1
|
Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Bank NB, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. bioRxiv 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.
Collapse
Affiliation(s)
- Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stamatina Fragkogianni
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Leslie Weber
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Araitz Alberdi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Baako
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oyku Ay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Estibaliz Lopez-Rodrigo
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rajya Kappagantula
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
2
|
Doe-Tetteh SA, Camp SY, Reales D, Crowdis J, Noronha AM, Wolff B, Alano T, Galle J, Duygu Selcuklu S, Viale A, Socci ND, Liu YL, Tew WP, Aghajanian C, Ladanyi M, He MX, AlDubayan SH, Mazor RD, Shpilberg O, Hershkovitz-Rokah O, Riancho JA, Hernandez JL, Gonzalez-Vela MC, Buthorn JJ, Wilson M, Webber AE, Yabe M, Petrova-Drus K, Rosenblum M, Durham BH, Abdel-Wahab O, Berger MF, Donoghue MT, Kung AL, Bender JG, Shukla NN, Funt SA, Dogan A, Soslow RA, Al-Ahmadie H, Feldman DR, Van Allen EM, Diamond EL, Solit DB. Overcoming Barriers to Tumor Genomic Profiling through Direct-to-Patient Outreach. Clin Cancer Res 2023; 29:2445-2455. [PMID: 36862133 PMCID: PMC10330105 DOI: 10.1158/1078-0432.ccr-22-3247] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/05/2023] [Accepted: 02/28/2023] [Indexed: 03/03/2023]
Abstract
PURPOSE To overcome barriers to genomic testing for patients with rare cancers, we initiated a program to offer free clinical tumor genomic testing worldwide to patients with select rare cancer subtypes. EXPERIMENTAL DESIGN Patients were recruited through social media outreach and engagement with disease-specific advocacy groups, with a focus on patients with histiocytosis, germ cell tumors (GCT), and pediatric cancers. Tumors were analyzed using the MSK-IMPACT next-generation sequencing assay with the return of results to patients and their local physicians. Whole-exome recapture was performed for female patients with GCTs to define the genomic landscape of this rare cancer subtype. RESULTS A total of 333 patients were enrolled, and tumor tissue was received for 288 (86.4%), with 250 (86.8%) having tumor DNA of sufficient quality for MSK-IMPACT testing. Eighteen patients with histiocytosis have received genomically guided therapy to date, of whom 17 (94%) have had clinical benefit with a mean treatment duration of 21.7 months (range, 6-40+). Whole-exome sequencing of ovarian GCTs identified a subset with haploid genotypes, a phenotype rarely observed in other cancer types. Actionable genomic alterations were rare in ovarian GCT (28%); however, 2 patients with ovarian GCTs with squamous transformation had high tumor mutational burden, one of whom had a complete response to pembrolizumab. CONCLUSIONS Direct-to-patient outreach can facilitate the assembly of cohorts of rare cancers of sufficient size to define their genomic landscape. By profiling tumors in a clinical laboratory, results could be reported to patients and their local physicians to guide treatment. See related commentary by Desai and Subbiah, p. 2339.
Collapse
Affiliation(s)
- Seyram A. Doe-Tetteh
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Sabrina Y. Camp
- Department of Medical Oncology, Dana Farber Cancer Institute
- Cancer Program, Broad Institute of MIT and Harvard
| | - Dalicia Reales
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Jett Crowdis
- Department of Medical Oncology, Dana Farber Cancer Institute
- Cancer Program, Broad Institute of MIT and Harvard
| | - Anne Marie Noronha
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Bernadette Wolff
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Department of Nursing, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Tina Alano
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Department of Nursing, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Jesse Galle
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - S. Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Nicholas D. Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Ying L. Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - William P. Tew
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Meng Xiao He
- Department of Medical Oncology, Dana Farber Cancer Institute
- Cancer Program, Broad Institute of MIT and Harvard
- Harvard Graduate Program in Biophysics, Boston, MA, 02115, USA
| | - Saud H. AlDubayan
- Department of Medical Oncology, Dana Farber Cancer Institute
- Cancer Program, Broad Institute of MIT and Harvard
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Roei David Mazor
- Clinic of Histiocytic Neoplasms, Institute of Hematology, Assuta Medical Center, Tel Aviv, Israel
| | - Ofer Shpilberg
- Clinic of Histiocytic Neoplasms, Institute of Hematology, Assuta Medical Center, Tel Aviv, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Oshrat Hershkovitz-Rokah
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel
- Translational Research Lab, Assuta Medical Center, Tel-Aviv, Israel
| | - Jose A. Riancho
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Jose L. Hernandez
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - M. Carmen Gonzalez-Vela
- Department of Pathology, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Justin J. Buthorn
- Department of Neurology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Manda Wilson
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Amy E. Webber
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Mariko Yabe
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Benjamin H. Durham
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Mark T.A. Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Julia Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Neerav N. Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Samuel A. Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Robert A. Soslow
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Darren R. Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute
- Cancer Program, Broad Institute of MIT and Harvard
| | - Eli L. Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| |
Collapse
|
3
|
Warrick JI, Hu W, Yamashita H, Walter V, Shuman L, Craig JM, Gellert LL, Castro MAA, Robertson AG, Kuo F, Ostrovnaya I, Sarungbam J, Chen YB, Gopalan A, Sirintrapun SJ, Fine SW, Tickoo SK, Kim K, Thomas J, Karan N, Gao SP, Clinton TN, Lenis AT, Chan TA, Chen Z, Rao M, Hollman TJ, Li Y, Socci ND, Chavan S, Viale A, Mohibullah N, Bochner BH, Pietzak EJ, Teo MY, Iyer G, Rosenberg JE, Bajorin DF, Kaag M, Merrill SB, Joshi M, Adam R, Taylor JA, Clark PE, Raman JD, Reuter VE, Chen Y, Funt SA, Solit DB, DeGraff DJ, Al-Ahmadie HA. Author Correction: FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation. Nat Commun 2022; 13:7920. [PMID: 36564410 PMCID: PMC9789140 DOI: 10.1038/s41467-022-35644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hironobu Yamashita
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lauren Shuman
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jenna M Craig
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lan L Gellert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Parana, Curitiba, Paraná, Brazil
| | - A Gordon Robertson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Fengshen Kuo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Judy Sarungbam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahussapont J Sirintrapun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samson W Fine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satish K Tickoo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwanghee Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jasmine Thomas
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nagar Karan
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sizhi Paul Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy N Clinton
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew T Lenis
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manisha Rao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyun Li
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Kaag
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suzanne B Merrill
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Monika Joshi
- Department of Medicine, Division of Hematology-Oncology, Penn State Cancer Institute, Hershey, PA, USA
| | - Rosalyn Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, MO, USA
| | - Peter E Clark
- Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Victor E Reuter
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Deparment of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Hikmat A Al-Ahmadie
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
4
|
Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Ovarian cancer mutational processes drive site-specific immune evasion. Nature 2022; 612:778-786. [PMID: 36517593 PMCID: PMC9771812 DOI: 10.1038/s41586-022-05496-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1-4 patterned by distinct mutational processes5,6, tumour heterogeneity7-9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11-13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.
Collapse
Affiliation(s)
- Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florian Uhlitz
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie L P Lim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Niyazov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arvin Eric B Ruiz
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin M Boehm
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J Fong
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Funnell
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eliyahu Havasov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samantha Leung
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arfath Pasha
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Druv M Patel
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maryam Pourmaleki
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rami Vanguri
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allen W Zhang
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vance Broach
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis S Chi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ginger J Gardner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah H Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Lennon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kara Long Roche
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yukio Sonoda
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oliver Zivanovic
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh N Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luke Geneslaw
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Maroldi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahelly Nunez
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthe Stylianou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahsa Vahdatinia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yonina Bykov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel N Grisham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Ying L Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Yulia Lakhman
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ines Nikolovski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Kelly
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jianjiong Gao
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Schietinger
- Weill Cornell Medical Center, New York, NY, USA
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire F Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical Center, New York, NY, USA.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
5
|
Warrick JI, Hu W, Yamashita H, Walter V, Shuman L, Craig JM, Gellert LL, Castro MAA, Robertson AG, Kuo F, Ostrovnaya I, Sarungbam J, Chen YB, Gopalan A, Sirintrapun SJ, Fine SW, Tickoo SK, Kim K, Thomas J, Karan N, Gao SP, Clinton TN, Lenis AT, Chan TA, Chen Z, Rao M, Hollman TJ, Li Y, Socci ND, Chavan S, Viale A, Mohibullah N, Bochner BH, Pietzak EJ, Teo MY, Iyer G, Rosenberg JE, Bajorin DF, Kaag M, Merrill SB, Joshi M, Adam R, Taylor JA, Clark PE, Raman JD, Reuter VE, Chen Y, Funt SA, Solit DB, DeGraff DJ, Al-Ahmadie HA. FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation. Nat Commun 2022; 13:6575. [PMID: 36323682 PMCID: PMC9630410 DOI: 10.1038/s41467-022-34251-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/06/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Cancers arising from the bladder urothelium often exhibit lineage plasticity with regions of urothelial carcinoma adjacent to or admixed with regions of divergent histomorphology, most commonly squamous differentiation. To define the biologic basis for and clinical significance of this morphologic heterogeneity, here we perform integrated genomic analyses of mixed histology bladder cancers with separable regions of urothelial and squamous differentiation. We find that squamous differentiation is a marker of intratumoral genomic and immunologic heterogeneity in patients with bladder cancer and a biomarker of intrinsic immunotherapy resistance. Phylogenetic analysis confirms that in all cases the urothelial and squamous regions are derived from a common shared precursor. Despite the presence of marked genomic heterogeneity between co-existent urothelial and squamous differentiated regions, no recurrent genomic alteration exclusive to the urothelial or squamous morphologies is identified. Rather, lineage plasticity in bladder cancers with squamous differentiation is associated with loss of expression of FOXA1, GATA3, and PPARG, transcription factors critical for maintenance of urothelial cell identity. Of clinical significance, lineage plasticity and PD-L1 expression is coordinately dysregulated via FOXA1, with patients exhibiting morphologic heterogeneity pre-treatment significantly less likely to respond to immune checkpoint inhibitors.
Collapse
Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hironobu Yamashita
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lauren Shuman
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jenna M Craig
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lan L Gellert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Parana, Curitiba, Paraná, Brazil
| | - A Gordon Robertson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Fengshen Kuo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Judy Sarungbam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahussapont J Sirintrapun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samson W Fine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satish K Tickoo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwanghee Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jasmine Thomas
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nagar Karan
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sizhi Paul Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy N Clinton
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew T Lenis
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manisha Rao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyun Li
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Kaag
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suzanne B Merrill
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Monika Joshi
- Department of Medicine, Division of Hematology-Oncology, Penn State Cancer Institute, Hershey, PA, USA
| | - Rosalyn Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, MO, USA
| | - Peter E Clark
- Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Victor E Reuter
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Deparment of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Hikmat A Al-Ahmadie
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
6
|
Salloum D, Singh K, Davidson NR, Cao L, Kuo D, Sanghvi VR, Jiang M, Lafoz MT, Viale A, Ratsch G, Wendel HG. A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes. J Immunol 2022; 209:1189-1199. [PMID: 36002234 PMCID: PMC9492650 DOI: 10.4049/jimmunol.2100537] [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] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/25/2022] [Indexed: 01/04/2023]
Abstract
The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
Collapse
Affiliation(s)
- Darin Salloum
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY
| | - Natalie R Davidson
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Linlin Cao
- Swiss Institute for Experimental Cancer Research, EPFL, Lausanne, Switzerland
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami FL
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Tello Lafoz
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Ratsch
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY;
| |
Collapse
|
7
|
Sanghvi V, Rust A, Leibold J, Lowe S, Viale A, Chodera J, Hendrickson RC, de Stanchina E, Wendel HG. Abstract PO029: Targeting non-canonical Hippo pathway in NRF2-mutant liver cancer. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.liverca22-po029] [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
NRF2 is an “undruggable” oncogenic transcription factor recurrently mutated in solid tumors such as liver and lung cancers. Our recent study demonstrates that NRF2 acts by coordinating the redox and metabolic stress responses as well as drug resistance programs in liver and other cancers. Developing an NRF2 inhibitor is a major goal of cancer drug discovery. Here, we identify the non-canonical Hippo pathway protein serine/threonine kinase 38 (STK38/NDR1) as a new NRF2 kinase that is a requirement for its stability and function. STK38 directly phosphorylates NRF2 at two sites (S33 and T559), and both sites contribute to full NRF2 activation. Loss of STK38 disables the redox response in NRF2 driven cancers and leads to tumor regression in vivo. Conversely, STK38 can also activate NRF2 and promote de novo liver cancer development in mice. This oncogenic effect is reflected in low frequency (3%) genomic amplifications in human liver cancers. Importantly, inhibition of the upstream STK38-activating mammalian Hippo kinases STK3/4 (MST2/1) by XMU-MP-1 inactivates STK38-NRF2 regulatory axis in vitroand in vivo. More importantly, XMU-MP-1 produces single agent activity against NRF2-driven liver and lung cancers in vivo in primary and patient derived xenograft (PDX)-based mouse models. In addition, we performed an in-silicoscreen and identified TAE-684 as an STK38 inhibitor that was subsequently confirmed to block STK38 activity in an in vitro kinase assay. TAE-684 treatment resulted in significant growth impairment of NRF2-mutant PDXs in vivo but no activity was observed in NRF2 wildtype counterparts. Together, these results uncover a surprising role of Hippo-related kinase STK38 in NRF2 activation and point to a paradoxical vulnerability in NRF2-driven cancers.
Citation Format: Viraj Sanghvi, Aleksander Rust, Josef Leibold, Scott Lowe, Agnes Viale, John Chodera, Ronald C. Hendrickson, Elisa de Stanchina, Hans-Guido Wendel. Targeting non-canonical Hippo pathway in NRF2-mutant liver cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in the Pathogenesis and Molecular Therapies of Liver Cancer; 2022 May 5-8; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(17_Suppl):Abstract nr PO029.
