1
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Lee N, Park SJ, Lange M, Tseyang T, Doshi MB, Kim TY, Song Y, Kim DI, Greer PL, Olzmann JA, Spinelli JB, Kim D. Selenium reduction of ubiquinone via SQOR suppresses ferroptosis. Nat Metab 2024; 6:343-358. [PMID: 38351124 DOI: 10.1038/s42255-024-00974-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
The canonical biological function of selenium is in the production of selenocysteine residues of selenoproteins, and this forms the basis for its role as an essential antioxidant and cytoprotective micronutrient. Here we demonstrate that, via its metabolic intermediate hydrogen selenide, selenium reduces ubiquinone in the mitochondria through catalysis by sulfide quinone oxidoreductase. Through this mechanism, selenium rapidly protects against lipid peroxidation and ferroptosis in a timescale that precedes selenoprotein production, doing so even when selenoprotein production has been eliminated. Our findings identify a regulatory mechanism against ferroptosis that implicates sulfide quinone oxidoreductase and expands our understanding of selenium in biology.
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Affiliation(s)
- Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Biomedical Science & Engineering, Dankook University, Cheonan, Republic of Korea.
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Mike Lange
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Tenzin Tseyang
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Mihir B Doshi
- Department of Biomedical Science & Engineering, Dankook University, Cheonan, Republic of Korea
| | | | - Yoseb Song
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - James A Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jessica B Spinelli
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Doshi MB, Lee N, Tseyang T, Ponomarova O, Goel HL, Spears M, Li R, Zhu LJ, Ashwood C, Simin K, Jang C, Mercurio AM, Walhout AJM, Spinelli JB, Kim D. Disruption of sugar nucleotide clearance is a therapeutic vulnerability of cancer cells. Nature 2023; 623:625-632. [PMID: 37880368 PMCID: PMC10709823 DOI: 10.1038/s41586-023-06676-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Identifying metabolic steps that are specifically required for the survival of cancer cells but are dispensable in normal cells remains a challenge1. Here we report a therapeutic vulnerability in a sugar nucleotide biosynthetic pathway that can be exploited in cancer cells with only a limited impact on normal cells. A systematic examination of conditionally essential metabolic enzymes revealed that UXS1, a Golgi enzyme that converts one sugar nucleotide (UDP-glucuronic acid, UDPGA) to another (UDP-xylose), is essential only in cells that express high levels of the enzyme immediately upstream of it, UGDH. This conditional relationship exists because UXS1 is required to prevent excess accumulation of UDPGA, which is produced by UGDH. UXS1 not only clears away UDPGA but also limits its production through negative feedback on UGDH. Excess UDPGA disrupts Golgi morphology and function, which impedes the trafficking of surface receptors such as EGFR to the plasma membrane and diminishes the signalling capacity of cells. UGDH expression is elevated in several cancers, including lung adenocarcinoma, and is further enhanced during chemoresistant selection. As a result, these cancer cells are selectively dependent on UXS1 for UDPGA detoxification, revealing a potential weakness in tumours with high levels of UGDH.
