JC, Davis AJ, Ly P, Lee KH, and Lewis NE

Biotechnology and Bioengineering 119:963-982 (2022)

Mechanistic origins of diverse genome rearrangements in cancer

Dahiya R, Hu Q, and Ly P

Seminars in Cell and Developmental Biology 123:100-109 (2022)

Chromothripsis drives the evolution of gene amplification in cancer

Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JS, Sun Y, Ellisman MH, Ren B, Campbell PJ, and Cleveland DW

Nature 591:137-141 (2021)

A POLE P286R mouse model of endometrial cancer recapitulates high mutational burden and immunotherapy response

Li HD, Li C, Zhang H, Hu Q, Zhang J, Cuevas IC, Sahoo SS, Aguilar M, Maurais EG, Zhang S, Wang X, Akbay EA, Li GM, Li B, Koduru P, Ly P, Fu YX, and Castrillon DH

Journal of Clinical Investigation Insight 5:138829 (2020)

Cellular and genomic approaches for exploring structural chromosomal rearrangements

Hu Q, Maurais EG, and Ly P

Chromosome Research 28:19-30 (2020)

TRIP13 and APC15 drive mitotic exit by turnover of interphase- and unattached kinetochore-produced MCC

Kim DH, Han JS, Ly P, Ye Q, McMahon M, Myung KJ, Corbett KD, and Cleveland DW

Nature Communications 9:4354 (2018)

Chromosomal instability drives metastasis through a cytosolic DNA response

Bakhoum SF, Ngo B, Laughney AM, Cavallo JA, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK, Duran M, Pauli C, Shaw C, Chadalavada K, Rajasekhar VK, Genovese G, Venkatesan S, Birkbak NJ, McGranahan N, Lundquist M, LaPlant Q, Healey JH, Elemento O, Chung CH, Lee NY, Imielenski M, Nanjangud G, Pe’er D, Cleveland DW, Powell SN, Lammerding J, Swanton C, and Cantley LC

Nature 553:467-472 (2018)

Interrogating cell division errors using random and chromosome-specific missegregation approaches

Ly P and Cleveland DW

Cell Cycle 16:1252-1258 (2017)

CENP-A is dispensable for mitotic centromere function after initial centromere/kinetochore assembly

Hoffmann S, Dumont M, Barra V, Ly P, Nechemia-Arbely Y, McMahon MA, Hervé S, Cleveland DW, and Fachinetti D

Cell Reports 17:2394-2404 (2016)

MYC is a major determinant of mitotic cell fate

Topham C, Tighe A, Ly P, Bennett A, Sloss O, Nelson L, Ridgway RA, Huels D, Littler S, Schandl C, Sun Y, Bechi B, Procter DJ, Sansom OJ, Cleveland DW, and Taylor SS

Cancer Cell 28:129-140 (2015)

DNA sequence-specific binding of CENP-B enhances the fidelity of human centromere function

Fachinetti D, Han JS, McMahon MA, Ly P, Abdullah A, Wong AJ, and Cleveland DW

Developmental Cell 33:314-327 (2015)

Cavin-3 dictates the balance between ERK and Akt signaling

Hernandez VJ, Weng J, Ly P, Pompey S, Dong H, Mishra L, Schwarz MA, Anderson RG, and Michaely P

eLife 2:e00905 (2013)

Aneuploid human colonic epithelial cells are sensitive to AICAR-induced growth inhibition through EGFR degradation

Ly P, Kim SB, Kaisani AA, Marian G, Wright WE, and Shay JW

Oncogene 32:3139-3146 (2013)

Mitigation of radiation-induced damage by targeting EGFR in noncancerous human epithelial cells

Kim SB, Ly P, Kaisani AA, Zhang L, Wright WE, and Shay JW