Collapse
Affiliation(s)
- Viraj Sanghvi
- 1University of Miami Miller School of Medicine, Miami,
| | | | | | - Scott Lowe
- 2Memorial Sloan Kettering Cancer Center, New York,
| | - Agnes Viale
- 2Memorial Sloan Kettering Cancer Center, New York,
| | - John Chodera
- 2Memorial Sloan Kettering Cancer Center, New York,
| | | | | | | |
Collapse
|
8
|
Bernard E, Tuechler H, Greenberg PL, Hasserjian RP, Arango Ossa JE, Nannya Y, Devlin SM, Creignou M, Pinel P, Monnier L, Gundem G, Medina-Martinez JS, Domenico D, Jädersten M, Germing U, Sanz G, van de Loosdrecht AA, Kosmider O, Follo MY, Thol F, Zamora L, Pinheiro RF, Pellagatti A, Elias HK, Haase D, Ganster C, Ades L, Tobiasson M, Palomo L, Della Porta MG, Takaori-Kondo A, Ishikawa T, Chiba S, Kasahara S, Miyazaki Y, Viale A, Huberman K, Fenaux P, Belickova M, Savona MR, Klimek VM, Santos FPS, Boultwood J, Kotsianidis I, Santini V, Solé F, Platzbecker U, Heuser M, Valent P, Ohyashiki K, Finelli C, Voso MT, Shih LY, Fontenay M, Jansen JH, Cervera J, Gattermann N, Ebert BL, Bejar R, Malcovati L, Cazzola M, Ogawa S, Hellström-Lindberg E, Papaemmanuil E. Molecular International Prognostic Scoring System for Myelodysplastic Syndromes. NEJM Evid 2022; 1:EVIDoa2200008. [PMID: 38319256 DOI: 10.1056/evidoa2200008] [Citation(s) in RCA: 238] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
MDS Molecular International Prognostic Scoring SystemSamples from over 2500 patients with MDS were profiled for gene mutations and used to develop the International Prognostic Scoring System-Molecular (IPSS-M). TP53multihit, FLT3 mutations, and MLLPTD were identified as top genetic predictors of adverse outcomes. IPSS-M improves prognostic discrimination across all clinical end points versus prior versions.
Collapse
Affiliation(s)
- Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | | | | | | | - Juan E Arango Ossa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, Institute of Medical Science, University of Tokyo, Tokyo
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm
| | - Philippe Pinel
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Lily Monnier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Gunes Gundem
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Juan S Medina-Martinez
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Dylan Domenico
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Martin Jädersten
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Guillermo Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid
- Health Research Institute La Fe, Valencia, Spain
| | - Arjan A van de Loosdrecht
- Department of Hematology, Amsterdam University Medical Center, Vrije University Medical Center, Amsterdam
| | - Olivier Kosmider
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris
| | - Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Lurdes Zamora
- Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncologia, Josep Carreras Leukaemia Research Institute, Barcelona
| | - Ronald F Pinheiro
- Drug Research and Development Center, Federal University of Ceara, Ceara, Brazil
| | - Andrea Pellagatti
- Radcliffe Department of Medicine, Oxford BRC Haematology Theme, University of Oxford, Oxford, United Kingdom
| | - Harold K Elias
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
| | - Detlef Haase
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Christina Ganster
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Lionel Ades
- Department of Hematology, Hôpital St Louis, and Paris University, Paris
| | - Magnus Tobiasson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm
| | - Laura Palomo
- Myelodysplastic Syndromes Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Senji Kasahara
- Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Agnes Viale
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York
| | - Kety Huberman
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York
| | - Pierre Fenaux
- Department of Hematology, Hôpital St Louis, and Paris University, Paris
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Michael R Savona
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
| | - Fabio P S Santos
- Oncology-Hematology Center, Hospital Israelita Albert Einstein, São Paulo
| | - Jacqueline Boultwood
- Radcliffe Department of Medicine, Oxford BRC Haematology Theme, University of Oxford, Oxford, United Kingdom
| | - Ioannis Kotsianidis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Valeria Santini
- Myelodysplastic syndromes Unit, Department of Experimental and Clinical Medicine, Hematology, Azienda Ospedaliero Universitaria Careggi, University of Florence, Florence, Italy
| | - Francesc Solé
- Myelodysplastic Syndromes Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Peter Valent
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna
| | | | - Carlo Finelli
- Institute of Hematology "Seràgnoli," Istituti di Ricovero e Cura a Carattere Scientifico Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Maria Teresa Voso
- Myelodysplastic syndromes Cooperative Group Gruppo Laziale Mielodisplasie (GROM-L), Department of Biomedicine and Prevention, Tor Vergata University, Rome
| | - Lee-Yung Shih
- Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taiwan
| | - Michaela Fontenay
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris
| | - Joop H Jansen
- Laboratory of Hematology, Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - José Cervera
- Department of Hematology and Genetics Unit, University Hospital La Fe, Valencia, Spain
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Howard Hughes Medical Institute, Dana-Farber Cancer Center, Boston
| | - Rafael Bejar
- University of California San Diego Moores Cancer Center, La Jolla, CA
| | - Luca Malcovati
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Mario Cazzola
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| |
Collapse
|
9
|
Vázquez-García I, Uhlitz F, Ceglia N, Lim JL, Wu M, Mohibullah N, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Paula ADC, Gardner GJ, Kim SH, Lennon M, Roche KL, Sonoda Y, Zivanovic O, Kundra R, Viale A, Bykov Y, Derakhshan FN, Geneslaw L, Maroldi A, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum N, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Abstract 2553: Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2553] [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
High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, a high degree of tumor heterogeneity and intraperitoneal spread. As immunotherapies have thus far proven ineffective in this disease, we sought to establish the determinants of immune recognition, avoidance and evasion in disease natural history to gain insight into the co-evolutionary processes underlying malignant progression and host immunity. Accordingly we linked mutational processes and anatomic sites of tumor foci as determinants of tumor microenvironment (TME) cellular phenotypes within and between patients using genome-based stratification of homologous recombination proficient (HRP) and deficient (HRD) disease subtypes, and profiling single cell phenotypes from ~1 million cells including cancer cells, T cells, myeloid cells and fibroblasts derived from single cell RNA sequencing, and in situ spatial profiling of histopathology, cancer cell, T cell and macrophage states of 160 tumor sites obtained from 42 treatment-naive patients. Mutational processes in HRD-Dup (BRCA1 mutant-like) tumors were associated with cancer cell-intrinsic JAK/STAT signaling and predominance of highly-differentiated dysfunctional CD8+ T cells in the TME; HRD-Del (BRCA2 mutant-like) tumors were associated with cancer cell-intrinsic NF-κB and TNFα signaling and expansion of M2-type macrophages; and foldback inversion (FBI, HRP) tumors were associated with cancer cell-intrinsic TGFβ signaling and overall immune exclusion, with a predominance of naive/central memory-like T cells. Increased neoantigen burden and HLA loss of heterozygosity (LOH) were defining genomic features of the HRD, but not FBI tumors. These mechanisms of escape from immune predation, with distinct signalling activity and losses of HLA allelic diversity in HRD tumors, connect evolutionary selection with immunological phenotypic states. Multi-region sampling revealed substantial spatial variation, highlighting site-specific properties of the ovary and fallopian tube as putative “immune-privileged” sites. These results establish that in patients with widespread intraperitoneal disease, the local properties of organ sites may determine malignant cell selection and immune pruning. Furthermore, we observed that spatial cellular topology is a major determinant of tumor-immune interactions by in situ protein measurements, revealing ubiquitous PD1-PDL1 interactions in HRD tumors. Together, our findings yield mechanistic insights for how distinct mutational processes in HGSOC lead to diverse patterns of within- and between- patient variation in immune resistance, which can be exploited to optimize future immuno-therapeutic treatment strategies.
Citation Format: Ignacio Vázquez-García, Florian Uhlitz, Nicholas Ceglia, Jamie L. Lim, Michelle Wu, Neeman Mohibullah, Arvin Eric B. Ruiz, Kevin M. Boehm, Viktoria Bojilova, Christopher J. Fong, Tyler Funnell, Diljot Grewal, Eliyahu Havasov, Samantha Leung, Arfath Pasha, Druv M. Patel, Maryam Pourmaleki, Nicole Rusk, Hongyu Shi, Rami Vanguri, Marc J. Williams, Allen W. Zhang, Vance Broach, Dennis S. Chi, Arnaud Da Cruz Paula, Ginger J. Gardner, Sarah H. Kim, Matthew Lennon, Kara Long Roche, Yukio Sonoda, Oliver Zivanovic, Ritika Kundra, Agnes Viale, Yonina Bykov, Fatemeh N. Derakhshan, Luke Geneslaw, Ana Maroldi, Andrea Schietinger, Travis J. Hollmann, Samuel F. Bakhoum, Robert A. Soslow, Lora H. Ellenson, Nadeem Abu-Rustum, Carol Aghajanian, Claire F. Friedman, Andrew McPherson, Britta Weigelt, MSK SPECTRUM Consortium, Dmitriy Zamarin, Sohrab P. Shah. Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2553.
Collapse
Affiliation(s)
| | | | | | - Jamie L. Lim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michelle Wu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Tyler Funnell
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diljot Grewal
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Arfath Pasha
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Druv M. Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Nicole Rusk
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongyu Shi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rami Vanguri
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Vance Broach
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dennis S. Chi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sarah H. Kim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Yukio Sonoda
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yonina Bykov
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Luke Geneslaw
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ana Maroldi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Doe-Tetteh SA, Camp SY, Crowdis J, Noronha AM, Reales D, Alano T, Viale A, Donoghue M, Socci ND, Berger MF, Al-Ahmadie HA, Funt SA, Feldman DR, Diamond EL, Van Allen EM, Solit DB. Overcoming barriers to tumor genomic profiling through direct patient social media outreach. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.6532] [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: 11/20/2022] Open
Abstract
6532 Background: Tumor genomic profiling is increasingly used to identify actionable genomic alterations as a guide to therapy selection. To overcome barriers to genomic testing for patients with rare cancers, we initiated a program to offer free clinical tumor genomic testing worldwide to patients with select rare cancer subtypes. Methods: Patients were recruited through social media outreach, engagement with disease advocacy groups, or via physician referral, with a focus on recruiting patients with histiocytosis, germ cell tumors and rare pediatric cancers. Tumor and patient-matched germline DNA were analyzed using the MSK-IMPACT targeted sequencing next generation sequencing panel with return of results to patients and their local physicians. Whole exome recapture of MSK-IMPACT DNA sequencing libraries was performed for patients with female germ cell tumors to define the genomic landscape of this rare cancer subtype. Results: 359 cancer patients expressed interest in the Make-an-IMPACT program, of whom 333 were enrolled. Tumor tissue was received for 288 (86.4%), with 250 (86.8%) having tumor DNA of sufficient quantity and quality for MSK-IMPACT testing. 14 histiocytosis patients have received genomically guided therapy to date, of whom 13 (93%) have had clinical benefit based on local MD response assessment with a mean treatment duration of 16.7 months (range 3-32+). Whole exome sequencing of ovarian GCTs identified a subset with fully haploid genotypes, a phenotype rarely observed in other cancer types. Actionable genomic alterations were rare in ovarian GCT (28%), however, 2 ovarian GCTs and squamous transformation had high tumor mutational burden, one of whom had a complete response to pembrolizumab. Conclusions: Social media outreach can facilitate the assembly of cohorts of rare cancers of sufficient size to define their genomic landscape. By profiling tumors in a clinical laboratory, results could be reported to patients and their local physicians where they could be used to guide treatment selection. This can also open the door to diversifying and being able to study the genomic landscape in a diverse cohort.
Collapse
Affiliation(s)
| | | | - Jett Crowdis
- Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
| | | | | | - Tina Alano
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | - David B. Solit
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, Kravis Center for Molecular Oncology, Sloan Kettering Institute, New York, NY
| |
Collapse
|
11
|
Shukla N, Levine MF, Gundem G, Domenico D, Spitzer B, Bouvier N, Arango-Ossa JE, Glodzik D, Medina-Martínez JS, Bhanot U, Gutiérrez-Abril J, Zhou Y, Fiala E, Stockfisch E, Li S, Rodriguez-Sanchez MI, O'Donohue T, Cobbs C, Roehrl MHA, Benhamida J, Iglesias Cardenas F, Ortiz M, Kinnaman M, Roberts S, Ladanyi M, Modak S, Farouk-Sait S, Slotkin E, Karajannis MA, Dela Cruz F, Glade Bender J, Zehir A, Viale A, Walsh MF, Kung AL, Papaemmanuil E. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Nat Commun 2022; 13:2485. [PMID: 35585047 PMCID: PMC9117241 DOI: 10.1038/s41467-022-30233-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.
Collapse
Affiliation(s)
- N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Domenico
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Glodzik
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Medina-Martínez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - U Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Gutiérrez-Abril
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Zhou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fiala
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - T O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Iglesias Cardenas
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Farouk-Sait
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Viale
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - E Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
12
|
Mohan P, Pasion J, Ciriello G, Lailler N, de Stanchina E, Viale A, van den Berg A, Diepstra A, Wendel HG, Sanghvi VR, Singh K. Frequent 4EBP1 Amplification Induces Synthetic Dependence on FGFR Signaling in Cancer. Cancers (Basel) 2022; 14:2397. [PMID: 35626002 PMCID: PMC9139685 DOI: 10.3390/cancers14102397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
The eIF4E translation initiation factor has oncogenic properties and concordantly, the inhibitory eIF4E-binding protein (4EBP1) is considered a tumor suppressor. The exact molecular effects of 4EBP1 activation in cancer are still unknown. Surprisingly, 4EBP1 is a target of genomic copy number gains (Chr. 8p11) in breast and lung cancer. We noticed that 4EBP1 gains are genetically linked to gains in neighboring genes, including WHSC1L1 and FGFR1. Our results show that FGFR1 gains act to attenuate the function of 4EBP1 via PI3K-mediated phosphorylation at Thr37/46, Ser65, and Thr70 sites. This implies that not 4EBP1 but instead FGFR1 is the genetic target of Chr. 8p11 gains in breast and lung cancer. Accordingly, these tumors show increased sensitivity to FGFR1 and PI3K inhibition, and this is a therapeutic vulnerability through restoring the tumor-suppressive function of 4EBP1. Ribosome profiling reveals genes involved in insulin signaling, glucose metabolism, and the inositol pathway to be the relevant translational targets of 4EBP1. These mRNAs are among the top 200 translation targets and are highly enriched for structure and sequence motifs in their 5'UTR, which depends on the 4EBP1-EIF4E activity. In summary, we identified the translational targets of 4EBP1-EIF4E that facilitate the tumor suppressor function of 4EBP1 in cancer.