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Affiliation(s)
- Mihir B Doshi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biomedical Science & Engineering, Dankook University, Cheonan, South Korea
| | - Tenzin Tseyang
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Olga Ponomarova
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hira Lal Goel
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Meghan Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Christopher Ashwood
- Glycomics Core, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Arthur M Mercurio
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Albertha J M Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jessica B Spinelli
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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3
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Spears ME, Lee N, Hwang S, Park SJ, Carlisle AE, Li R, Doshi MB, Armando AM, Gao J, Simin K, Zhu LJ, Greer PL, Quehenberger O, Torres EM, Kim D. De novo sphingolipid biosynthesis necessitates detoxification in cancer cells. Cell Rep 2022; 40:111415. [PMID: 36170811 PMCID: PMC9552870 DOI: 10.1016/j.celrep.2022.111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/19/2021] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Sphingolipids play important signaling and structural roles in cells. Here, we find that during de novo sphingolipid biosynthesis, a toxic metabolite is formed with critical implications for cancer cell survival. The enzyme catalyzing the first step in this pathway, serine palmitoyltransferase complex (SPT), is upregulated in breast and other cancers. SPT is dispensable for cancer cell proliferation, as sphingolipids can be salvaged from the environment. However, SPT activity introduces a liability as its product, 3-ketodihydrosphingosine (3KDS), is toxic and requires clearance via the downstream enzyme 3-ketodihydrosphingosine reductase (KDSR). In cancer cells, but not normal cells, targeting KDSR induces toxic 3KDS accumulation leading to endoplasmic reticulum (ER) dysfunction and loss of proteostasis. Furthermore, the antitumor effect of KDSR disruption can be enhanced by increasing metabolic input (via high-fat diet) to allow greater 3KDS production. Thus, de novo sphingolipid biosynthesis entails a detoxification requirement in cancer cells that can be therapeutically exploited.
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Affiliation(s)
- Meghan E Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sunyoung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anne E Carlisle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Mihir B Doshi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aaron M Armando
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Jenny Gao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Oswald Quehenberger
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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4
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Lee N, Carlisle AE, Peppers A, Park SJ, Doshi MB, Spears ME, Kim D. xCT-Driven Expression of GPX4 Determines Sensitivity of Breast Cancer Cells to Ferroptosis Inducers. Antioxidants (Basel) 2021; 10:antiox10020317. [PMID: 33672555 PMCID: PMC7923775 DOI: 10.3390/antiox10020317] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Inducers of ferroptosis such as the glutathione depleting agent Erastin and the GPX4 inhibitor Rsl-3 are being actively explored as potential therapeutics in various cancers, but the factors that determine their sensitivity are poorly understood. Here, we show that expression levels of both subunits of the cystine/glutamate antiporter xCT determine the expression of GPX4 in breast cancer, and that upregulation of the xCT/selenocysteine biosynthesis/GPX4 production axis paradoxically renders the cancer cells more sensitive to certain types of ferroptotic stimuli. We find that GPX4 is strongly upregulated in a subset of breast cancer tissues compared to matched normal samples, and that this is tightly correlated with the increased expression of the xCT subunits SLC7A11 and SLC3A2. Erastin depletes levels of the antioxidant selenoproteins GPX4 and GPX1 in breast cancer cells by inhibiting xCT-dependent extracellular reduction which is required for selenium uptake and selenocysteine biosynthesis. Unexpectedly, while breast cancer cells are resistant compared to nontransformed cells against oxidative stress inducing drugs, at the same time they are hypersensitive to lipid peroxidation and ferroptosis induced by Erastin or Rsl-3, indicating that they are 'addicted' to the xCT/GPX4 axis. Our findings provide a strategic basis for targeting the anti-ferroptotic machinery of breast cancer cells depending on their xCT status, which can be further explored.
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Affiliation(s)
- Namgyu Lee
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
| | - Anne E. Carlisle
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
| | - Austin Peppers
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA;
| | - Mihir B. Doshi
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
| | - Meghan E. Spears
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
| | - Dohoon Kim
- Cell and Cancer Biology, Department of Molecular, University of Massachusetts Medical School, Worcester, MA 01604, USA; (N.L.); (A.E.C.); (A.P.); (M.B.D.); (M.E.S.)
