Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid

Christopher Douville¹, Samuel Curtis¹, Mahmoud Summers¹, Tej D Azad², Jordina Rincon-Torroella³, Yuxuan Wang¹, Austin Mattox¹, Bracha Avigdor¹, Jonathan Dudley⁴, Joshua Materi², Divyaansh Raj², Sumil Nair², Debarati Bhanja⁵, Kyle Tuohy⁵, Lisa Dobbyn¹, Maria Popoli¹, Janine Ptak¹, Nadine Nehme¹, Natalie Silliman¹, Cherie Blair¹, Kathy Judge¹, Gary L Gallia², Mari Groves², Christopher M Jackson², Eric M Jackson², John Laterra⁶, Michael Lim⁷, Debraj Mukherjee², Jon Weingart², Jarushka Naidoo⁸, Carl Koschmann⁹, Natalya Smith⁵, Karisa C Schreck¹⁰, Carlos A Pardo⁶, Michael Glantz⁵, Matthias Holdhoff¹¹, Kenneth W Kinzler¹, Nickolas Papadopoulos¹, Bert Vogelstein¹², Chetan Bettegowda¹³

Affiliations

¹ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
² Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
³ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
⁴ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
⁵ Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA.
⁶ Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
⁷ Department of Neurosurgery, Stanford University, Palo Alto, CA, USA.
⁸ Department of Oncology, Beaumont Hospital, Dublin, Ireland.
⁹ Division of Pediatric Oncology, University of Michigan, Ann Arbor, MI, USA.
¹⁰ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
¹¹ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
¹² Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
¹³ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA. Electronic address: cbetteg1@jhmi.edu.

PMID: 37552989
PMCID: PMC10439243
DOI: 10.1016/j.xcrm.2023.101148

Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid

Christopher Douville et al. Cell Rep Med. 2023.

. 2023 Aug 15;4(8):101148.

doi: 10.1016/j.xcrm.2023.101148. Epub 2023 Aug 7.

Authors

Affiliations

¹ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
² Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
³ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
⁴ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
⁵ Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA.
⁶ Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
⁷ Department of Neurosurgery, Stanford University, Palo Alto, CA, USA.
⁸ Department of Oncology, Beaumont Hospital, Dublin, Ireland.
⁹ Division of Pediatric Oncology, University of Michigan, Ann Arbor, MI, USA.
¹⁰ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
¹¹ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
¹² Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
¹³ Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA. Electronic address: cbetteg1@jhmi.edu.

PMID: 37552989
PMCID: PMC10439243
DOI: 10.1016/j.xcrm.2023.101148

Abstract

It is often challenging to distinguish cancerous from non-cancerous lesions in the brain using conventional diagnostic approaches. We introduce an analytic technique called Real-CSF (repetitive element aneuploidy sequencing in CSF) to detect cancers of the central nervous system from evaluation of DNA in the cerebrospinal fluid (CSF). Short interspersed nuclear elements (SINEs) are PCR amplified with a single primer pair, and the PCR products are evaluated by next-generation sequencing. Real-CSF assesses genome-wide copy-number alterations as well as focal amplifications of selected oncogenes. Real-CSF was applied to 280 CSF samples and correctly identified 67% of 184 cancerous and 96% of 96 non-cancerous brain lesions. CSF analysis was considerably more sensitive than standard-of-care cytology and plasma cell-free DNA analysis in the same patients. Real-CSF therefore has the capacity to be used in combination with other clinical, radiologic, and laboratory-based data to inform the diagnosis and management of patients with suspected cancers of the brain.

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Conflict of interest statement

Declaration of interests B.V., K.W.K., and N.P. are founders of Thrive Earlier Detection, an Exact Sciences Company. K.W.K., N.P., and C.D. are consultants to Thrive Earlier Detection. B.V., K.W.K., N.P., and C.D. hold equity in Exact Sciences. B.V., K.W.K., and N.P. are founders of and own equity in ManaT Bio. K.W.K. and N.P. are consultants to and own equity in Haystack Oncology, Neophore, and Personal Genome Diagnostics. K.W.K., B.V., and N.P. hold equity in and are consultants to CAGE Pharma. B.V. is a consultant to and holds equity in Catalio Capital Management and may be a consultant to and hold equity in Haystack Oncology. B.V. owns equity in CAGE, Neophore, and Personal Genome Diagnostics. C. Bettegowda is a consultant to Depuy-Synthes, Bionaut Labs, Haystack Oncology, and Galectin Therapeutics. C. Bettegowda is a co-founder of OrisDx. C. Bettegowda and C.D. are co-founders of Belay Diagnostics. The companies named above, as well as other companies, have licensed previously described technologies related to the work described in this paper from Johns Hopkins University. B.V., K.W.K., N.P., C. Bettegowda, and C.D. are inventors on some of these technologies. Licenses to these technologies are or will be associated with equity or royalty payments to the inventors as well as to Johns Hopkins University. Patent applications on the work described in this paper may be filed by Johns Hopkins University. The terms of all these arrangements are being managed by Johns Hopkins University in accordance with its conflict of interest policies. M.H. is on the data safety monitoring board for Parexel and Advarra and has received an honorarium from Pfizer. K.S. received an honorarium from Springworks Therapeutics and receives research funding from Springworks Therapeutics. J.N. receives research funding from Merck, AstraZeneca, BMS, Amgen, Novartis, and Roche/Genetech and is a consulting/advisory board for Merck, AstraZeneca, BMS, Amgen, Novartis, Roche/Genetech, Takeda, Pfizer, Daiichi Sankyo, and NGM Biosciences. C.J. is a co-founder with equity interest in Egret Therapeutics and receives research support from Biohaven.

Figures

**Figure 1**
Representative focal changes used in Real-CSF The Real-CSF focal panel calls focal changes surrounding the following genes: (A) 1.5 M focal amplification of MDM4 at 1q32.1 (chr1: 203,800,000–205,300,000 hg19); (B) 3.5 MB focal amplification of CDK4 at 12q14.1 (chr12: 57,600,000–61,100,000 hg19); (C) 1.5 MB focal amplification of EGFR at 7p11.2 (chr7: 54,200,000–55,700,000 hg19); and (D) 2.5 MB focal amplification of ERBB2 17q12 (chr17: 35,300,000–37,800,000 hg19)

**Figure 2**
Evaluation of Real-CSF (A) Comparison of performance of Real-CSF in the training and validation partitions. Medulloblastoma is not illustrated in this figure because it was not included in the training set. (B) Comparison of performance of Real-CSF with cytology. (C) Comparison of Real-CSF performance in CSF and plasma. Error bars represent confidence intervals as calculated by the Wilson score interval.

**Figure 3**
Venn diagrams (A) Overlap of samples identified based on the global aneuploidy score (GAS) and panel of focal amplifications. (B) Overlap of calls based on cytology and Real-CSF. (C) Overlap of Real-CSF calls in matched CSF and plasma samples.

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References

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Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid

Affiliations

Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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Grants and funding

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Full Text Sources