Collapse
Affiliation(s)
- Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Joyce Pasion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, CH-1005 Lausanne, Switzerland;
| | - Nathalie Lailler
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA;
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.v.d.B.); (A.D.)
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.v.d.B.); (A.D.)
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (J.P.); (H.-G.W.)
| | - Viraj R. Sanghvi
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Kamini Singh
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY 10461, USA
| |
Collapse
|
13
|
Hussain SS, Majumdar R, Moore GM, Narang H, Buechelmaier E, Bazil MJ, Ravindran PT, Leeman J, Li Y, Jalan M, Anderson KS, Farina A, Soni R, Mohibullah N, Hamzic E, Rong-Mullins X, Sifuentes C, Damerla RR, Viale A, Powell SN, Higginson D. Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell. Nucleic Acids Res 2021; 49:e74. [PMID: 33877327 PMCID: PMC8287935 DOI: 10.1093/nar/gkab262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 11/10/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.
Collapse
Affiliation(s)
- Suleman S Hussain
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Grace M Moore
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Himanshi Narang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erika S Buechelmaier
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Maximilian J Bazil
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jonathan E Leeman
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02189, USA
| | - Yi Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Anderson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Farina
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rekha Soni
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neeman Mohibullah
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edin Hamzic
- Biocomputix, Sarajevo, 71000, Bosnia and Herzegovina
| | - Xiaoqing Rong-Mullins
- Department of Biostatistics, The Ohio State University College of Public Health, Columbus, OH 43210, USA
| | | | - Rama R Damerla
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
14
|
Samoila A, Sosa J, Padilla J, Wutkowski M, Vanness K, Viale A, Berger M, Houck-Loomis B, Pessin M, Peerschke EI. Developing Quality Programs for Cell-Free DNA (cfDNA) Extraction from Peripheral Blood. J Appl Lab Med 2021; 5:788-797. [PMID: 32603443 DOI: 10.1093/jalm/jfaa050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/09/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis using peripheral blood represents an exciting, minimally invasive technology for cancer diagnosis and monitoring. The reliability of testing is dependent on the accuracy and sensitivity of specific molecular analyses to detect tumor-associated genomic variants and on the quantity and quality of cfDNA available for testing. Specific guidelines for standardization and design of appropriate quality programs focused specifically on cfDNA isolation are lacking, as are standardized quality control reagents. CONTENT This report describes and illustrates quality control and quality assurance processes, supported by generation of in-house quality control material, to ensure the reliability of the preanalytical phase of cfDNA analysis. SUMMARY We have developed a robust quality program to support high-volume automated cfDNA extraction from peripheral blood by implementing processes and procedures designed to monitor the adequacy of specimen collection, specimen stability, efficiency of cfDNA extraction, and cfDNA quality.
Collapse
Affiliation(s)
- Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jose Sosa
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica Padilla
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Wutkowski
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katelynd Vanness
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian Houck-Loomis
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ellinor I Peerschke
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
15
|
Tsui DWY, Cheng ML, Shady M, Yang JL, Stephens D, Won H, Srinivasan P, Huberman K, Meng F, Jing X, Patel J, Hasan M, Johnson I, Gedvilaite E, Houck-Loomis B, Socci ND, Selcuklu SD, Seshan VE, Zhang H, Chakravarty D, Zehir A, Benayed R, Arcila M, Ladanyi M, Funt SA, Feldman DR, Li BT, Razavi P, Rosenberg J, Bajorin D, Iyer G, Abida W, Scher HI, Rathkopf D, Viale A, Berger MF, Solit DB. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients. Genome Med 2021; 13:96. [PMID: 34059130 PMCID: PMC8165771 DOI: 10.1186/s13073-021-00898-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 03/02/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. METHODS Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). RESULTS cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. CONCLUSIONS cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
Collapse
Affiliation(s)
- Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Weill Cornell Medical College, Weill Cornell University, New York, USA.
- Present Address: PetDx, Inc., La Jolla, USA.
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
- Present Address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Maha Shady
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
| | - Julie L Yang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dennis Stephens
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Xiaohong Jing
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: NYU Langone Health, New York, USA
| | - Juber Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maysun Hasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Brian Houck-Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Samuel A Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jonathan Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Cornell Medical College, Weill Cornell University, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
| |
Collapse
|
16
|
Shukla N, Levine M, Gundem G, Spitzer B, Gutierrez-Abril J, Bouvier N, Arango Ossa JE, Medina-Martinez J, Stockfisch E, O'Donohue T, Zehir A, Viale A, Modak S, Dela Cruz FS, Slotkin EK, Karajannis MA, Glade Bender JL, Walsh MF, Kung A, Papaemmanuil E. Feasibility and clinical utility of cancer whole genome and transcriptome sequencing for pediatric and young adult solid tumors. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.3063] [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: 11/20/2022] Open
Abstract
3063 Background: Next generation sequencing (NGS) assays have accelerated the identification of mutations and potential matched targeted therapies for patients with cancer. However, a significant proportion of patients do not derive clinical benefit from targeted panel sequencing approaches. Cancer whole genome and transcriptome sequencing (cWGTS) offers the opportunity to fully characterize tumors, but are challenged by significant cost and computational resource requirements, concerns of assay sensitivity, and the need to deliver curated results within clinically relevant time frames. We performed a prospective study to evaluate the feasibility and utility of cWGTS in pediatric and young adults with solid tumors. Methods: We developed an automated analytical workflow (Isabl) for the QC and processing of cWGTS data to include ensembl variant calling for germline and somatic substitutions, indels, and structural variants; fusion genes; gene expression; and mutation signatures. Treatment biomarkers were annotated using OncoKB with generation of a clinical prototype report. We tested the feasibility of cWGTS implementation, evaluated its analytical validity compared to standard diagnostic assays, and characterized the clinical utility of incremental findings in a prospective study of children and young adults treated at Memorial Sloan Kettering Cancer Center. Results: A total of 114 patients were enrolled. Standard NGS assays (MSK-IMPACT, MSK-Fusion) identified clinically relevant biomarkers in 22% of cases. The cWGTS process was completed, from sample acquisition to summary report, in less than 12 days. Comparison against clinically reported NGS results demonstrated high precision and recall for reported mutations (98.8%) with high concordance across variant allele representations (r2> 0.73). cWGTS identified additional oncogenic mutations not captured by targeted sequencing in 49% of patients. Furthermore, incremental findings, beyond those identified by NGS assays, of direct clinical relevance (diagnostic, prognostic, therapy guiding) were identified in 26% of patients. Importantly, < 5% of the incremental findings would have been captured by whole exome or transcriptome sequencing alone. Of possible therapeutic relevance, cWGTS analyses revealed a significantly higher tumor mutation burden than previously reported (range: 0 - 11.23). Conclusions: We demonstrate feasibility, analytical validity and clinical utility of cWGTS approaches in pediatric and young adult cancer patients, with nearly half of all patients having incremental findings that were not captured by standard targeted NGS approaches.
Collapse
Affiliation(s)
- Neerav Shukla
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Max Levine
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunes Gundem
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shakeel Modak
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Andrew Kung
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | |
Collapse
|
17
|
Singh K, Lin J, Lecomte N, Mohan P, Gokce A, Sanghvi VR, Jiang M, Grbovic-Huezo O, Burčul A, Stark SG, Romesser PB, Chang Q, Melchor JP, Beyer RK, Duggan M, Fukase Y, Yang G, Ouerfelli O, Viale A, de Stanchina E, Stamford AW, Meinke PT, Rätsch G, Leach SD, Ouyang Z, Wendel HG. Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules. Cancer Res 2021; 81:2002-2014. [PMID: 33632898 PMCID: PMC8137674 DOI: 10.1158/0008-5472.can-20-2929] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 08/30/2020] [Revised: 12/01/2020] [Accepted: 02/22/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signaling. Here, we show that the eIF4A RNA helicase is required for translation of key KRAS signaling molecules and that pharmacological inhibition of eIF4A has single-agent activity against murine and human PDAC models at safe dose levels. EIF4A was uniquely required for the translation of mRNAs with long and highly structured 5' untranslated regions, including those with multiple G-quadruplex elements. Computational analyses identified these features in mRNAs encoding KRAS and key downstream molecules. Transcriptome-scale ribosome footprinting accurately identified eIF4A-dependent mRNAs in PDAC, including critical KRAS signaling molecules such as PI3K, RALA, RAC2, MET, MYC, and YAP1. These findings contrast with a recent study that relied on an older method, polysome fractionation, and implicated redox-related genes as eIF4A clients. Together, our findings highlight the power of ribosome footprinting in conjunction with deep RNA sequencing in accurately decoding translational control mechanisms and define the therapeutic mechanism of eIF4A inhibitors in PDAC. SIGNIFICANCE: These findings document the coordinate, eIF4A-dependent translation of RAS-related oncogenic signaling molecules and demonstrate therapeutic efficacy of eIF4A blockade in pancreatic adenocarcinoma.
Collapse
Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut
| | - Nicolas Lecomte
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Askan Gokce
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Olivera Grbovic-Huezo
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Stefan G Stark
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Computer Science, Biomedical Informatics, ETH, Zürich, Zürich, Switzerland
| | - Paul B Romesser
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Qing Chang
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jerry P Melchor
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Rachel K Beyer
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mark Duggan
- Tri-Institutional Drug Development Initiative, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Yoshiyuki Fukase
- Tri-Institutional Drug Development Initiative, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Guangli Yang
- The Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ouathek Ouerfelli
- The Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Andrew W Stamford
- Tri-Institutional Drug Development Initiative, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Peter T Meinke
- Tri-Institutional Drug Development Initiative, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Computer Science, Biomedical Informatics, ETH, Zürich, Zürich, Switzerland
| | - Steven D Leach
- Molecular Systems Biology and Surgery, Geisel School of Medicine, Dartmouth, Norris Cotton Cancer Center at Dartmouth-Hitchcock, Lebanon, New Hampshire
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York.
| |
Collapse
|
18
|
Sanghvi VR, Mohan P, Singh K, Cao L, Berishaj M, Wolfe AL, Schatz JH, Lailler N, de Stanchina E, Viale A, Wendel HG. NRF2 Activation Confers Resistance to eIF4A Inhibitors in Cancer Therapy. Cancers (Basel) 2021; 13:cancers13040639. [PMID: 33562682 PMCID: PMC7915661 DOI: 10.3390/cancers13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary eIF4A-targeted translational inhibitors, such as silvestrol and its analogues, have emerged as strong anticancer therapies. Here, we tested the efficacy of eIF4A inhibition across a large and diverse panel of cancer cell lines and found B cell lymphomas to be the most sensitive group. Moreover, we performed a genetic screen and identified NRF2 activation as a major mechanism of resistance to silvestrol and related eIF4A inhibitors. Mechanistically, NRF2 activation broadly increases protein synthesis, and this effect is more pronounced on specific mRNAs that require eIF4A for translation. Finally, blocking NRF2 function by preventing its deglycation restores silvestrol sensitivity in cells that harbor NRF2 activation. Overall, our findings indicate that eIF4A inhibitors are a feasible therapeutic option against lymphoma and other cancers and that NRF2 activation status may be an important predictor of their efficacy. Abstract Inhibition of the eIF4A RNA helicase with silvestrol and related compounds is emerging as a powerful anti-cancer strategy. We find that a synthetic silvestrol analogue (CR-1-31 B) has nanomolar activity across many cancer cell lines. It is especially active against aggressive MYC+/BCL2+ B cell lymphomas and this likely reflects the eIF4A-dependent translation of both MYC and BCL2. We performed a genome-wide CRISPR/Cas9 screen and identified mechanisms of resistance to this new class of therapeutics. We identify three negative NRF2 regulators (KEAP1, CUL3, CAND1) whose inactivation is sufficient to cause CR1-31-B resistance. NRF2 is known to alter the oxidation state of translation factors and cause a broad increase in protein production. We find that NRF2 activation particularly increases the translation of some eIF4A-dependent mRNAs and restores MYC and BCL2 production. We know that NRF2 functions depend on removal of sugar adducts by the frutosamine-3-kinase (FN3K). Accordingly, loss of FN3K results in NRF2 hyper-glycation and inactivation and resensitizes cancer cells to eIF4A inhibition. Together, our findings implicate NRF2 in the translation of eIF4A-dependent mRNAs and point to FN3K inhibition as a new strategy to block NRF2 functions in cancer.
Collapse
Affiliation(s)
- Viraj R. Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Correspondence:
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
| | - Linlin Cao
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
- Swiss Institute of Experimental Cancer Research, EPFL, 1015 Lausanne, Switzerland
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
| | - Andrew L. Wolfe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
- Hellen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
| | - Jonathan H. Schatz
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
- Department of Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Nathalie Lailler
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Elisa de Stanchina
- Department of Antitumor Assessment Core and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (N.L.); (A.V.)
