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Parry EM, Leshchiner I, Guièze R, Johnson C, Tausch E, Parikh SA, Lemvigh C, Broséus J, Hergalant S, Messer C, Utro F, Levovitz C, Rhrissorrakrai K, Li L, Rosebrock D, Yin S, Deng S, Slowik K, Jacobs R, Huang T, Li S, Fell G, Redd R, Lin Z, Knisbacher BA, Livitz D, Schneider C, Ruthen N, Elagina L, Taylor-Weiner A, Persaud B, Martinez A, Fernandes SM, Purroy N, Anandappa AJ, Ma J, Hess J, Rassenti LZ, Kipps TJ, Jain N, Wierda W, Cymbalista F, Feugier P, Kay NE, Livak KJ, Danysh BP, Stewart C, Neuberg D, Davids MS, Brown JR, Parida L, Stilgenbauer S, Getz G, Wu CJ. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome. Nat Med 2023; 29:158-169. [PMID: 36624313 PMCID: PMC10155825 DOI: 10.1038/s41591-022-02113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 10/28/2022] [Indexed: 01/11/2023]
Abstract
Richter syndrome (RS) arising from chronic lymphocytic leukemia (CLL) exemplifies an aggressive malignancy that develops from an indolent neoplasm. To decipher the genetics underlying this transformation, we computationally deconvoluted admixtures of CLL and RS cells from 52 patients with RS, evaluating paired CLL-RS whole-exome sequencing data. We discovered RS-specific somatic driver mutations (including IRF2BP2, SRSF1, B2M, DNMT3A and CCND3), recurrent copy-number alterations beyond del(9p21)(CDKN2A/B), whole-genome duplication and chromothripsis, which were confirmed in 45 independent RS cases and in an external set of RS whole genomes. Through unsupervised clustering, clonally related RS was largely distinct from diffuse large B cell lymphoma. We distinguished pathways that were dysregulated in RS versus CLL, and detected clonal evolution of transformation at single-cell resolution, identifying intermediate cell states. Our study defines distinct molecular subtypes of RS and highlights cell-free DNA analysis as a potential tool for early diagnosis and monitoring.
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Affiliation(s)
- Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Romain Guièze
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- CHU de Clermont-Ferrand, Clermont-Ferrand, France
- Université Clermont Auvergne, EA7453 CHELTER, Clermont-Ferrand, France
| | | | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | | | - Camilla Lemvigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julien Broséus
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU-Nancy, service d'hématologie biologique, pôle laboratoires, Nancy, France
| | - Sébastien Hergalant
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
| | - Conor Messer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Filippo Utro
- IBM Research, Yorktown Heights, New York, NY, USA
| | | | | | - Liang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Stephanie Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kara Slowik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raquel Jacobs
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Geoff Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robert Redd
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziao Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Christof Schneider
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Neil Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Bria Persaud
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aina Martinez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Annabelle J Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jialin Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julian Hess
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Z Rassenti
- Moores Cancer Center, Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Kipps
- Moores Cancer Center, Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nitin Jain
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florence Cymbalista
- Laboratoire d'hématologie, Hôpital Avicenne-AP-HP, INSERM U978- Université Sorbonne Paris Nord, Bobigny, France
| | - Pierre Feugier
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU Nancy, service d'hématologie clinique, Nancy, France
| | - Neil E Kay
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laxmi Parida
- IBM Research, Yorktown Heights, New York, NY, USA
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Ostano P, Mello-Grand M, Sesia D, Gregnanin I, Peraldo-Neia C, Guana F, Jachetti E, Farsetti A, Chiorino G. Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma. Int J Mol Sci 2020; 21:ijms21031078. [PMID: 32041153 PMCID: PMC7037893 DOI: 10.3390/ijms21031078] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 12/20/2022] Open
Abstract
Neuroendocrine prostate cancer (NEPC) can arise de novo, but much more commonly occurs as a consequence of a selective pressure from androgen deprivation therapy or androgen receptor antagonists used for prostate cancer (PCa) treatment. The process is known as neuroendocrine transdifferentiation. There is little molecular characterization of NEPCs and consequently there is no standard treatment for this kind of tumors, characterized by highly metastases rates and poor survival. For this purpose, we profiled 54 PCa samples with more than 10-years follow-up for gene and miRNA expression. We divided samples into two groups (NE-like vs. AdenoPCa), according to their clinical and molecular features. NE-like tumors were characterized by a neuroendocrine fingerprint made of known neuroendocrine markers and novel molecules, including long non-coding RNAs and components of the estrogen receptor signaling. A gene expression signature able to predict NEPC was built and tested on independently published datasets. This study identified molecular features (protein-coding, long non-coding, and microRNAs), at the time of surgery, that may anticipate the NE transformation process of prostate adenocarcinoma. Our results may contribute to improving the diagnosis and treatment of this subgroup of tumors for which traditional therapy regimens do not show beneficial effects.
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Affiliation(s)
- Paola Ostano
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Maurizia Mello-Grand
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Debora Sesia
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Ilaria Gregnanin
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Caterina Peraldo-Neia
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Francesca Guana
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
| | - Elena Jachetti
- Department of Research, Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Antonella Farsetti
- National Research Council - Institute of Analysis, Systems and Computer Science –CNR-IASI, 00185 Rome, Italy;
| | - Giovanna Chiorino
- Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, via Malta 3, 13900 Biella, Italy; (P.O.); (M.M.-G.); (D.S.); (I.G.); (C.P.-N.); (F.G.)
- Correspondence:
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9
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Aggarwal R, Huang J, Alumkal J, Feng FY, Zhang L, Stuart JM, Small EJ. Reply to A. Dalla Volta et al. J Clin Oncol 2019; 37:351-352. [DOI: 10.1200/jco.18.01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rahul Aggarwal
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Jiaoti Huang
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Joshi Alumkal
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Felix Y. Feng
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Li Zhang
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Joshua M. Stuart
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
| | - Eric J. Small
- Rahul Aggarwal, MD, University of California San Francisco, San Francisco, CA; Jiaoti Huang, MD, PhD, Duke University, Durham, NC; Joshi Alumkal, MD, Oregon Health Sciences University, Portland, OR; Felix Y. Feng, MD and Li Zhang, PhD, University of California San Francisco, San Francisco, CA; Joshua M. Stuart, PhD, University of California Santa Cruz, Santa Cruz, CA; and Eric J. Small, MD, University of California San Francisco, San Francisco, CA
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