1
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O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Res 2022; 82:3950-3961. [PMID: 36273492 PMCID: PMC9633439 DOI: 10.1158/0008-5472.can-21-4335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/20/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Abstract
Over one million cases of gastric cancer are diagnosed each year globally, and the metastatic disease continues to have a poor prognosis. A significant proportion of gastric tumors have defects in the DNA damage response pathway, creating therapeutic opportunities through synthetic lethal approaches. Several small-molecule inhibitors of ATR, a key regulator of the DNA damage response, are now in clinical development as targeted agents for gastric cancer. Here, we performed a large-scale CRISPR interference screen to discover genetic determinants of response and resistance to ATR inhibitors (ATRi) in gastric cancer cells. Among the top hits identified as mediators of ATRi response were UPF2 and other components of the nonsense-mediated decay (NMD) pathway. Loss of UPF2 caused ATRi resistance across multiple gastric cancer cell lines. Global proteomic, phosphoproteomic, and transcriptional profiling experiments revealed that cell-cycle progression and DNA damage responses were altered in UPF2-mutant cells. Further studies demonstrated that UPF2-depleted cells failed to accumulate in G1 following treatment with ATRi. UPF2 loss also reduced transcription–replication collisions, which has previously been associated with ATRi response, thereby suggesting a possible mechanism of resistance. Our results uncover a novel role for NMD factors in modulating response to ATRi in gastric cancer, highlighting a previously unknown mechanism of resistance that may inform the clinical use of these drugs.
Significance:
Loss of NMD proteins promotes resistance to ATR inhibitors in gastric cancer cells, which may provide a combination of therapeutic targets and biomarkers to improve the clinical utility of these drugs.
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Affiliation(s)
- Patrick C. O'Leary
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Huadong Chen
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Yagmur U. Doruk
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Tess Williamson
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Benjamin Polacco
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Andrew S. McNeal
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Tanushree Shenoy
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Nupura Kale
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Julia Carnevale
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
| | - Erica Stevenson
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - David A. Quigley
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 6Department of Urology, University of California San Francisco, San Francisco, California
- 7Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
| | - Felix Y. Feng
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 6Department of Urology, University of California San Francisco, San Francisco, California
- 8Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Danielle L. Swaney
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Nevan J. Krogan
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Minkyu Kim
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Morgan E. Diolaiti
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Alan Ashworth
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
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2
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McNeal AS, Belote RL, Zeng H, Urquijo M, Barker K, Torres R, Curtin M, Shain AH, Andtbacka RHI, Holmen S, Lum DH, McCalmont TH, VanBrocklin MW, Grossman D, Wei ML, Lang UE, Judson-Torres RL. BRAF V600E induces reversible mitotic arrest in human melanocytes via microrna-mediated suppression of AURKB. eLife 2021; 10:e70385. [PMID: 34812139 PMCID: PMC8610417 DOI: 10.7554/elife.70385] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/12/2021] [Indexed: 12/22/2022] Open
Abstract
Benign melanocytic nevi frequently emerge when an acquired BRAFV600E mutation triggers unchecked proliferation and subsequent arrest in melanocytes. Recent observations have challenged the role of oncogene-induced senescence in melanocytic nevus formation, necessitating investigations into alternative mechanisms for the establishment and maintenance of proliferation arrest in nevi. We compared the transcriptomes of melanocytes from healthy human skin, nevi, and melanomas arising from nevi and identified a set of microRNAs as highly expressed nevus-enriched transcripts. Two of these microRNAs-MIR211-5p and MIR328-3p-induced mitotic failure, genome duplication, and proliferation arrest in human melanocytes through convergent targeting of AURKB. We demonstrate that BRAFV600E induces a similar proliferation arrest in primary human melanocytes that is both reversible and conditional. Specifically, BRAFV600E expression stimulates either arrest or proliferation depending on the differentiation state of the melanocyte. We report genome duplication in human melanocytic nevi, reciprocal expression of AURKB and microRNAs in nevi and melanomas, and rescue of arrested human nevus cells with AURKB expression. Taken together, our data describe an alternative molecular mechanism for melanocytic nevus formation that is congruent with both experimental and clinical observations.
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Affiliation(s)
- Andrew S McNeal
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Hanlin Zeng
- Huntsman Cancer Inst.Salt Lake CityUnited States
| | | | | | - Rodrigo Torres
- University of California, San FranciscoSan FranciscoUnited States
| | | | - A Hunter Shain
- University of California, San FranciscoSan FranciscoUnited States
| | - Robert HI Andtbacka
- Huntsman Cancer Inst.Salt Lake CityUnited States
- University of UtahSalt Lake CityUnited States
| | - Sheri Holmen
- Huntsman Cancer Inst.Salt Lake CityUnited States
- University of UtahSalt Lake CityUnited States
| | - David H Lum
- Huntsman Cancer Inst.Salt Lake CityUnited States
| | | | - Matt W VanBrocklin
- Huntsman Cancer Inst.Salt Lake CityUnited States
- University of UtahSalt Lake CityUnited States
| | - Douglas Grossman
- Huntsman Cancer Inst.Salt Lake CityUnited States
- University of UtahSalt Lake CityUnited States
| | - Maria L Wei
- University of California, San FranciscoSan FranciscoUnited States
| | - Ursula E Lang
- University of California, San FranciscoSan FranciscoUnited States
| | - Robert L Judson-Torres
- Huntsman Cancer Inst.Salt Lake CityUnited States
- University of UtahSalt Lake CityUnited States
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3
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Tang J, Fewings E, Chang D, Zeng H, Liu S, Jorapur A, Belote RL, McNeal AS, Tan TM, Yeh I, Arron ST, Judson-Torres RL, Bastian BC, Shain AH. The genomic landscapes of individual melanocytes from human skin. Nature 2020; 586:600-605. [PMID: 33029006 PMCID: PMC7581540 DOI: 10.1038/s41586-020-2785-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/03/2020] [Indexed: 01/13/2023]
Abstract
Every cell in the human body has a unique set of somatic mutations, yet it remains difficult to comprehensively genotype an individual cell1. Here, we developed solutions to overcome this obstacle in the context of normal human skin, thus offering the first glimpse into the genomic landscapes of individual melanocytes from human skin. As expected, sun-shielded melanocytes had fewer mutations than sun-exposed melanocytes. However, within sun-exposed sites, melanocytes on chronically sun-exposed skin (e.g. the face) displayed a lower mutation burden than melanocytes on intermittently sun-exposed skin (e.g. the back). Melanocytes located adjacent to a skin cancer had higher mutation burdens than melanocytes from donors without skin cancer, implying that the mutation burden of normal skin can be harnessed to measure cumulative sun damage and skin cancer risk. Moreover, melanocytes from healthy skin commonly harbor pathogenic mutations, though these mutations tended to be weakly oncogenic, likely explaining why they did not give rise to discernible lesions. Phylogenetic analyses identified groups of related melanocytes, suggesting that melanocytes spread throughout skin as fields of clonally related cells, invisible to the naked eye. Overall, our study offers an unprecedented view into the genomic landscapes of individual melanocytes, revealing key insights into the causes and origins of melanoma.