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (P.M.); (K.S.); (L.C.); (M.B.); (A.L.W.); (J.H.S.); (H.-G.W.)
| |
Collapse
|
19
|
Cheng ML, Donoghue MTA, Audenet F, Wong NC, Pietzak EJ, Bielski CM, Isharwal S, Iyer G, Funt S, Bagrodia A, Bajorin DF, Reuter VE, Eng J, Joseph G, Bourque C, Bromberg M, Ling L, Selcuklu SD, Arcila ME, Tsui DWY, Zehir A, Viale A, Berger MF, Bosl GJ, Sheinfeld J, Van Allen E, Taylor BS, Al-Ahmadie H, Solit DB, Feldman DR. Germ Cell Tumor Molecular Heterogeneity Revealed Through Analysis of Primary and Metastasis Pairs. JCO Precis Oncol 2020; 4:2000166. [PMID: 33163850 DOI: 10.1200/po.20.00166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Although primary germ cell tumors (GCTs) have been extensively characterized, molecular analysis of metastatic sites has been limited. We performed whole-exome sequencing and targeted next-generation sequencing on paired primary and metastatic GCT samples in a patient cohort enriched for cisplatin-resistant disease. PATIENTS AND METHODS Tissue sequencing was performed on 100 tumor specimens from 50 patients with metastatic GCT, and sequencing of plasma cell-free DNA was performed for a subset of patients. RESULTS The mutational landscape of primary and metastatic pairs from GCT patients was highly discordant (68% of all somatic mutations were discordant). Whereas genome duplication was common and highly concordant between primary and metastatic samples, only 25% of primary-metastasis pairs had ≥ 50% concordance at the level of DNA copy number alterations (CNAs). Evolutionary-based analyses revealed that most mutations arose after CNAs at the respective loci in both primary and metastatic samples, with oncogenic mutations enriched in the set of early-occurring mutations versus variants of unknown significance (VUSs). TP53 pathway alterations were identified in nine cisplatin-resistant patients and had the highest degree of concordance in primary and metastatic specimens, consistent with their association with this treatment-resistant phenotype. CONCLUSION Analysis of paired primary and metastatic GCT specimens revealed significant molecular heterogeneity for both CNAs and somatic mutations. Among loci demonstrating serial genetic evolution, most somatic mutations arose after CNAs, but oncogenic mutations were enriched in the set of early-occurring mutations as compared with VUSs. Alterations in TP53 were clonal when present and shared among primary-metastasis pairs.
Collapse
Affiliation(s)
- Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - François Audenet
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan C Wong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eugene J Pietzak
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Craig M Bielski
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Isharwal
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Samuel Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Aditya Bagrodia
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jana Eng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gabriella Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caitlin Bourque
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Bromberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lilan Ling
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - George J Bosl
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joel Sheinfeld
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| |
Collapse
|
20
|
Hanrahan AJ, Sylvester BE, Chang MT, Elzein A, Gao J, Han W, Liu Y, Xu D, Gao SP, Gorelick AN, Jones AM, Kiliti AJ, Nissan MH, Nimura CA, Poteshman AN, Yao Z, Gao Y, Hu W, Wise HC, Gavrila EI, Shoushtari AN, Tiwari S, Viale A, Abdel-Wahab O, Merghoub T, Berger MF, Rosen N, Taylor BS, Solit DB. Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer. Cancer Res 2020; 80:4233-4243. [PMID: 32641410 PMCID: PMC7541597 DOI: 10.1158/0008-5472.can-20-0865] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 03/16/2020] [Revised: 04/18/2020] [Accepted: 07/02/2020] [Indexed: 01/06/2023]
Abstract
Despite significant advances in cancer precision medicine, a significant hurdle to its broader adoption remains the multitude of variants of unknown significance identified by clinical tumor sequencing and the lack of biologically validated methods to distinguish between functional and benign variants. Here we used functional data on MAP2K1 and MAP2K2 mutations generated in real-time within a co-clinical trial framework to benchmark the predictive value of a three-part in silico methodology. Our computational approach to variant classification incorporated hotspot analysis, three-dimensional molecular dynamics simulation, and sequence paralogy. In silico prediction accurately distinguished functional from benign MAP2K1 and MAP2K2 mutants, yet drug sensitivity varied widely among activating mutant alleles. These results suggest that multifaceted in silico modeling can inform patient accrual to MEK/ERK inhibitor clinical trials, but computational methods need to be paired with laboratory- and clinic-based efforts designed to unravel variabilities in drug response. SIGNIFICANCE: Leveraging prospective functional characterization of MEK1/2 mutants, it was found that hotspot analysis, molecular dynamics simulation, and sequence paralogy are complementary tools that can robustly prioritize variants for biologic, therapeutic, and clinical validation.See related commentary by Whitehead and Sebolt-Leopold, p. 4042.
Collapse
Affiliation(s)
- Aphrothiti J Hanrahan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brooke E Sylvester
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arijh Elzein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- The Graduate Program in Pharmacology, The Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, New York
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Sizhi P Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander N Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Alexis M Jones
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amber J Kiliti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Moriah H Nissan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clare A Nimura
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abigail N Poteshman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhan Yao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Mechanism-Based Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yijun Gao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Mechanism-Based Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah C Wise
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena I Gavrila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander N Shoushtari
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Shakuntala Tiwari
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Rosen
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Mechanism-Based Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| |
Collapse
|
21
|
Kothari P, Marass F, Yang JL, Stewart CM, Stephens D, Patel J, Hasan M, Jing X, Meng F, Enriquez J, Huberman K, Viale A, Francis JH, Berger MF, Shukla N, Abramson DH, Dunkel IJ, Tsui DW. Cell‐free DNA profiling in retinoblastoma patients with advanced intraocular disease: An MSKCC experience. Cancer Med 2020; 9:6093-6101. [PMID: 32633890 PMCID: PMC7476838 DOI: 10.1002/cam4.3144] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 10/11/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
Purpose The enucleation rate for retinoblastoma has dropped from over 95% to under 10% in the past 10 years as a result of improvements in therapy. This reduces access to tumor tissue for molecular profiling, especially in unilateral retinoblastoma, and hinders the confirmation of somatic RB1 mutations necessary for genetic counseling. Plasma cell‐free DNA (cfDNA) has provided a platform for noninvasive molecular profiling in cancer, but its applicability in low tumor burden retinoblastoma has not been shown. We analyzed cfDNA collected from 10 patients with available tumor tissue to determine whether sufficient tumorderived cfDNA is shed in plasma from retinoblastoma tumors to enable noninvasive RB1 mutation detection. Methods Tumor tissue was collected from eye enucleations in 10 patients diagnosed with advanced intra‐ocular unilateral retinoblastoma, three of which went on to develop metastatic disease. Tumor RB1 mutation status was determined using an FDA‐cleared tumor sequencing assay, MSK‐IMPACT. Plasma samples were collected before eye enucleation and analyzed with a customized panel targeting all exons of RB1. Results Tumor‐guided genotyping detected 10 of the 13 expected somatic RB1 mutations in plasma cfDNA in 8 of 10 patients (average variant allele frequency 3.78%). Without referring to RB1 status in the tumor, de novo mutation calling identified 7 of the 13 expected RB1 mutations (in 6 of 10 patients) with high confidence. Conclusion Plasma cfDNA can detect somatic RB1 mutations in patients with unilateral retinoblastoma. Since intraocular biopsies are avoided in these patients because of concern about spreading tumor, cfDNA can potentially offer a noninvasive platform to guide clinical decisions about treatment, follow‐up schemes, and risk of metastasis.
Collapse
Affiliation(s)
| | - Francesco Marass
- ETH Zurich Basel Switzerland
- SIB Swiss Institute of Bioinformatics Basel Switzerland
| | - Julie L. Yang
- Memorial Sloan Kettering Cancer Center New York NY USA
| | | | | | - Juber Patel
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Maysun Hasan
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Xiaohong Jing
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Fanli Meng
- Memorial Sloan Kettering Cancer Center New York NY USA
| | | | - Kety Huberman
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Jasmine H. Francis
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Michael F. Berger
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Neerav Shukla
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - David H. Abramson
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Ira J. Dunkel
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Dana W.Y. Tsui
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| |
Collapse
|
22
|
Singh K, Lin J, Lecomte N, Mohan P, Gokce A, Sanghvi V, Olivera GH, Jiang M, Burčul A, Stark S, Viale A, Romesser PB, Destanchia E, Bagni R, Rätsch G, Leach SD, Ouyang Z, Wendel HG. Abstract B44: KRAS and RAS signaling network is co-regulated and can be therapeutically blocked by targeting eIF4A dependent translation program. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
New and effective therapeutics are urgently needed for the treatment of pancreatic ductal adenocarcinoma (PDAC). The eIF4A/DDX2 RNA helicase drives translation of mRNAs with highly structured 5′UTRs. The natural compound silvestrol and synthetic analogues are potent and selective inhibitors of eIF4A1/2 that show promising activity in models of hematologic malignancies. Here, we show silvestrol analogues have nanomolar activity against PDAC cell lines and organoids in vitro. Moreover, we see single-agent activity in the KRAS/p53 mouse PDAC model and also against PDAC xenograft and primary, patient-derived PDAC tumors. These therapeutic effects occur at nontoxic dose levels. Transcriptome-wide ribosome profiling, analyses of protein and gene expression, and translation reporter studies reveal that KRAS and the RAS signaling network is co-regulated by translation in an eIF4A dependent manner. eIF4A inhibitors block an oncogenic translation program in PDAC cells that includes G-quadruplex containing mRNAs such as KRAS, MYC, YAP1, MET, SMAD3, TGFβ and other components of the RAS signaling network. Together, our data indicate that pharmacologic inhibition of eIF4A disrupts oncoproteins production and shows efficacy across several PDAC models.
Citation Format: Kamini Singh, Jianan Lin, Nicolas Lecomte, Prathibha Mohan, Askan Gokce, Viraj Sanghvi, Grbovic-Huezo Olivera, Man Jiang, Antonija Burčul, Stefan Stark, Agnes Viale, Paul B. Romesser, Elisa Destanchia, Rachel Bagni, Gunnar Rätsch, Steve D. Leach, Zhengqing Ouyang, Hans-Guido Wendel. KRAS and RAS signaling network is co-regulated and can be therapeutically blocked by targeting eIF4A dependent translation program [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B44.
Collapse
Affiliation(s)
- Kamini Singh
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Jianan Lin
- 2The Jackson Laboratory for Genomic Medicine, New York, NY,
| | - Nicolas Lecomte
- 3David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Prathibha Mohan
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Askan Gokce
- 3David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Viraj Sanghvi
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Grbovic-Huezo Olivera
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Man Jiang
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Antonija Burčul
- 4Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Stefan Stark
- 5Biomedical Informatics, Department of Computer Science, ETH, Zurich, Switzerland,
| | - Agnes Viale
- 6Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Paul B. Romesser
- 7Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Elisa Destanchia
- 8Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | - Gunnar Rätsch
- 5Biomedical Informatics, Department of Computer Science, ETH, Zurich, Switzerland,
| | - Steve D. Leach
- 10Molecular Systems Biology and Surgery, Geisel School of Medicine, Dartmouth, Norris Cotton Cancer Center at Dartmouth-Hitchcock, Lebanon, NH,
| | - Zhengqing Ouyang
- 11Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- 1Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY,
| |
Collapse
|
23
|
Datta J, Smith JJ, Chatila WK, McAuliffe JC, Kandoth C, Vakiani E, Frankel TL, Ganesh K, Wasserman I, Lipsyc-Sharf M, Guillem J, Nash GM, Paty PB, Weiser MR, Saltz LB, Berger MF, Jarnagin WR, Balachandran V, Kingham TP, Kemeny NE, Cercek A, Garcia-Aguilar J, Taylor BS, Viale A, Yaeger R, Solit DB, Schultz N, D'Angelica MI. Coaltered Ras/B-raf and TP53 Is Associated with Extremes of Survivorship and Distinct Patterns of Metastasis in Patients with Metastatic Colorectal Cancer. Clin Cancer Res 2019; 26:1077-1085. [PMID: 31719050 DOI: 10.1158/1078-0432.ccr-19-2390] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [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: 07/24/2019] [Revised: 09/27/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE We aimed to investigate genomic correlates underlying extremes of survivorship in metastatic colorectal cancer and their applicability in informing survival in distinct subsets of patients with metastatic colorectal cancer. EXPERIMENTAL DESIGN We examined differences in oncogenic somatic alterations between metastatic colorectal cancer cohorts demonstrating extremes of survivorship following complete metastasectomy: ≤2-year (n = 17) and ≥10-year (n = 18) survivors. Relevant genomic findings, and their association with overall survival (OS), were validated in two independent datasets of 935 stage IV and 443 resected stage I-IV patients. RESULTS In the extremes-of-survivorship cohort, significant co-occurrence of KRAS hotspot mutations and TP53 alterations was observed in ≤2-year survivors (P < 0.001). When validating these findings in the independent cohort of 935 stage IV patients, incorporation of the cumulative effect of any oncogenic Ras/B-raf (i.e., either KRAS, NRAS, or BRAF) and TP53 alteration generated three prognostic clusters: (i) TP53-altered alone (median OS, 132 months); (ii) Ras/B-raf-altered alone (65 months) or Ras/B-raf- and TP53 pan-wild-type (60 months); and (iii) coaltered Ras/B-raf-TP53 (40 months; P < 0.0001). Coaltered Ras/B-raf-TP53 was independently associated with mortality (HR, 2.47; 95% confidence interval, 1.91-3.21; P < 0.001). This molecular profile predicted survival in the second independent cohort of 443 resected stage I-IV patients. Coaltered Ras/B-raf-TP53 was associated with worse OS in patients with liver (n = 490) and lung (n = 172) but not peritoneal surface (n = 149) metastases. Moreover, coaltered Ras/B-raf-TP53 tumors were significantly more likely to involve extrahepatic metastatic sites with limited salvage options. CONCLUSIONS Genomic analysis of extremes of survivorship following colorectal cancer metastasectomy identifies a prognostic role for coaltered Ras/B-raf-TP53 and its association with distinct patterns of colorectal cancer metastasis.
