Program Director

Principal Investigator

Chetan
Bettegowda
Awardee Organization

Johns Hopkins University
United States

Fiscal Year
2022
Activity Code
R37
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Interrogating malignant gliomas using released tumor DNA in cerebrospinal fluid

Approximately 17,000 individuals each year are diagnosed with a malignant glioma in the United States and the vast majority of these patients will succumb to their disease. Given the lack of clinically available biomarkers for CNS malignancies, the conventional method for disease monitoring in these patients is radiographic. Unfortunately, anatomic changes detected by MRI and CT scans are often non-specific and lag behind progressing or regressing disease. Moreover, it can be difficult to discriminate between treatment effect and cancer growth with imaging alone. Patients must, therefore, have additional surgeries for definitive tissue diagnosis or inappropriately wait for radiographic findings to change as their disease progresses unabated. As a result, there is an incredible need for more sensitive and specific tumor biomarkers in neurooncology. We and others have shown that most cancers shed cell free molecules of tumor derived DNA into the circulation and that these molecules can be quantified as a measure of disease burden. Brain tumors are the exception to the rule and rarely shed detectable levels DNA into the bloodstream. However, we have provocative data to suggest that malignant gliomas shed cell free molecules of tumor derived DNA into the cerebrospinal fluid (CSF-tDNA). CSF-tDNA can be distinguished from DNA derived from normal cells by the presence of disease defining somatic mutations. Levels of CSF-tDNA can be quantified using sensitive digital sequencing based assays, such “Safe-SeqS”. In Aim 1, we will use Safe-SeqS to quantify CSF-tDNA levels in longitudinal spinal fluid samples derived from 20 patients with malignant gliomas. We will determine how closely CSF-tDNA levels correlate with disease status as measured by clinical, radiographic and pathological findings. If successful, this approach will accurately assess tumor response and identify those patients at highest risk for recurrence, thus enabling the clinician to alter treatment regimens. There are also burgeoning data to suggest that all cancers, including malignant gliomas, evolve over time in response to various selection pressures, including treatment. These genetic changes have important clinical implications but currently there are no minimally invasive clinical assays that are capable of providing insights into the glioma genotype. As a result, in Aim 2, we will perform whole exome sequencing directly on the CSF and compare to exomic sequencing results from matched tumor/normal samples. This will allow us to understand what fraction of tumor genotype can be detected by analyzing the CSF directly. In order to determine the background mutation rate in CSF, in Aim 3 we will perform Safe-SeqS directly on the CSF of 50 individuals without any history of cancer. At the completion of this grant, we hope to validate CSF-tDNA as a candidate biomarker for individuals with malignant glioma and set the stage for large scale clinical trials that can be conducted to demonstrate clinical utility.