- Correspondence:
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5
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Panzarino NJ, Krais JJ, Cong K, Peng M, Mosqueda M, Nayak SU, Bond SM, Calvo JA, Doshi MB, Bere M, Ou J, Deng B, Zhu LJ, Johnson N, Cantor SB. Replication Gaps Underlie BRCA Deficiency and Therapy Response. Cancer Res 2020; 81:1388-1397. [PMID: 33184108 PMCID: PMC8026497 DOI: 10.1158/0008-5472.can-20-1602] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/02/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Defects in DNA repair and the protection of stalled DNA replication forks are thought to underlie the chemosensitivity of tumors deficient in the hereditary breast cancer genes BRCA1 and BRCA2 (BRCA). Challenging this assumption are recent findings that indicate chemotherapies, such as cisplatin used to treat BRCA-deficient tumors, do not initially cause DNA double-strand breaks (DSB). Here, we show that ssDNA replication gaps underlie the hypersensitivity of BRCA-deficient cancer and that defects in homologous recombination (HR) or fork protection (FP) do not. In BRCA-deficient cells, ssDNA gaps developed because replication was not effectively restrained in response to stress. Gap suppression by either restoration of fork restraint or gap filling conferred therapy resistance in tissue culture and BRCA patient tumors. In contrast, restored FP and HR could be uncoupled from therapy resistance when gaps were present. Moreover, DSBs were not detected after therapy when apoptosis was inhibited, supporting a framework in which DSBs are not directly induced by genotoxic agents, but rather are induced from cell death nucleases and are not fundamental to the mechanism of action of genotoxic agents. Together, these data indicate that ssDNA replication gaps underlie the BRCA cancer phenotype, "BRCAness," and we propose they are fundamental to the mechanism of action of genotoxic chemotherapies. SIGNIFICANCE: This study suggests that ssDNA replication gaps are fundamental to the toxicity of genotoxic agents and underlie the BRCA-cancer phenotype "BRCAness," yielding promising biomarkers, targets, and opportunities to resensitize refractory disease.See related commentary by Canman, p. 1214.
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Affiliation(s)
| | - John J Krais
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ke Cong
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Min Peng
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Michelle Mosqueda
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sumeet U Nayak
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Samuel M Bond
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jennifer A Calvo
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Mihir B Doshi
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Matt Bere
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jianhong Ou
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Bin Deng
- The University of Vermont, Burlington, Vermont
| | - Lihua J Zhu
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Neil Johnson
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sharon B Cantor
- University of Massachusetts Medical School, Worcester, Massachusetts.
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6
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Carlisle AE, Lee N, Matthew-Onabanjo AN, Spears ME, Park SJ, Youkana D, Doshi MB, Peppers A, Li R, Joseph AB, Smith M, Simin K, Zhu LJ, Greer PL, Shaw LM, Kim D. Selenium detoxification is required for cancer-cell survival. Nat Metab 2020; 2:603-611. [PMID: 32694795 PMCID: PMC7455022 DOI: 10.1038/s42255-020-0224-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/28/2020] [Indexed: 12/21/2022]
Abstract
The micronutrient selenium is incorporated via the selenocysteine biosynthesis pathway into the rare amino acid selenocysteine, which is required in selenoproteins such as glutathione peroxidases and thioredoxin reductases1,2. Here, we show that selenophosphate synthetase 2 (SEPHS2), an enzyme in the selenocysteine biosynthesis pathway, is essential for survival of cancer, but not normal, cells. SEPHS2 is required in cancer cells to detoxify selenide, an intermediate that is formed during selenocysteine biosynthesis. Breast and other cancer cells are selenophilic, owing to a secondary function of the cystine/glutamate antiporter SLC7A11 that promotes selenium uptake and selenocysteine biosynthesis, which, by allowing production of selenoproteins such as GPX4, protects cells against ferroptosis. However, this activity also becomes a liability for cancer cells because selenide is poisonous and must be processed by SEPHS2. Accordingly, we find that SEPHS2 protein levels are elevated in samples from people with breast cancer, and that loss of SEPHS2 impairs growth of orthotopic mammary-tumour xenografts in mice. Collectively, our results identify a vulnerability of cancer cells and define the role of selenium metabolism in cancer.