Collapse
Affiliation(s)
- Jashodeep Datta
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Surgery, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, Florida
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John C McAuliffe
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Montefiore Medical Center, Bronx, New York
| | - Cyriac Kandoth
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy L Frankel
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Karuna Ganesh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isaac Wasserman
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marla Lipsyc-Sharf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jose Guillem
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Garrett M Nash
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip B Paty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - T Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy E Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
24
|
Perera D, Ghossein R, Camacho N, Senbabaoglu Y, Seshan V, Li J, Bouvier N, Boucai L, Viale A, Socci ND, Untch BR, Gonen M, Knauf J, Fagin JA, Berger M, Tuttle RM. Genomic and Transcriptomic Characterization of Papillary Microcarcinomas With Lateral Neck Lymph Node Metastases. J Clin Endocrinol Metab 2019; 104:4889-4899. [PMID: 31237614 PMCID: PMC6733494 DOI: 10.1210/jc.2019-00431] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/19/2019] [Indexed: 02/08/2023]
Abstract
CONTEXT Most papillary microcarcinomas (PMCs) are indolent and subclinical. However, as many as 10% can present with clinically significant nodal metastases. OBJECTIVE AND DESIGN Characterization of the genomic and transcriptomic landscape of PMCs presenting with or without clinically important lymph node metastases. SUBJECTS AND SAMPLES Formalin-fixed paraffin-embedded PMC samples from 40 patients with lateral neck nodal metastases (pN1b) and 71 patients with PMC with documented absence of nodal disease (pN0). OUTCOME MEASURES To interrogate DNA alterations in 410 genes commonly mutated in cancer and test for differential gene expression using a custom NanoString panel of 248 genes selected primarily based on their association with tumor size and nodal disease in the papillary thyroid cancer TCGA project. RESULTS The genomic landscapes of PMC with or without pN1b were similar. Mutations in TERT promoter (3%) and TP53 (1%) were exclusive to N1b cases. Transcriptomic analysis revealed differential expression of 43 genes in PMCs with pN1b compared with pN0. A random forest machine learning-based molecular classifier developed to predict regional lymph node metastasis demonstrated a negative predictive value of 0.98 and a positive predictive value of 0.72 at a prevalence of 10% pN1b disease. CONCLUSIONS The genomic landscape of tumors with pN1b and pN0 disease was similar, whereas 43 genes selected primarily by mining the TCGA RNAseq data were differentially expressed. This bioinformatics-driven approach to the development of a custom transcriptomic assay provides a basis for a molecular classifier for pN1b risk stratification in PMC.
Collapse
Affiliation(s)
- Dilmi Perera
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Yasin Senbabaoglu
- Department of Bioinformatics & Computational Biology, Genentech, South San Francisco, California
| | | | - Juan Li
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Boucai
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Brian R Untch
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gonen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey Knauf
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Berger
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - R Michael Tuttle
- Memorial Sloan Kettering Cancer Center, New York, New York
- Correspondence and Reprint Requests: R. Michael Tuttle, MD, Endocrinology Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021. E-mail:
| |
Collapse
|
25
|
Sanghvi VR, Leibold J, Mina M, Mohan P, Berishaj M, Li Z, Miele MM, Lailler N, Zhao C, de Stanchina E, Viale A, Akkari L, Lowe SW, Ciriello G, Hendrickson RC, Wendel HG. The Oncogenic Action of NRF2 Depends on De-glycation by Fructosamine-3-Kinase. Cell 2019; 178:807-819.e21. [PMID: 31398338 PMCID: PMC6693658 DOI: 10.1016/j.cell.2019.07.031] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/23/2019] [Accepted: 07/17/2019] [Indexed: 12/28/2022]
Abstract
The NRF2 transcription factor controls a cell stress program that is implicated in cancer and there is great interest in targeting NRF2 for therapy. We show that NRF2 activity depends on Fructosamine-3-kinase (FN3K)-a kinase that triggers protein de-glycation. In its absence, NRF2 is extensively glycated, unstable, and defective at binding to small MAF proteins and transcriptional activation. Moreover, the development of hepatocellular carcinoma triggered by MYC and Keap1 inactivation depends on FN3K in vivo. N-acetyl cysteine treatment partially rescues the effects of FN3K loss on NRF2 driven tumor phenotypes indicating a key role for NRF2-mediated redox balance. Mass spectrometry reveals that other proteins undergo FN3K-sensitive glycation, including translation factors, heat shock proteins, and histones. How glycation affects their functions remains to be defined. In summary, our study reveals a surprising role for the glycation of cellular proteins and implicates FN3K as targetable modulator of NRF2 activity in cancer.
Collapse
Affiliation(s)
- Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Josef Leibold
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Mina
- Department of Computational Biology, University of Lausanne, 1005 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhuoning Li
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew M Miele
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nathalie Lailler
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chunying Zhao
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core and Molecular Pharmacology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Leila Akkari
- Oncode Institute, Tumor Biology and Immunology division, the Netherlands Cancer Institute, 1006 BE, Amsterdam, the Netherlands
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, 1005 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland
| | - Ronald C Hendrickson
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
26
|
Jonsson P, Bandlamudi C, Cheng ML, Srinivasan P, Chavan SS, Friedman ND, Rosen EY, Richards AL, Bouvier N, Selcuklu SD, Bielski CM, Abida W, Mandelker D, Birsoy O, Zhang L, Zehir A, Donoghue MTA, Baselga J, Offit K, Scher HI, O'Reilly EM, Stadler ZK, Schultz N, Socci ND, Viale A, Ladanyi M, Robson ME, Hyman DM, Berger MF, Solit DB, Taylor BS. Tumour lineage shapes BRCA-mediated phenotypes. Nature 2019; 571:576-579. [PMID: 31292550 PMCID: PMC7048239 DOI: 10.1038/s41586-019-1382-1] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [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: 01/03/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Mutations in BRCA1 and BRCA2 predispose individuals to certain cancers1-3, and disease-specific screening and preventative strategies have reduced cancer mortality in affected patients4,5. These classical tumour-suppressor genes have tumorigenic effects associated with somatic biallelic inactivation, although haploinsufficiency may also promote the formation and progression of tumours6,7. Moreover, BRCA1/2-mutant tumours are often deficient in the repair of double-stranded DNA breaks by homologous recombination8-13, and consequently exhibit increased therapeutic sensitivity to platinum-containing therapy and inhibitors of poly-(ADP-ribose)-polymerase (PARP)14,15. However, the phenotypic and therapeutic relevance of mutations in BRCA1 or BRCA2 remains poorly defined in most cancer types. Here we show that in the 2.7% and 1.8% of patients with advanced-stage cancer and germline pathogenic or somatic loss-of-function alterations in BRCA1/2, respectively, selective pressure for biallelic inactivation, zygosity-dependent phenotype penetrance, and sensitivity to PARP inhibition were observed only in tumour types associated with increased heritable cancer risk in BRCA1/2 carriers (BRCA-associated cancer types). Conversely, among patients with non-BRCA-associated cancer types, most carriers of these BRCA1/2 mutation types had evidence for tumour pathogenesis that was independent of mutant BRCA1/2. Overall, mutant BRCA is an indispensable founding event for some tumours, but in a considerable proportion of other cancers, it appears to be biologically neutral-a difference predominantly conditioned by tumour lineage-with implications for disease pathogenesis, screening, design of clinical trials and therapeutic decision-making.
Collapse
Affiliation(s)
- Philip Jonsson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noah D Friedman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - José Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- AstraZeneca, Waltham, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
27
|
Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med 2019; 216:1509-1524. [PMID: 31142587 PMCID: PMC6605752 DOI: 10.1084/jem.20181726] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 09/10/2018] [Revised: 02/22/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. Specifically, MYC drives the translation of most protein components of the electron transport chain in lymphoma cells, and many of these effects are independent from proliferation. Specific interactions of MYC-sensitive RNA-binding proteins (e.g., SRSF1/RBM42) with 5'UTR sequence motifs mediate many of these changes. Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. Together, our findings reveal MYC effects on the translation of key metabolic enzymes and immune receptors in lymphoma cells.
Collapse
Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald C Hendrickson
- Proteomics and Microchemistry, Memorial Sloan- Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
28
|
Sinn BV, Fu C, Lau R, Litton J, Tsai TH, Murthy R, Tam A, Andreopoulou E, Gong Y, Murthy R, Gould R, Zhang Y, King TA, Viale A, Andrade V, Giri D, Salgado R, Laios I, Sotiriou C, Marginean EC, Kwiatkowski DN, Layman RM, Booser D, Hatzis C, Vicente Valero V, Fraser Symmans W. SET ER/PR: a robust 18-gene predictor for sensitivity to endocrine therapy for metastatic breast cancer. NPJ Breast Cancer 2019; 5:16. [PMID: 31231679 PMCID: PMC6542807 DOI: 10.1038/s41523-019-0111-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022] Open
Abstract
There is a clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SETER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to preanalytical and analytical influences. We tested SETER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand-binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients. Higher SETER/PR index in metastatic samples predicted longer PFS and OS when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1-98% of ESR1 transcripts (all had high SETER/PR index). A signature based on probe sets with good preanalytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SETER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.
Collapse
Affiliation(s)
- Bruno V. Sinn
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institut of Health, Berlin, Germany
| | - Chunxiao Fu
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rosanna Lau
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jennifer Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Tsung-Heng Tsai
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rashmi Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alda Tam
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Eleni Andreopoulou
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Yun Gong
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Ravi Murthy
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rebekah Gould
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Ya Zhang
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Tari A. King
- Department of Surgery, Brigham and Women’s Hospital and Dana Farber Cancer Institute, Boston, MA USA
| | - Agnes Viale
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Victor Andrade
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
- Department of Pathology, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Dilip Giri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Ioanna Laios
- Department of Pathology, Institut Jules Bordet, Brussels, Belgium
| | - Christos Sotiriou
- Translational Breast Cancer Laboratory, Institut Jules Bordet, Brussels, Belgium
| | | | - Danielle N. Kwiatkowski
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rachel M. Layman
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Daniel Booser
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christos Hatzis
- Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - V. Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - W. Fraser Symmans
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| |
Collapse
|
29
|
Damerla RR, Lee NY, You D, Soni R, Shah R, Reyngold M, Katabi N, Wu V, McBride SM, Tsai CJ, Riaz N, Powell SN, Babady NE, Viale A, Higginson DS. Detection of Early Human Papillomavirus-Associated Cancers by Liquid Biopsy. JCO Precis Oncol 2019; 3. [PMID: 31485558 DOI: 10.1200/po.18.00276] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE A circulating tumor DNA (ctDNA) test to detect plasma Epstein-Barr viral DNA can be used to screen for early nasopharyngeal cancers; however, the reported sensitivity of viral ctDNA tests to detect human papillomavirus (HPV)-associated cancers is modest. We assessed the utility of droplet digital polymerase chain reaction (ddPCR) to detect early-stage HPV-associated cancers using sequential HPV16 and HPV33 assays that account for HPV subtype distribution and subtype sequence variants. PATIENTS AND METHODS We collected plasma specimens from 97 HPV-positive patients with oropharyngeal squamous cell carcinoma and eight patients with HPV-positive anal squamous cell carcinoma, each with locoregionally confined disease. Negative controls included samples from seven patients with HPV-negative head and neck cancers and 20 individuals without cancer. RESULTS Of 97 patients with nonmetastatic, locoregionally confined oropharyngeal squamous cell carcinoma, 90 patients had detectable HPV16 ctDNA and three patients had HPV33 ctDNA, indicating an overall sensitivity of 95.6%. Seven of eight patients with early anal cancer were HPV16 ctDNA positive. No HPV ctDNA was detected in 27 negative controls, indicating 100% specificity. HPV16 ctDNA was detected in 19 of 19 patients with low-volume disease, defined as patients with a single, asymptomatic positive lymph node (N1) or an isolated T1-2 asymptomatic primary tumor. HPV16 ctDNA levels directly corresponded to tumor responses to chemoradiation and surgery. CONCLUSION With an updated understanding of HPV subtypes and sequence variation, HPV ctDNA by ddPCR is highly sensitive and specific, identifying HPV16 and HPV33 subtypes in a similar distribution as reported in major genomic profiling studies. The detection of small tumors indicates that HPV16 and HPV33 ctDNA ddPCR could be readily used in early detection screening trials and in disease response monitoring, analogous to Epstein-Barr virus DNA.
Collapse
Affiliation(s)
| | - Nancy Y Lee
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Daoqui You
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Rekha Soni
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Rachna Shah
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Nora Katabi
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Vanessa Wu
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Nadeem Riaz
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Agnes Viale
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | |
Collapse
|
30
|
Okada T, Sinha S, Esposito I, Schiavon G, López-Lago MA, Su W, Pratilas CA, Abele C, Hernandez JM, Ohara M, Okada M, Viale A, Heguy A, Socci ND, Sapino A, Seshan VE, Long S, Inghirami G, Rosen N, Giancotti FG. Author Correction: The Rho GTPase Rnd1 suppresses mammary tumorigenesis and EMT by restraining Ras-MAPK signalling. Nat Cell Biol 2019; 21:534. [PMID: 30842593 DOI: 10.1038/s41556-019-0288-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published the same blot was inadvertently presented as both p-Rb and Cyclin A in Fig. 2a. This blot corresponds to the p-Rb panel, as can be seen in the unprocessed version of these blots in Supplementary Fig. 9. The corrected version of the panel is shown below, together with a completely uncropped image of both blots. In addition, in the 'Viral transduction' section of the Methods, the pLKO.1 plasmids encoding short hairpin RNAs targeting human Rnd1 were incorrectly listed as clones TRCN0000018338 and TRCN0000039977. The correct clone numbers are TRCN0000047434 and TRCN0000047435.