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Affiliation(s)
- Jessica Tang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Eleanor Fewings
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hanlin Zeng
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Shanshan Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aparna Jorapur
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rachel L Belote
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Andrew S McNeal
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tuyet M Tan
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sarah T Arron
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert L Judson-Torres
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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4
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Zeng H, Jorapur A, Shain AH, Lang UE, Torres R, Zhang Y, McNeal AS, Botton T, Lin J, Donne M, Bastian IN, Yu R, North JP, Pincus L, Ruben BS, Joseph NM, Yeh I, Bastian BC, Judson RL. Bi-allelic Loss of CDKN2A Initiates Melanoma Invasion via BRN2 Activation. Cancer Cell 2018; 34:56-68.e9. [PMID: 29990501 PMCID: PMC6084788 DOI: 10.1016/j.ccell.2018.05.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 02/12/2018] [Accepted: 05/30/2018] [Indexed: 02/03/2023]
Abstract
Loss of the CDKN2A tumor suppressor is associated with melanoma metastasis, but the mechanisms connecting the phenomena are unknown. Using CRISPR-Cas9 to engineer a cellular model of melanoma initiation from primary human melanocytes, we discovered that a lineage-restricted transcription factor, BRN2, is downstream of CDKN2A and directly regulated by E2F1. In a cohort of melanocytic tumors that capture distinct progression stages, we observed that CDKN2A loss coincides with both the onset of invasive behavior and increased BRN2 expression. Loss of the CDKN2A protein product p16INK4A permitted metastatic dissemination of human melanoma lines in mice, a phenotype rescued by inhibition of BRN2. These results demonstrate a mechanism by which CDKN2A suppresses the initiation of melanoma invasion through inhibition of BRN2.
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Affiliation(s)
- Hanlin Zeng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Aparna Jorapur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - A Hunter Shain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Ursula E Lang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Rodrigo Torres
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Yuntian Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Andrew S McNeal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Thomas Botton
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Donne
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ingmar N Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Richard Yu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Faculty of Medicine, University of British Columbia, Vancouver, BC V6T1Z3, Canada
| | - Jeffrey P North
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Laura Pincus
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Beth S Ruben
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Palo Alto Medical Foundation, Palo Alto, CA 94301, USA
| | - Nancy M Joseph
- Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA.
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5
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McNeal AS, Liu K, Nakhate V, Natale CA, Duperret EK, Capell BC, Dentchev T, Berger SL, Herlyn M, Seykora JT, Ridky TW. CDKN2B Loss Promotes Progression from Benign Melanocytic Nevus to Melanoma. Cancer Discov 2015; 5:1072-85. [PMID: 26183406 DOI: 10.1158/2159-8290.cd-15-0196] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/09/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Deletion of the entire CDKN2B-CDKN2A gene cluster is among the most common genetic events in cancer. The tumor-promoting effects are generally attributed to loss of CDKN2A-encoded p16 and p14ARF tumor suppressors. The degree to which the associated CDKN2B-encoded p15 loss contributes to human tumorigenesis is unclear. Here, we show that CDKN2B is highly upregulated in benign melanocytic nevi, contributes to maintaining nevus melanocytes in a growth-arrested premalignant state, and is commonly lost in melanoma. Using primary melanocytes isolated directly from freshly excised human nevi naturally expressing the common BRAF(V600E)-activating mutation, nevi progressing to melanoma, and normal melanocytes engineered to inducibly express BRAF(V600E), we show that BRAF activation results in reversible, TGFβ-dependent, p15 induction that halts proliferation. Furthermore, we engineer human skin grafts containing nevus-derived melanocytes to establish a new, architecturally faithful, in vivo melanoma model, and demonstrate that p15 loss promotes the transition from benign nevus to melanoma. SIGNIFICANCE Although BRAF(V600E) mutations cause melanocytes to initially proliferate into benign moles, mechanisms responsible for their eventual growth arrest are unknown. Using melanocytes from human moles, we show that BRAF activation leads to a CDKN2B induction that is critical for restraining BRAF oncogenic effects, and when lost, contributes to melanoma.
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Affiliation(s)
- Andrew S McNeal
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin Liu
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vihang Nakhate
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christopher A Natale
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth K Duperret
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brian C Capell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tzvete Dentchev
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - John T Seykora
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Todd W Ridky
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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