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Affiliation(s)
- Anne E Carlisle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Asia N Matthew-Onabanjo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Meghan E Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Daniel Youkana
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mihir B Doshi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Austin Peppers
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Alexander B Joseph
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Miles Smith
- Environmental Testing and Research Laboratories, Leominster, MA, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Leslie M Shaw
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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7
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Hong AL, Tseng YY, Wala JA, Kim WJ, Kynnap BD, Doshi MB, Kugener G, Sandoval GJ, Howard TP, Li J, Yang X, Tillgren M, Ghandi M, Sayeed A, Deasy R, Ward A, McSteen B, Labella KM, Keskula P, Tracy A, Connor C, Clinton CM, Church AJ, Crompton BD, Janeway KA, Van Hare B, Sandak D, Gjoerup O, Bandopadhayay P, Clemons PA, Schreiber SL, Root DE, Gokhale PC, Chi SN, Mullen EA, Roberts CW, Kadoch C, Beroukhim R, Ligon KL, Boehm JS, Hahn WC. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. eLife 2019; 8:44161. [PMID: 30860482 PMCID: PMC6436895 DOI: 10.7554/elife.44161] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of SMARCB1 for survival. Through integration of RNAi and CRISPR-Cas9 loss-of-function genetic screens and a small-molecule screen, we found that the ubiquitin-proteasome system (UPS) was essential in RMC. Inhibition of the UPS caused a G2/M arrest due to constitutive accumulation of cyclin B1. These observations extend across cancers that harbor SMARCB1 loss, which also require expression of the E2 ubiquitin-conjugating enzyme, UBE2C. Our studies identify a synthetic lethal relationship between SMARCB1-deficient cancers and reliance on the UPS which provides the foundation for a mechanism-informed clinical trial with proteasome inhibitors. Renal medullary carcinoma (RMC for short) is a rare type of kidney cancer that affects teenagers and young adults. These patients are usually of African descent and carry one of the two genetic changes that cause sickle cell anemia. RMC is an aggressive disease without effective treatments and patients survive, on average, for only six to eight months after their diagnosis. Recent genetic studies found that most RMC cells have mutations that prevent them from producing a protein called SMARCB1. SMARCB1 normally acts as a so-called tumor suppressor, preventing cells from becoming cancerous. However, it was not clear whether RMCs always have to lose SMARCB1 if they are to survive and grow. Often, diseases are studied using laboratory-grown cells and tissues that have certain features of the disease. No such models had been created for RMC, which has slowed efforts to understand how the disease develops and find new treatments for it. Hong et al. therefore worked with patients to develop new lines of cells that can be used to study RMC in the laboratory. These RMC cells started dying when they were given copies of the SMARCB1 gene, which supports the theory that RMCs have to lose SMARCB1 in order to grow. Hong et al. then used a set of genetic reagents that can suppress or delete genes that are targeted by drugs, and followed this by testing a range of drugs on the RMC cells. Drugs and genetic reagents that reduced the activity of the proteasome – the structure inside cells that gets rid of old or unwanted proteins – caused the RMC cells to die. These proteasome inhibitor drugs also killed other kinds of cancer cells with SMARCB1 mutations. Proteasome inhibitors are already used to treat different types of cancer. Potentially, a clinical trial could be run to see if they will treat patients whose cancers lack SMARCB1. Further work is also needed to determine the exact link between SMARCB1 and the proteasome.