Collapse
Affiliation(s)
- Tomoyo Okada
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, 10065, USA
| | - Surajit Sinha
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Ilaria Esposito
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Gaia Schiavon
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Breast Unit, Royal Marsden Hospital, London, SW3 6JJ, UK
| | - Miguel A López-Lago
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Surgery and Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, 10065, USA
| | - Wenjing Su
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Christine A Pratilas
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Pediatrics, Memorial Hospital, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21287, USA
| | - Cristina Abele
- Department of Biomedical Sciences and Human Oncology, Center of Experimental Medicine and Research, University of Torino, Torino, 10126, Italy
| | - Jonathan M Hernandez
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Surgery, Memorial Hospital, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Masahiro Ohara
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Agnes Viale
- Genomics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Adriana Heguy
- Geoffrey Beene Translational Oncology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Pathology, Office for Collaborative Science, New York University, New York, 10016, USA
| | - Nicholas D Socci
- Bioinformatics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Anna Sapino
- Department of Medical Sciences, Center of Experimental Medicine and Research, University of Torino, Torino, 10126, Italy
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Hospital, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Stephen Long
- Structural Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Giorgio Inghirami
- Department of Biomedical Sciences and Human Oncology, Center of Experimental Medicine and Research, University of Torino, Torino, 10126, Italy.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, 10065, USA
| | - Neal Rosen
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.,Department of Medicine, Memorial Hospital, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Filippo G Giancotti
- Cell Biology Program, Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.
| |
Collapse
|
31
|
Narayan RR, Goldman DA, Gonen M, Reichel J, Huberman KH, Raj S, Viale A, Kemeny NE, Allen PJ, Balachandran VP, D'Angelica MI, DeMatteo RP, Drebin JA, Jarnagin WR, Kingham TP. Peripheral Circulating Tumor DNA Detection Predicts Poor Outcomes After Liver Resection for Metastatic Colorectal Cancer. Ann Surg Oncol 2019; 26:1824-1832. [PMID: 30706231 DOI: 10.1245/s10434-019-07201-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Liver resection can be curative for well-selected metastatic colorectal cancer (CRC) patients. Circulating tumor DNA (ctDNA) has shown promise as a biomarker for tumor dynamics and recurrence following CRC resection. This prospective pilot study investigated the use of ctDNA to predict disease outcome in resected CRC patients. METHODS Between November 2014 and November 2015, 60 patients with CRC were identified and prospectively enrolled. During liver resection, blood was drawn from peripheral (PERIPH), portal (PV), and hepatic (HV) veins, and 3-4 weeks postoperatively from a peripheral vein (POSTOP). Kappa statistics were used to compare mutated (mt) genes in tissue and ctDNA. Disease-specific and disease-free survival (DSS and DFS) were assessed from surgery with Kaplan-Meier and Cox methods. RESULTS For the 59 eligible patients, the most commonly mutated genes were TP53 (mtTP53: 47.5%) and APC (mtAPC: 50.8%). Substantial to almost-perfect agreement was seen between ctDNA from PERIPH and PV (mtTP53: 89.8%, κ = 0.73, 95% confidence interval [CI] 0.53-0.93; mtAPC: 94.9%, κ = 0.83, 95% CI 0.64-1.00), as well as HV (mtTP53: 91.5%, κ = 0.78, 95% CI 0.60-0.96; mtAPC: 91.5%, κ = 0.73, 95% CI 0.51-0.95). Tumor mutations and PERIPH ctDNA had fair-to-moderate agreement (mtTP53: 72.9%, κ = 0.44, 95% CI 0.23-0.66; mtAPC: 61.0%, κ = 0.23, 95% CI 0.04-0.42). Detection of PERIPH mtTP53 was associated with worse 2-year DSS (mt+ 79% vs. mt- 90%, P = 0.024). CONCLUSIONS Peripheral blood reflects the perihepatic ctDNA signature. Disagreement between tissue and ctDNA mutations may reflect the true natural history of tumor genes or an assay limitation. Peripheral ctDNA detection before liver resection is associated with worse DSS.
Collapse
Affiliation(s)
- Raja R Narayan
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Debra A Goldman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Reichel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kety H Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sandeep Raj
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy E Kemeny
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter J Allen
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vinod P Balachandran
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael I D'Angelica
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald P DeMatteo
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey A Drebin
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William R Jarnagin
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - T Peter Kingham
- Department of Surgery, Hepatopancreatobiliary Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
32
|
Harding JJ, Lowery MA, Shih AH, Schvartzman JM, Hou S, Famulare C, Patel M, Roshal M, Do RK, Zehir A, You D, Selcuklu SD, Viale A, Tallman MS, Hyman DM, Reznik E, Finley LWS, Papaemmanuil E, Tosolini A, Frattini MG, MacBeth KJ, Liu G, Fan B, Choe S, Wu B, Janjigian YY, Mellinghoff IK, Diaz LA, Levine RL, Abou-Alfa GK, Stein EM, Intlekofer AM. Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition. Cancer Discov 2018; 8:1540-1547. [PMID: 30355724 DOI: 10.1158/2159-8290.cd-18-0877] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/09/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023]
Abstract
Somatic mutations in cytosolic or mitochondrial isoforms of isocitrate dehydrogenase (IDH1 or IDH2, respectively) contribute to oncogenesis via production of the metabolite 2-hydroxyglutarate (2HG). Isoform-selective IDH inhibitors suppress 2HG production and induce clinical responses in patients with IDH1- and IDH2-mutant malignancies. Despite the promising activity of IDH inhibitors, the mechanisms that mediate resistance to IDH inhibition are poorly understood. Here, we describe four clinical cases that identify mutant IDH isoform switching, either from mutant IDH1 to mutant IDH2 or vice versa, as a mechanism of acquired clinical resistance to IDH inhibition in solid and liquid tumors. SIGNIFICANCE: IDH-mutant cancers can develop resistance to isoform-selective IDH inhibition by "isoform switching" from mutant IDH1 to mutant IDH2 or vice versa, thereby restoring 2HG production by the tumor. These findings underscore a role for continued 2HG production in tumor progression and suggest therapeutic strategies to prevent or overcome resistance.This article is highlighted in the In This Issue feature, p. 1494.
Collapse
Affiliation(s)
- James J Harding
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maeve A Lowery
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan H Shih
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan M Schvartzman
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shengqi Hou
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard K Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - S Duygu Selcuklu
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin S Tallman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Early Drug Development Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Guowen Liu
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts
| | - Bin Fan
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts
| | - Sung Choe
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts
| | - Bin Wu
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts
| | - Yelena Y Janjigian
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross L Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ghassan K Abou-Alfa
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York.,Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
33
|
Razavi P, Chang MT, Xu G, Bandlamudi C, Ross DS, Vasan N, Cai Y, Bielski CM, Donoghue MTA, Jonsson P, Penson A, Shen R, Pareja F, Kundra R, Middha S, Cheng ML, Zehir A, Kandoth C, Patel R, Huberman K, Smyth LM, Jhaveri K, Modi S, Traina TA, Dang C, Zhang W, Weigelt B, Li BT, Ladanyi M, Hyman DM, Schultz N, Robson ME, Hudis C, Brogi E, Viale A, Norton L, Dickler MN, Berger MF, Iacobuzio-Donahue CA, Chandarlapaty S, Scaltriti M, Reis-Filho JS, Solit DB, Taylor BS, Baselga J. The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers. Cancer Cell 2018; 34:427-438.e6. [PMID: 30205045 PMCID: PMC6327853 DOI: 10.1016/j.ccell.2018.08.008] [Citation(s) in RCA: 578] [Impact Index Per Article: 96.3] [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: 12/11/2017] [Revised: 07/15/2018] [Accepted: 08/09/2018] [Indexed: 02/06/2023]
Abstract
We integrated the genomic sequencing of 1,918 breast cancers, including 1,501 hormone receptor-positive tumors, with detailed clinical information and treatment outcomes. In 692 tumors previously exposed to hormonal therapy, we identified an increased number of alterations in genes involved in the mitogen-activated protein kinase (MAPK) pathway and in the estrogen receptor transcriptional machinery. Activating ERBB2 mutations and NF1 loss-of-function mutations were more than twice as common in endocrine resistant tumors. Alterations in other MAPK pathway genes (EGFR, KRAS, among others) and estrogen receptor transcriptional regulators (MYC, CTCF, FOXA1, and TBX3) were also enriched. Altogether, these alterations were present in 22% of tumors, mutually exclusive with ESR1 mutations, and associated with a shorter duration of response to subsequent hormonal therapies.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms, Male/drug therapy
- Breast Neoplasms, Male/genetics
- Breast Neoplasms, Male/pathology
- Drug Resistance, Neoplasm/genetics
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Genomics
- Humans
- MAP Kinase Signaling System/genetics
- Male
- Middle Aged
- Mutation
- Neurofibromin 1/genetics
- Neurofibromin 1/metabolism
- Prospective Studies
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Young Adult
Collapse
Affiliation(s)
- Pedram Razavi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guotai Xu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neil Vasan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanyan Cai
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Craig M Bielski
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruchi Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Komal Jhaveri
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shanu Modi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tiffany A Traina
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chau Dang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wen Zhang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clifford Hudis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maura N Dickler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge S Reis-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - José Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
34
|
Lee JY, Schizas M, Geyer FC, Selenica P, Piscuoglio S, Sakr RA, Ng CKY, Carniello JVS, Towers R, Giri DD, de Andrade VP, Papanastasiou AD, Viale A, Harris RS, Solit DB, Weigelt B, Reis-Filho JS, King TA. Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma. Clin Cancer Res 2018; 25:674-686. [PMID: 30185420 DOI: 10.1158/1078-0432.ccr-18-1103] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Lobular carcinoma in situ (LCIS) is a preinvasive lesion of the breast. We sought to define its genomic landscape, whether intralesion genetic heterogeneity is present in LCIS, and the clonal relatedness between LCIS and invasive breast cancers.Experimental Design: We reanalyzed whole-exome sequencing (WES) data and performed a targeted amplicon sequencing validation of mutations identified in 43 LCIS and 27 synchronous more clinically advanced lesions from 24 patients [9 ductal carcinomas in situ (DCIS), 13 invasive lobular carcinomas (ILC), and 5 invasive ductal carcinomas (IDC)]. Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic trees were defined using validated computational methods. RESULTS WES of 43 LCIS lesions revealed a genomic profile similar to that previously reported for ILCs, with CDH1 mutations present in 81% of the lesions. Forty-two percent (18/43) of LCIS were found to be clonally related to synchronous DCIS and/or ILCs, with clonal evolutionary patterns indicative of clonal selection and/or parallel/branched progression. Intralesion genetic heterogeneity was higher among LCIS clonally related to DCIS/ILC than in those nonclonally related to DCIS/ILC. A shift from aging to APOBEC-related mutational processes was observed in the progression from LCIS to DCIS and/or ILC in a subset of cases. CONCLUSIONS Our findings support the contention that LCIS has a repertoire of somatic genetic alterations similar to that of ILCs, and likely constitutes a nonobligate precursor of breast cancer. Intralesion genetic heterogeneity is observed in LCIS and should be considered in studies aiming to develop biomarkers of progression from LCIS to more advanced lesions.
Collapse
Affiliation(s)
- Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michail Schizas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Russell Towers
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor P de Andrade
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Agnes Viale
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Reuben S Harris
- Howard Hughes Medical Institute, Masonic Cancer Center, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
35
|
Patel J, Hasan M, Meng F, Jing X, Perera D, Reichel J, Gedvilaite E, Yang J, Shady M, Raj S, Srinivasan P, Johnson I, Wang J, Jarosz M, Samoila A, Viale A, Li B, Razavi P, Tsui D, Berger M. Abstract 5598: Development and optimization of a comprehensive high-sensitivity NGS cancer assay and bioinformatics pipeline for plasma cfDNA profiling. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5598] [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
The accessibility of tumor-derived cell-free DNA (cfDNA) in blood plasma provides a means to non-invasively profile somatic mutations in solid tumor patients. Clinical applications include longitudinal monitoring of disease burden and acquired drug resistance, identification of clinically relevant alterations and mutation signatures, and detection of minimal residual disease. However, the low fraction of tumor-derived cfDNA in plasma in many patients requires assays and bioinformatics methods that are much more sensitive than have been used for traditional tissue-based analysis.
The design of our cfDNA NGS panel is based on prospectively-collected clinical sequencing data obtained from more than 20,000 patients at Memorial Sloan Kettering Cancer Center using MSK-IMPACT, a custom 468-gene sequencing test authorized by the FDA for somatic mutation profiling. Exons harboring hotspot mutations, clinically actionable mutations, and elevated somatic mutation rates were selected for inclusion in the cfDNA panel. Additional non-coding content was included to enable optimal detection of selected copy number alterations, regions of loss of heterozygosity, rearrangement breakpoints, and microsatellite instability. Altogether the panel contains 208 kilobases of sequence from 129 cancer genes. Ultra-deep sequencing and unique molecular indexing enable PCR-generated replicate sequences to be collapsed into error-free consensus sequences, thereby facilitating the high-confidence detection of mutations present at low allele fractions.
We developed an open source bioinformatics tool, Marianas, for collapsing PCR replicates into consensus sequences and computing associated quality and performance metrics. Marianas incorporates many empirically derived features that lead to significant noise reduction. It efficiently processes a bam file with 20,000X coverage in 20 minutes on a single processor. We benchmarked the performance of Marianas against other available tools for collapsing and consensus base calling. The relative contributions of sources of error such as barcode contamination and sample
cross-talk during PCR and sequencing were also quantified. We found that using unique dual sample indexes in multiplexed sequencing runs was essential to suppress these sources of noise.
Applying these aggregated methods to analyze plasma cfDNA samples obtained from patients across a range of solid tumor types and disease stages, we were able to reliably detect clinically relevant mutations with variant allele fractions below 0.003, including subclonal mutations associated with acquired drug resistance. This approach, when applied prospectively on clinical specimens, has the potential to facilitate diagnosis, prognosis, and treatment selection in an era of precision oncology.
Citation Format: Juber Patel, Maysun Hasan, Fanli Meng, Xiaohong Jing, Dilmi Perera, Jonathan Reichel, Erika Gedvilaite, Julie Yang, Maha Shady, Sandeep Raj, Preethi Srinivasan, Ian Johnson, Jiashi Wang, Mirna Jarosz, Aliaksandra Samoila, Agnes Viale, Bob Li, Pedram Razavi, Dana Tsui, Michael Berger. Development and optimization of a comprehensive high-sensitivity NGS cancer assay and bioinformatics pipeline for plasma cfDNA profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5598.