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Affiliation(s)
- Andrew L Hong
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jeremiah A Wala
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Won-Jun Kim
- Dana-Farber Cancer Institute, Boston, United States
| | | | - Mihir B Doshi
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Gabriel J Sandoval
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Ji Li
- Dana-Farber Cancer Institute, Boston, United States
| | - Xiaoping Yang
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Mahmhoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Abeer Sayeed
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Rebecca Deasy
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Abigail Ward
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | - Brian McSteen
- Rare Cancer Research Foundation, Durham, United States
| | | | - Paula Keskula
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Adam Tracy
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Cora Connor
- RMC Support, North Charleston, United States
| | - Catherine M Clinton
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - Brian D Crompton
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Katherine A Janeway
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - David Sandak
- Rare Cancer Research Foundation, Durham, United States
| | - Ole Gjoerup
- Dana-Farber Cancer Institute, Boston, United States
| | - Pratiti Bandopadhayay
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Susan N Chi
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | - Elizabeth A Mullen
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - Cigall Kadoch
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
| | - Keith L Ligon
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
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8
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Hong AL, Guerriero JL, Doshi MB, Kynnap BD, Kim WJ, Schinzel AC, Modiste R, Schlauch AJ, Adam RM, Kwiatkowski DJ, Beroukhim R, Letai A, Rosenberg JE, Hahn WC. MCL1 and DEDD Promote Urothelial Carcinoma Progression. Mol Cancer Res 2019; 17:1294-1304. [PMID: 30777879 DOI: 10.1158/1541-7786.mcr-18-0963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/26/2018] [Accepted: 02/14/2019] [Indexed: 12/16/2022]
Abstract
Focal amplification of chromosome 1q23.3 in patients with advanced primary or relapsed urothelial carcinomas is associated with poor survival. We interrogated chromosome 1q23.3 and the nearby focal amplicon 1q21.3, as both are associated with increased lymph node disease in patients with urothelial carcinoma. Specifically, we assessed whether the oncogene MCL1 that resides in 1q21.3 and the genes that reside in the 1q23.3 amplicon were required for the proliferation or survival of urothelial carcinoma. We observed that suppressing MCL1 or the death effector domain-containing protein (DEDD) in the cells that harbor amplifications of 1q21.3 or 1q23.3, respectively, inhibited cell proliferation. We also found that overexpression of MCL1 or DEDD increased anchorage independence growth in vitro and increased experimental metastasis in vivo in the nonamplified urothelial carcinoma cell line, RT112. The expression of MCL1 confers resistance to a range of apoptosis inducers, while the expression of DEDD led to resistance to TNFα-induced apoptosis. These observations identify MCL1 and DEDD as genes that contribute to aggressive urothelial carcinoma. IMPLICATIONS: These studies identify MCL1 and DEDD as genes that contribute to aggressive urothelial carcinomas.
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Affiliation(s)
- Andrew L Hong
- Boston Children's Hospital, Boston, Massachusetts.,Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Mihir B Doshi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Won Jun Kim
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | | | | | - David J Kwiatkowski
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Brigham and Women's Hospital, Boston, Massachusetts
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Jonathan E Rosenberg
- Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Brigham and Women's Hospital, Boston, Massachusetts
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9
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Hong AL, Tseng YY, Kynnap BD, Doshi MB, Wala J, Sandoval G, Church AJ, Mullen E, Kadoch C, Roberts CW, Beroukhim R, Boehm JS, Hahn WC. Abstract B18: Modeling renal medullary carcinomas identifies druggable vulnerabilities in SMARCB1-deficient cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-b18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Renal medullary carcinomas (RMCs) are thought to be driven by the loss of tumor suppressor, SMARCB1. These rare kidney cancers carry a very poor prognosis and primarily affect African American adolescents and young adults with sickle cell trait. From two patients with RMC, we have identified by whole-genome sequencing mechanisms of SMARCB1 loss (e.g., inactivating fusion events involving SMARCB1). We developed in vitro models of primary and relapsed metastatic disease. We performed biochemical and functional studies to conclusively show that RMC is dependent on loss of SMARCB1, similar to rhabdoid tumors and atypical teratoid/rhabdoid tumors. Furthermore, we performed small-molecule screens, pooled CRISPR-Cas9 knockout, and RNAi suppression screens focused on druggable cancer targets. Integration of these orthogonal methods identifies a core set of targets that may provide a rational approach to therapeutic targeting for this rare kidney cancer and other SMARCB1-deficient cancers.
Citation Format: Andrew L. Hong, Yuen-Yi Tseng, Bryan D. Kynnap, Mihir B. Doshi, Jeremiah Wala, Gabriel Sandoval, Alanna J. Church, Elizabeth Mullen, Cigall Kadoch, Charles W.M. Roberts, Rameen Beroukhim, Jesse S. Boehm, William C. Hahn. Modeling renal medullary carcinomas identifies druggable vulnerabilities in SMARCB1-deficient cancers [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B18.
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10
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Hong AL, Tseng YY, Kynnap BD, Doshi MB, Sandoval G, Oh C, Sayeed A, Shubhroz G, Church AJ, Keskula P, Peng A, Clemons PA, Tsherniak A, Vazquez F, Rodriguez-Galindo C, Janeway KA, Garraway LA, Schreiber SL, Root DE, Mullen E, Stegmaier K, Kadoch C, Roberts CW, Boehm JS, Hahn WC. Abstract B17: Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-b17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Renal medullary carcinoma is a rare kidney cancer that is primarily seen in adolescent and young adult African American patients with sickle cell trait. Prognosis is poor and treatment options are limited. We have developed several cell line models that recapitulate the primary and relapsed metastatic samples from a patient who succumbed to this disease. We have confirmed by whole exome sequencing that our models have sickle cell trait and loss of heterozygosity of the SMARCB1 loci, both hallmarks of this disease. By RNA-sequencing, we see a lack of SMARCB1 transcription. We have further shown dependency of our models to SMARCB1 re-expression thus suggesting that this cancer is indeed driven by loss of SMARCB1 at a functional level. We performed pooled CRISPR-Cas9 and RNAi loss of function screens and a small molecule screen focused on druggable cancer targets based on our previous work in parallel to a genome-wide pooled CRISPR-Cas9 loss of function screen. Integrating these complementary and orthogonal methods, we identified a number of targets for further validation. These targets, when combined may provide a rational approach to therapeutic targeting for this rare kidney cancer.
Citation Format: Andrew L. Hong, Yuen-Yi Tseng, Bryan D. Kynnap, Mihir B. Doshi, Gabriel Sandoval, Coyin Oh, Abeer Sayeed, Gill Shubhroz, Alanna J. Church, Paula Keskula, Anson Peng, Paul A. Clemons, Aviad Tsherniak, Francisca Vazquez, Carlos Rodriguez-Galindo, Katherine A. Janeway, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Elizabeth Mullen, Kimberly Stegmaier, Cigall Kadoch, Charles W.M. Roberts, Jesse S. Boehm, William C. Hahn. Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B17.
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Affiliation(s)
| | | | | | | | | | - Coyin Oh
- 2Broad Institute, Cambridge, MA,
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11
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Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting. Cancer Discov 2016; 6:914-29. [PMID: 27260156 PMCID: PMC4972686 DOI: 10.1158/2159-8290.cd-16-0154] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/31/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions. SIGNIFICANCE We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Cancer Discov; 6(8); 914-29. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Munoz et al., p. 900This article is highlighted in the In This Issue feature, p. 803.
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Affiliation(s)
- Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Barbara A Weir
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Francisca Vazquez
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Cheng-Zhong Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Uri Ben-David
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Mihir B Doshi
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Stanley Gill
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Han Xu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi D Ali
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sasha Pantel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Coyin Oh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gregory Kryukov
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Kimberly Stegmaier
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Boston Children's Hospital, Boston, Massachusetts
| | - Charles W Roberts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts. St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Todd R Golub
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.
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12
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Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CWM, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS. Integrated genetic and pharmacologic interrogation of rare cancers. Nat Commun 2016; 7:11987. [PMID: 27329820 PMCID: PMC4917959 DOI: 10.1038/ncomms11987] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm that this cell line recapitulates the histology and harbours the majority of the somatic genetic alterations found in a metastatic lesion isolated at first relapse. We then perform pooled CRISPR-Cas9 and RNAi loss-of-function screens and a small-molecule screen focused on druggable cancer targets. Integrating these three complementary and orthogonal methods, we identify CDK4 and XPO1 as potential therapeutic targets in this cancer, which has no known alterations in these genes. These observations establish an approach that integrates new patient-derived models, functional genomics and chemical screens to facilitate the discovery of targets in rare cancers.