Collapse
Affiliation(s)
- Juber Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maysun Hasan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fanli Meng
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaohong Jing
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dilmi Perera
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Julie Yang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maha Shady
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sandeep Raj
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ian Johnson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Agnes Viale
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bob Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana Tsui
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | |
Collapse
|
36
|
Chang MT, Penson A, Desai NB, Socci ND, Shen R, Seshan VE, Kundra R, Abeshouse A, Viale A, Cha EK, Hao X, Reuter VE, Rudin CM, Bochner BH, Rosenberg JE, Bajorin DF, Schultz N, Berger MF, Iyer G, Solit DB, Al-Ahmadie HA, Taylor BS. Small-Cell Carcinomas of the Bladder and Lung Are Characterized by a Convergent but Distinct Pathogenesis. Clin Cancer Res 2018; 24:1965-1973. [PMID: 29180607 PMCID: PMC5965261 DOI: 10.1158/1078-0432.ccr-17-2655] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [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: 09/13/2017] [Revised: 10/23/2017] [Accepted: 11/22/2017] [Indexed: 01/06/2023]
Abstract
Purpose: Small-cell carcinoma of the bladder (SCCB) is a rare and aggressive neuroendocrine tumor with a dismal prognosis and limited treatment options. As SCCB is histologically indistinguishable from small-cell lung cancer, a shared pathogenesis and cell of origin has been proposed. The aim of this study is to determine whether SCCBs arise from a preexisting urothelial carcinoma or share a molecular pathogenesis in common with small-cell lung cancer.Experimental Design: We performed an integrative analysis of 61 SCCB tumors to identify histology- and organ-specific similarities and differences.Results: SCCB has a high somatic mutational burden driven predominantly by an APOBEC-mediated mutational process. TP53, RB1, and TERT promoter mutations were present in nearly all samples. Although these events appeared to arise early in all affected tumors and likely reflect an evolutionary branch point that may have driven small-cell lineage differentiation, they were unlikely the founding transforming event, as they were often preceded by diverse and less common driver mutations, many of which are common in bladder urothelial cancers, but not small-cell lung tumors. Most patient tumors (72%) also underwent genome doubling (GD). Although arising at different chronologic points in the evolution of the disease, GD was often preceded by biallelic mutations in TP53 with retention of two intact copies.Conclusions: Our findings indicate that small-cell cancers of the bladder and lung have a convergent but distinct pathogenesis, with SCCBs arising from a cell of origin shared with urothelial bladder cancer. Clin Cancer Res; 24(8); 1965-73. ©2017 AACRSee related commentary by Oser and Jänne, p. 1775.
Collapse
Affiliation(s)
- Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Alexander Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neil B Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Abeshouse
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eugene K Cha
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xueli Hao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
37
|
Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, Zhang J, Walsh MF, Nichols KE, Joseph V, Snyder C, Vachon CM, McKay JD, Wang SP, Jayabalan DS, Jacobs LM, Becirovic D, Waller RG, Artomov M, Viale A, Patel J, Phillip J, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager SL, Godley LA, Churpek J, Garber JE, Anderson KC, Daly MJ, Roeder RG, Dumontet C, Lynch HT, Mullighan CG, Camp NJ, Offit K, Klein RJ, Yu H, Cerchietti L, Lipkin SM. Germline Lysine-Specific Demethylase 1 ( LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma. Cancer Res 2018; 78:2747-2759. [PMID: 29559475 DOI: 10.1158/0008-5472.can-17-1900] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/07/2017] [Accepted: 03/16/2018] [Indexed: 01/03/2023]
Abstract
Given the frequent and largely incurable occurrence of multiple myeloma, identification of germline genetic mutations that predispose cells to multiple myeloma may provide insight into disease etiology and the developmental mechanisms of its cell of origin, the plasma cell (PC). Here, we identified familial and early-onset multiple myeloma kindreds with truncating mutations in lysine-specific demethylase 1 (LSD1/KDM1A), an epigenetic transcriptional repressor that primarily demethylates histone H3 on lysine 4 and regulates hematopoietic stem cell self-renewal. In addition, we found higher rates of germline truncating and predicted deleterious missense KDM1A mutations in patients with multiple myeloma unselected for family history compared with controls. Both monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma cells have significantly lower KDM1A transcript levels compared with normal PCs. Transcriptome analysis of multiple myeloma cells from KDM1A mutation carriers shows enrichment of pathways and MYC target genes previously associated with myeloma pathogenesis. In mice, antigen challenge followed by pharmacologic inhibition of KDM1A promoted PC expansion, enhanced secondary immune response, elicited appearance of serum paraprotein, and mediated upregulation of MYC transcriptional targets. These changes are consistent with the development of MGUS. Collectively, our findings show that KDM1A is the first autosomal-dominant multiple myeloma germline predisposition gene providing new insights into its mechanistic roles as a tumor suppressor during post-germinal center B-cell differentiation.Significance: KDM1A is the first germline autosomal dominant predisposition gene identified in multiple myeloma and provides new insights into multiple myeloma etiology and the mechanistic role of KDM1A as a tumor suppressor during post-germinal center B-cell differentiation. Cancer Res; 78(10); 2747-59. ©2018 AACR.
Collapse
Affiliation(s)
- Xiaomu Wei
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Department of Biological Statistics and Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York
| | | | - Siwei Chen
- Department of Biological Statistics and Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York
| | - Gang Wu
- St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Maria V Revuelta
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jian Sun
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jinghui Zhang
- St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Kim E Nichols
- St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Vijai Joseph
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | | | | | | | | | | | | | | | - Mykyta Artomov
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Agnes Viale
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - Jude Phillip
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | | | | | | | - Ruben Niesvizky
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ola Landgren
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | | | | | | | | | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | | | | | | | - Kenneth Offit
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York.
| | | | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
38
|
Momtaz P, Pentsova E, Abdel-Wahab O, Diamond E, Hyman D, Merghoub T, You D, Gasmi B, Viale A, Chapman PB. Quantification of tumor-derived cell free DNA(cfDNA) by digital PCR (DigPCR) in cerebrospinal fluid of patients with BRAFV600 mutated malignancies. Oncotarget 2018; 7:85430-85436. [PMID: 27863426 PMCID: PMC5356746 DOI: 10.18632/oncotarget.13397] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [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: 10/04/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
Tumor-derived cell free DNA (cfDNA) can be detected in plasma. We hypothesized that mutated BRAF V600 cfDNA could be quantified in the cerebrospinal fluid (CSF) of patients with central nervous system (CNS) metastases. We collected CSF from patients with BRAF V600E or K-mutated melanoma (N=8) or BRAF V600E mutated Erdheim-Chester Disease (ECD) (N=3) with suspected central nervous system (CNS) involvement on the basis of neurological symptoms (10/11), MRI imaging (8/11), or both. Tumor-derived cfDNA was quantified by digital PCR in the CSF of 6/11 patients (range from 0.15-10.56 copies/μL). Conventional cytology was negative in all patients except in the two patients with markedly elevated levels of tumor-derived cfDNA. In 2 patients with serial measurements, CSF tumor-derived cfDNA levels reflected response to treatment or progressive disease. CSF tumor-derived cfDNA has the potential to serve as a diagnostic tool that complements MRI and may be more sensitive than conventional cytology.
Collapse
Affiliation(s)
- Parisa Momtaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Elena Pentsova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Omar Abdel-Wahab
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Eli Diamond
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Daoqi You
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Billel Gasmi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Paul B Chapman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York, USA
| |
Collapse
|
39
|
Crago AM, Socci ND, Qin LX, Wilder F, O'Connor R, Craig A, Houdt WV, Weinhold N, Kandoth C, Viale A, Antonescu C, Singer S. Abstract PR16: Multiplatform analysis of paired primary and recurrent well- and dedifferentiated liposarcoma samples defines copy number alterations as dominant drivers of initiation and progression. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-pr16] [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
Objective: Initiation of well-differentiated (WD) and dedifferentiated (DD) liposarcoma is driven by 12q13-15 amplification and consequent MDM2 and CDK4 overexpression, but mechanisms that regulate the variable biologic behavior of WD/DD tumors remain poorly understood. We used a multiplatform analysis of paired WD and DD samples to identify genomic events with potential to contribute to liposarcomagenesis.
Methods: From serial tumor resections performed on the same patient, we collected paired WD/DD (n=7) or WD/WD (n=2) test samples and normal tissue. Samples were analyzed using whole-exome sequencing, array comparative genomic hybridization (aCGH), Solexa small RNA sequencing, and, in a subset, RNA-seq. Findings were validated in WD/DD cohorts analyzed by custom capture array (n=201), aCGH (n=210), Affymetrix U133A microarrays (n=146), and Solexa (n=118). Lentivirus was used to deliver shRNA to WD cells in vitro; proliferation was assayed by CyQuant, differentiation by immunoblot/oil red O staining, and gene expression by Illumina microarrays.
Results: 12q13-15 amplification was observed in all WD/DD test and validation samples. Among WD samples, 1q21-24 and 6q23-25 amplifications were found in test samples and in 28% and 18% of the validation set, respectively. Of genes upregulated in WD vs. normal fat test samples, 465 were validated in the larger cohort [≥2-fold change (FC), FDR<0.05]. 53% of these genes lie within regions of copy number alteration (CNA); 8% were predicted targets of 12q-encoded miRNAs. shRNA targeting of MDM2 or drug inhibition of CDK4 in vitro negatively regulated 11% of the genes, including AURKA and its regulators TPX2 and KIF11. 6q23-25 amplification was associated with local recurrence (LR) after primary WD resection (HR 10.9, p<0.001) and with overexpression of CCDC28A and TAB2, an AP-1 regulator (1.7- and 1.9-FC, FDRs<0.05). In 6q23-25-amplified WD cells, shRNA-mediated TAB2 inhibition reduced proliferation by >90%. Comparison of matched WD/DD samples showed retained amplification of 12q13-15 and 6q23-25 after progression. In contrast to WD, DD showed strong association of the 6q23-25 CNA with increased expression of 6q genes TCF21 and HBS1L (16- and 4-FC, FDRs<0.001), but not TAB2 or CCDC28A, suggesting that additional progression events alter the oncogenic effects of initiation-associated CNAs in DD vs WD. Direct comparison of paired DD/WD test samples revealed recurrent 13q loss arising during dedifferentiation (n=3). 13q loss was found in 28% of the DD validation set and associated with reduced expression of 13q genes MYCBP2 and IRS2, regulators of insulin signaling. shRNA inhibition of MYCBP2 or IRS2 in vitro had little effect on WD differentiation, but inhibition of both genes decreased levels of PPARG, FABP4, PLIN and oil red O staining (70% reduction). Uncommon mutations in genes regulating steroid-hormone activation (e.g., NCOA6, KMT2C), adaptive immunity (e.g., LILRA1, NFKB1), and RTK signaling (e.g., NRG1, FGFR1) were identified in 11%, 6%, and 11% of WD/DD samples, respectively, but did not associate with differentiation.
Conclusions: Genes upregulated during WD initiation are commonly located in regions of CNA or regulated by 12q23-25 oncogenes MDM2 and CDK4 (e.g., AURKA, a potential therapeutic target). 6q23-26 amplification, observed in subsets of both WD and DD, associates with LR of WD, but expression of 6q23-26 genes with potential to modulate oncogenesis (e.g., TAB2 vs TCF21) differs in WD and DD tumors, suggesting that the CNA may differentially modulate early and late disease. Losses affecting broad chromosome regions such as 13q likely mediate progression by affecting multiple regulators of adipogenesis pathways (e.g., insulin signaling), while mutations have little effect on dedifferentiation.
Citation Format: Aimee M. Crago, Nicholas D. Socci, Li-Xuan Qin, Fatima Wilder, Rachael O'Connor, Amanda Craig, Willem van Houdt, Nils Weinhold, Cyriac Kandoth, Agnes Viale, Cristina Antonescu, Sam Singer. Multiplatform analysis of paired primary and recurrent well- and dedifferentiated liposarcoma samples defines copy number alterations as dominant drivers of initiation and progression [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR16.
Collapse
Affiliation(s)
| | | | - Li-Xuan Qin
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fatima Wilder
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Amanda Craig
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Nils Weinhold
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sam Singer
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
40
|
Yaeger R, Chatila WK, Lipsyc MD, Hechtman JF, Cercek A, Sanchez-Vega F, Jayakumaran G, Middha S, Zehir A, Donoghue MTA, You D, Viale A, Kemeny N, Segal NH, Stadler ZK, Varghese AM, Kundra R, Gao J, Syed A, Hyman DM, Vakiani E, Rosen N, Taylor BS, Ladanyi M, Berger MF, Solit DB, Shia J, Saltz L, Schultz N. Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer. Cancer Cell 2018; 33:125-136.e3. [PMID: 29316426 PMCID: PMC5765991 DOI: 10.1016/j.ccell.2017.12.004] [Citation(s) in RCA: 507] [Impact Index Per Article: 84.5] [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: 08/02/2017] [Revised: 10/26/2017] [Accepted: 12/09/2017] [Indexed: 02/07/2023]
Abstract
Metastatic colorectal cancers (mCRCs) are clinically heterogeneous, but the genomic basis of this variability remains poorly understood. We performed prospective targeted sequencing of 1,134 CRCs. We identified splice alterations in intronic regions of APC and large in-frame deletions in CTNNB1, increasing oncogenic WNT pathway alterations to 96% of CRCs. Right-sided primary site in microsatellite stable mCRC was associated with shorter survival, older age at diagnosis, increased mutations, and enrichment of oncogenic alterations in KRAS, BRAF, PIK3CA, AKT1, RNF43, and SMAD4 compared with left-sided primaries. Left-sided tumors frequently had no identifiable genetic alteration in mitogenic signaling, but exhibited higher mitogenic ligand expression. Our results suggest different pathways to tumorigenesis in right- and left-sided microsatellite stable CRC that may underlie clinical differences.
Collapse
Affiliation(s)
- Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marla D Lipsyc
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaclyn F Hechtman
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gowtham Jayakumaran
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daoqi You
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nancy Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neil H Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aijazuddin Syed
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Efsevia Vakiani
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jinru Shia
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Leonard Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
41
|
Momtaz P, Harding JJ, Ariyan C, Coit DG, Merghoub T, Gasmi B, You D, Viale A, Panageas KS, Samoila A, Postow MA, Wolchok JD, Chapman PB. Four-month course of adjuvant dabrafenib in patients with surgically resected stage IIIC melanoma characterized by a BRAFV600E/K mutation. Oncotarget 2017; 8:105000-105010. [PMID: 29285228 PMCID: PMC5739615 DOI: 10.18632/oncotarget.21072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We tested the hypothesis that a 4-month course of adjuvant dabrafenib in stage IIIC BRAF-mutated melanoma would improve 2 year RFS from 24% to 51%, and that tumor-derived cell free DNA (cfDNA) in plasma would correlate with and predict recurrence. METHODS Patients with stage IIIC BRAF V600E/K mutated melanoma who were free of disease after surgical resection received 4 months of adjuvant dabrafenib. Patients were evaluated with imaging at baseline, at the end of cycles 2, 4, 6, then every 3 months until disease relapse or 2 years, whichever came first. Serial blood samples were collected for evaluation of cfDNA at the same time. RESULTS 21/23 patients enrolled were evaluable; 2 patients withdrew consent during the first week of treatment. The 2 year RFS was 28.6% (95% CI 12-48%). The estimated overall survival at 2 years was 78% (95% CI 51-91%). cfDNA detection had a 53% sensitivity in relapsing patients but cfDNA detection did not provide lead-time advantage over CT scanning. CONCLUSION A 4-month course of adjuvant dabrafenib did not result in a detectable improvement in 2-year RFS. cfDNA was less sensitive than standard CT imaging and did not provide a lead-time advantage in detecting relapse.