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Affiliation(s)
- Andrew L. Hong
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Glenn S. Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Oliver Jonas
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Jaime H. Cheah
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Bryan D. Kynnap
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Mihir B. Doshi
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Coyin Oh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Stephanie C. Meyer
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alanna J. Church
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Shubhroz Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Craig M. Bielski
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alma Imamovic
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Gregory V. Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Paul A. Clemons
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Brian D. Crompton
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alykhan F. Shamji
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Carlos Rodriguez-Galindo
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Katherine A. Janeway
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Charles W. M. Roberts
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Kimberly Stegmaier
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paul van Hummelen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Michael J. Cima
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Robert S. Langer
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Levi A. Garraway
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Stuart L. Schreiber
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David E. Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - William C. Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
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13
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Hong AL, Cowley GS, Tseng YY, Cheah JH, Jonas O, Doshi MB, Kynnap BD, Oh C, Meyer S, Clemons P, Burger M, Vazquez F, Weir B, Kryukov GV, Church A, Imamovic A, Tsherniak A, Bielski C, Crompton B, Mullen E, Roberts C, Rodriguez-Galindo C, Janeway KA, Stegmaier K, Hummelen PV, Langer R, Garraway LA, Schreiber SL, Root DE, Boehm JS, Hahn WC. Abstract B38: Developing a functional genomics platform to interrogate rare pediatric cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.pedca15-b38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Of pediatric solid tumors, as many as 10% of tumors are categorized as rare. Many of these rare tumors lack standard effective known therapy. The ability to identify vulnerabilities for many rare tumors has been significantly limited by the lack of in vitro and in vivo models. Furthermore, current approaches to study such vulnerabilities are usually limited to a specific compound or target. Our objectives were 1) to develop a platform to collect tumor samples and generate in vitro models and 2) to develop systematic and orthogonal approaches focused on currently known druggable cancer targets to identify vulnerabilities in these difficult to treat cancers. We have developed a proof of concept cell line from a patient who succumbed to progressive undifferentiated sarcoma treated on an aggressive multi-therapy regimen. This cell line, in its early passages, has novel gene fusions that match that of the primary tumor. Furthermore, even at early passages, this cell line was amenable to high throughput functional screens. Using a targeted pooled shRNA screen (employing matched seed controls) and an analogous CRISPR screen we identified dependencies to XPO1 and CDK4. In parallel, compounds against these targets were identified in a small molecule compound screen. These targetable dependencies were further validated in vivo with a micro-dosing device. These observations identify new targets in this rare malignancy. Furthermore, this suggests that the interrogation of patient derived cell lines facilitates the identification of testable therapeutic approaches.
Citation Format: Andrew L. Hong, Glenn S. Cowley, Yuen-Yi Tseng, Jaime H. Cheah, Oliver Jonas, Mihir B. Doshi, Bryan D. Kynnap, Coyin Oh, Stephanie Meyer, Paul Clemons, Michael Burger, Francisca Vazquez, Barbara Weir, Gregory V. Kryukov, Alanna Church, Alma Imamovic, Aviad Tsherniak, Craig Bielski, Brian Crompton, Elizabeth Mullen, Charles Roberts, Carlos Rodriguez-Galindo, Katherine A. Janeway, Kimberly Stegmaier, Paul van Hummelen, Robert Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Jesse S. Boehm, William C. Hahn. Developing a functional genomics platform to interrogate rare pediatric cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B38.
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Affiliation(s)
| | | | | | - Jaime H. Cheah
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | - Oliver Jonas
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | | | | | - Coyin Oh
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | - Paul Clemons
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | - Barbara Weir
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | - Robert Langer
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
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