Collapse
Affiliation(s)
- Parisa Momtaz
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Harding
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Charlotte Ariyan
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Daniel G Coit
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Billel Gasmi
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Daoqi You
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | - Michael A Postow
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Jedd D Wolchok
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Paul B Chapman
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
42
|
Cheng M, Yang J, Shady M, Ulz P, Heitzer E, Socci N, Seshan V, Offin M, Stephens D, Makhnin A, Tandon N, Datta S, Selcuklu D, Huberman K, Vanness K, Gedvilaite E, Viale A, Arcila M, Ladanyi M, Chaft J, Rudin C, Berger M, Solit D, Li B, Tsui D. OA 10.05 Non-Invasive Molecular Profiling in NSCLC by Targeted and Whole Exome Analysis of Plasma cfDNA. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
43
|
Grommes C, Pastore A, Palaskas N, Tang SS, Campos C, Schartz D, Codega P, Nichol D, Clark O, Hsieh WY, Rohle D, Rosenblum M, Viale A, Tabar VS, Brennan CW, Gavrilovic IT, Kaley TJ, Nolan CP, Omuro A, Pentsova E, Thomas AA, Tsyvkin E, Noy A, Palomba ML, Hamlin P, Sauter CS, Moskowitz CH, Wolfe J, Dogan A, Won M, Glass J, Peak S, Lallana EC, Hatzoglou V, Reiner AS, Gutin PH, Huse JT, Panageas KS, Graeber TG, Schultz N, DeAngelis LM, Mellinghoff IK. Ibrutinib Unmasks Critical Role of Bruton Tyrosine Kinase in Primary CNS Lymphoma. Cancer Discov 2017; 7:1018-1029. [PMID: 28619981 DOI: 10.1158/2159-8290.cd-17-0613] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 12/22/2022]
Abstract
Bruton tyrosine kinase (BTK) links the B-cell antigen receptor (BCR) and Toll-like receptors with NF-κB. The role of BTK in primary central nervous system (CNS) lymphoma (PCNSL) is unknown. We performed a phase I clinical trial with ibrutinib, the first-in-class BTK inhibitor, for patients with relapsed or refractory CNS lymphoma. Clinical responses to ibrutinib occurred in 10 of 13 (77%) patients with PCNSL, including five complete responses. The only PCNSL with complete ibrutinib resistance harbored a mutation within the coiled-coil domain of CARD11, a known ibrutinib resistance mechanism. Incomplete tumor responses were associated with mutations in the B-cell antigen receptor-associated protein CD79B. CD79B-mutant PCNSLs showed enrichment of mammalian target of rapamycin (mTOR)-related gene sets and increased staining with PI3K/mTOR activation markers. Inhibition of the PI3K isoforms p110α/p110δ or mTOR synergized with ibrutinib to induce cell death in CD79B-mutant PCNSL cells.Significance: Ibrutinib has substantial activity in patients with relapsed or refractory B-cell lymphoma of the CNS. Response rates in PCNSL were considerably higher than reported for diffuse large B-cell lymphoma outside the CNS, suggesting a divergent molecular pathogenesis. Combined inhibition of BTK and PI3K/mTOR may augment the ibrutinib response in CD79B-mutant human PCNSLs. Cancer Discov; 7(9); 1018-29. ©2017 AACR.See related commentary by Lakshmanan and Byrd, p. 940This article is highlighted in the In This Issue feature, p. 920.
Collapse
Affiliation(s)
- Christian Grommes
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Alessandro Pastore
- Department of Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicolaos Palaskas
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah S Tang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carl Campos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Derrek Schartz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paolo Codega
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donna Nichol
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Owen Clark
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wan-Ying Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Rohle
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Viviane S Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cameron W Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Igor T Gavrilovic
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Thomas J Kaley
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Craig P Nolan
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Antonio Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Alissa A Thomas
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elina Tsyvkin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ariela Noy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - M Lia Palomba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Paul Hamlin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Craig S Sauter
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Craig H Moskowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Julia Wolfe
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Minhee Won
- NRG Oncology Statistics and Data Management Center, Philadelphia, Pennsylvania
| | - Jon Glass
- Department of Neurosurgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Scott Peak
- Department of Neurosurgery, The Permanente Medical Group, Sacramento, California
| | - Enrico C Lallana
- Department of Neuro-Oncology, The Permanente Medical Group, Redwood City, California
| | - Vaios Hatzoglou
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anne S Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip H Gutin
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason T Huse
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, University of California, Los Angeles, California
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lisa M DeAngelis
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Neurology, Weill Cornell Medical College, New York, New York
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurology, Weill Cornell Medical College, New York, New York.,Department of Pharmacology, Weill Cornell Medical College, New York, New York
| |
Collapse
|
44
|
Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 2017. [PMID: 28514453 DOI: 10.1038/nature22367.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.
Collapse
Affiliation(s)
- Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ellen L Horste
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Peter Lauer
- Aduro Biotech, Inc., Berkeley, California 94720, USA
| | - Taha Merghoub
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Matthew D Hellmann
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jedd D Wolchok
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| |
Collapse
|
45
|
Shukla NN, Patel JA, Magnan H, Zehir A, You D, Tang J, Meng F, Samoila A, Slotkin EK, Ambati SR, Chou AJ, Wexler LH, Meyers PA, Peerschke EI, Viale A, Berger MF, Ladanyi M. Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patients with EWSR1 fusion-positive sarcomas. JCO Precis Oncol 2017; 2017. [PMID: 29629425 DOI: 10.1200/po.16.00028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Ewing Sarcoma (ES) and Desmoplastic Small Round Cell Tumors (DSRCT) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Patients and Methods To investigate the feasibility of identifying EWSR1 fusions in plasma derived cell-free DNA (cfDNA) from ES and DSRCT patients, we evaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomic EWSR1 fusion breakpoints in formalin-fixed, paraffin-embedded tumor DNA using a broad, hybridization capture-based next generation sequencing (NGS) panel, followed by design of patient-specific droplet digital PCR (ddPCR) assays for plasma cfDNA interrogation . The second approach employed a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA which included EWSR1 as well as several other genes with potential prognostic utility. Results EWSR1 fusions were identified in 11/11 (100%) ES and 5/6 (83%) DSRCT samples by ddPCR, while 10/11 (91%) and 4/6 (67%) were identified by NGS. The ddPCR approach had higher sensitivity, ranging between 0.009-0.018% sensitivity. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor sequencing results. Conclusion These results provide a compelling rationale for an integrated approach utilizing both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.
Collapse
Affiliation(s)
- Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juber A Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center New York, New York
| | - Heather Magnan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center New York, New York
| | - Jiabin Tang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center New York, New York
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center New York, New York
| | - Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Srikanth R Ambati
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander J Chou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ellinor I Peerschke
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
46
|
Sacco V, Viale A, Noris Chiorda B, Sini C, Salvadori G, Fiorino C, Di Muzio N, Cozzarini C. EP-1815: Technical aspects and setup irradiation of rats using a clinical accelerator. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)32178-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
47
|
Ng CKY, Bidard FC, Piscuoglio S, Geyer FC, Lim RS, de Bruijn I, Shen R, Pareja F, Berman SH, Wang L, Pierga JY, Vincent-Salomon A, Viale A, Norton L, Sigal B, Weigelt B, Cottu P, Reis-Filho JS. Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases. Clin Cancer Res 2017; 23:4402-4415. [PMID: 28351929 DOI: 10.1158/1078-0432.ccr-16-3115] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 01/17/2017] [Accepted: 03/22/2017] [Indexed: 12/21/2022]
Abstract
Purpose: Paired primary breast cancers and metachronous metastases after adjuvant treatment are reported to differ in their clonal composition and genetic alterations, but it is unclear whether these differences stem from the selective pressures of the metastatic process, the systemic therapies, or both. We sought to define the repertoire of genetic alterations in breast cancer patients with de novo metastatic disease who had not received local or systemic therapy.Experimental Design: Up to two anatomically distinct core biopsies of primary breast cancers and synchronous distant metastases from nine patients who presented with metastatic disease were subjected to high-depth whole-exome sequencing. Mutations, copy number alterations and their cancer cell fractions, and mutation signatures were defined using state-of-the-art bioinformatics methods. All mutations identified were validated with orthogonal methods.Results: Genomic differences were observed between primary and metastatic deposits, with a median of 60% (range 6%-95%) of shared somatic mutations. Although mutations in known driver genes including TP53, PIK3CA, and GATA3 were preferentially clonal in both sites, primary breast cancers and their synchronous metastases displayed spatial intratumor heterogeneity. Likely pathogenic mutations affecting epithelial-to-mesenchymal transition-related genes, including SMAD4, TCF7L2, and TCF4 (ITF2), were found to be restricted to or enriched in the metastatic lesions. Mutational signatures of trunk mutations differed from those of mutations enriched in the primary tumor or the metastasis in six cases.Conclusions: Synchronous primary breast cancers and metastases differ in their repertoire of somatic genetic alterations even in the absence of systemic therapy. Mutational signature shifts might contribute to spatial intratumor genetic heterogeneity. Clin Cancer Res; 23(15); 4402-15. ©2017 AACR.
Collapse
Affiliation(s)
- Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Francois-Clement Bidard
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronglai Shen
- Department of Biostatistics and Epidemiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel H Berman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France.,University Paris Descartes, Paris, France
| | | | - Agnes Viale
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Larry Norton
- Breast Medicine Service, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Brigitte Sigal
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
48
|
Singh K, Lecomte N, Stark S, Burčul A, Olivera GH, Grimont A, Viale A, Mohan P, Jiang M, Destanchia E, Gokce A, Rätsch G, Leach SD, Wendel HG. Abstract A45: Targeting eIF4A dependent translation as therapeutics in pancreatic cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.transcontrol16-a45] [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
RNA translation is activated in aggressive pancreatic cancer and at the same time is also refractory to mTOR inhibition. We have used a translation inhibitor for eIF4A, RNA helicase that is downstream of mTOR signaling and can be functionally targeted in pancreatic cancer. We establish that Silvestrol and its analog CR-31B showed potent anti-tumor activity in pancreatic cancer cell lines in vitro and in vivo. Silvestrol/CR-31B reduced pancreatic cancer cells and organoids growth derived from mouse model of pancreatic cancer and human patient samples in vitro. Further we identify the genome wide translational targets of Silvestrol in pancreatic cancer cell line that lacks response to mTOR signaling through loss of EIF4EBP1. Silvestrol down regulate translation of many key oncogenes and others cellular factors involved in oncogenic signaling specific to pancreatic cancer. Silvestrol targets were also enriched for G-quadruplex structure in their 5' UTR. With this study we establish a new mechanism of targeting pancreatic cancer cells through translation inhibition and identify newer proteins as therapeutic targets that are regulated independent of mTOR signaling.
Citation Format: Kamini Singh, Nicolas Lecomte, Stefan Stark, Antonija Burčul, Grbovic-Huezo Olivera, Adrien Grimont, Agnes Viale, Prathibha Mohan, Man Jiang, Elisa Destanchia, Askan Gokce, Gunnar Rätsch, Steve D. Leach, Hans-Guido Wendel. Targeting eIF4A dependent translation as therapeutics in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr A45.
Collapse
Affiliation(s)
- Kamini Singh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Stefan Stark
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Man Jiang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Askan Gokce
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | |
Collapse
|
49
|
Singh K, Stark SG, Viale A, Mohan P, Jiang M, Rätsch G, Wendel HG. Abstract A56: Targeting eIF4A dependent translation as therapeutics in pancreatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.panca16-a56] [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
Pancreatic cancer is one of the most aggressive cancers with no targeted therapy available. RNA translation is activated in aggressive pancreatic cancer and at the same time is also refractory to mTor inhibition. We have used a translation inhibitor for eIF4A, RNA helicase that is downstream of mTOR signaling and can be functionally targeted in pancreatic cancer. We establish that Silvestrol and its analog CR-31B showed potent anti-tumor activity in pancreatic cancer cell lines in vitro and in vivo. Silvestrol/CR-31B reduced pancreatic cancer cells and organoids growth derived from mouse model of pancreatic cancer and human patient samples in vitro. Further we identify the genome wide translational targets of Silvestrol in pancreatic cancer cell line that lacks response to mTOR signaling through loss of EIF4EBP1. Silvestrol down regulate translation of many key oncogenes and others cellular factors involved in oncogenic signaling in pancreatic cancer. Silvestrol targets were also enriched for G-quadruplex structure in their 5’UTR. With this study we establish a new mechanism of targeting pancreatic cancer cells through translation inhibition and identify more proteins as therapeutic targets that are regulated independent of mTOR signaling.
Citation Format: Kamini Singh, Stefan G. Stark, Agnes Viale, Prathibha Mohan, Man Jiang, Gunnar Rätsch, Hans-Guido Wendel.{Authors}. Targeting eIF4A dependent translation as therapeutics in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A56.
Collapse
Affiliation(s)
- Kamini Singh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Man Jiang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | |
Collapse
|
50
|
Lowery M, You D, Samoila A, Peerschke E, Viale A, Patel R, Selcuklu D, Rusek M, Cercek A, Kemeny N, Harding J, Mellinghoff I, Tap W, Abou-Alfa G, Moynahan M. Detection of IDH1 mutations in circulating free DNA in patients with cholangiocarcinoma. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)33021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|