Publications

  • Chen D, Nauen DW, Park HC, Li D, Yuan W, Li A, Guan H, Kut C, Chaichana KL, Bettegowda C, Quiñones-Hinojosa A, Li X. Label-free imaging of human brain tissue at subcellular resolution for potential rapid intra-operative assessment of glioma surgery. Theranostics. 2021 May 24;11(15):7222-7234. doi: 10.7150/thno.59244. eCollection 2021. PMID: 34158846
  • Douglass J, Hsiue EH, Mog BJ, Hwang MS, DiNapoli SR, Pearlman AH, Miller MS, Wright KM, Azurmendi PA, Wang Q, Paul S, Schaefer A, Skora AD, Molin MD, Konig MF, Liu Q, Watson E, Li Y, Murphy MB, Pardoll DM, Bettegowda C, Papadopoulos N, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S. Bispecific antibodies targeting mutant RAS neoantigens. Science immunology. 2021 Mar 1;6. (57). PMID: 33649101
  • Douville C, Cohen JD, Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Schoen RE, Tie J, Gibbs P, Goggins M, Wolfgang CL, Wang TL, Shih IM, Karchin R, Lennon AM, Hruban RH, Tomasetti C, Bettegowda C, Kinzler KW, Papadopoulos N, Vogelstein B. Assessing aneuploidy with repetitive element sequencing. Proceedings of the National Academy of Sciences of the United States of America. 2020 Mar 3;117(9):4858-4863. Epub 2020 Feb 19. PMID: 32075918
  • Azad TD, Jin MC, Bernhardt LJ, Bettegowda C. Liquid biopsy for pediatric diffuse midline glioma: a review of circulating tumor DNA and cerebrospinal fluid tumor DNA. Neurosurgical focus. 2020 Jan 1;48(1):E9. PMID: 31896079
  • Hsiue EH, Wright KM, Douglass J, Hwang MS, Mog BJ, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Wang Q, Schaefer A, Miller MS, Skora AD, Azurmendi PA, Murphy MB, Liu Q, Watson E, Li Y, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Gabelli SB, Zhou S. Targeting a neoantigen derived from a common TP53 mutation. Science (New York, N.Y.). 2021 Mar 5;371. (6533). Epub 2021 Mar 1. PMID: 33649166
  • Pearlman AH, Hwang MS, Konig MF, Hsiue EH, Douglass J, DiNapoli SR, Mog BJ, Bettegowda C, Pardoll DM, Gabelli SB, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Targeting public neoantigens for cancer immunotherapy. Nature cancer. 2021 May;2(5):487-497. Epub 2021 May 17. PMID: 34676374
  • Konig MF, Powell M, Staedtke V, Bai RY, Thomas DL, Fischer N, Huq S, Khalafallah AM, Koenecke A, Xiong R, Mensh B, Papadopoulos N, Kinzler KW, Vogelstein B, Vogelstein JT, Athey S, Zhou S, Bettegowda C. Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists. The Journal of clinical investigation. 2020 Jul 1;130(7):3345-3347. PMID: 32352407
  • Hwang MS, Mog BJ, Douglass J, Pearlman AH, Hsiue EH, Paul S, DiNapoli SR, Konig MF, Pardoll DM, Gabelli SB, Bettegowda C, Papadopoulos N, Vogelstein B, Zhou S, Kinzler KW. Targeting loss of heterozygosity for cancer-specific immunotherapy. Proceedings of the National Academy of Sciences of the United States of America. 2021 Mar 23;118. (12). PMID: 33731480
  • Lee B, Mahmud I, Pokhrel R, Murad R, Yuan M, Stapleton S, Bettegowda C, Jallo G, Eberhart CG, Garrett T, Perera RJ. Medulloblastoma cerebrospinal fluid reveals metabolites and lipids indicative of hypoxia and cancer-specific RNAs. Acta neuropathologica communications. 2022 Feb 24;10(1):25. PMID: 35209946
  • Zhang M, Iyer RR, Azad TD, Wang Q, Garzon-Muvdi T, Wang J, Liu A, Burger P, Eberhart C, Rodriguez FJ, Sciubba DM, Wolinsky JP, Gokaslan Z, Groves ML, Jallo GI, Bettegowda C. Genomic Landscape of Intramedullary Spinal Cord Gliomas. Scientific reports. 2019 Dec 10;9(1):18722. PMID: 31822682
  • Hwang MS, Miller MS, Thirawatananond P, Douglass J, Wright KM, Hsiue EH, Mog BJ, Aytenfisu TY, Murphy MB, Aitana Azurmendi P, Skora AD, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Bettegowda C, Pardoll DM, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens. Nature communications. 2021 Sep 6;12(1):5271. PMID: 34489470
  • Hsu PJ, Yan K, Shi H, Izumchenko E, Agrawal N. Molecular biology of oral cavity squamous cell carcinoma. Oral oncology. 2020 Mar;102:104552. Epub 2020 Jan 7. PMID: 31918173
  • Paul S, Pearlman AH, Douglass J, Mog BJ, Hsiue EH, Hwang MS, DiNapoli SR, Konig MF, Brown PA, Wright KM, Sur S, Gabelli SB, Li Y, Ghiaur G, Pardoll DM, Papadopoulos N, Bettegowda C, Kinzler KW, Zhou S, Vogelstein B. TCR β chain-directed bispecific antibodies for the treatment of T cell cancers. Science translational medicine. 2021 Mar 10;13. (584). Epub 2021 Mar 1. PMID: 33649188
  • Cohen JD, Douville C, Dudley JC, Mog BJ, Popoli M, Ptak J, Dobbyn L, Silliman N, Schaefer J, Tie J, Gibbs P, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B. Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands. Nature biotechnology. 2021 Oct;39(10):1220-1227. Epub 2021 May 3. PMID: 33941929
  • Mattox AK, Yan H, Bettegowda C. The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors. Neuro-oncology. 2019 Dec 17;21(12):1509-1518. PMID: 31595305
  • Pearlman AH, Hwang MS, Konig MF, Hsiue EH, Douglass J, DiNapoli SR, Mog BJ, Bettegowda C, Pardoll DM, Gabelli SB, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Author Correction: Targeting public neoantigens for cancer immunotherapy. Nature cancer. 2021 Aug;2(8):865-867. PMID: 35122030
  • Shanmugam A, Hariharan AK, Hasina R, Nair JR, Katragadda S, Irusappan S, Ravichandran A, Veeramachaneni V, Bettadapura R, Bhati M, Ramaswamy V, Rao VUS, Bagadia RK, Manjunath A, Manjunath NML, Solomon MC, Maji S, Bahadur U, Bettegowda C, Papadopoulos N, Lingen MW, Hariharan R, Gupta V, Agrawal N, Izumchenko E. Ultrasensitive detection of tumor-specific mutations in saliva of patients with oral cavity squamous cell carcinoma. Cancer. 2021 May 15;127(10):1576-1589. Epub 2020 Dec 21. PMID: 33405231
  • Lennon AM, Buchanan AH, Kinde I, Warren A, Honushefsky A, Cohain AT, Ledbetter DH, Sanfilippo F, Sheridan K, Rosica D, Adonizio CS, Hwang HJ, Lahouel K, Cohen JD, Douville C, Patel AA, Hagmann LN, Rolston DD, Malani N, Zhou S, Bettegowda C, Diehl DL, Urban B, Still CD, Kann L, Woods JI, Salvati ZM, Vadakara J, Leeming R, Bhattacharya P, Walter C, Parker A, Lengauer C, Klein A, Tomasetti C, Fishman EK, Hruban RH, Kinzler KW, Vogelstein B, Papadopoulos N. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science (New York, N.Y.). 2020 Jul 3;369. (6499). Epub 2020 Apr 28. PMID: 32345712
  • Naidoo J, Schreck KC, Fu W, Hu C, Carvajal-Gonzalez A, Connolly RM, Santa-Maria CA, Lipson EJ, Holdhoff M, Forde PM, Douville C, Riemer J, Barnes A, Redmond KJ, Kleinberg L, Page B, Aygun N, Kinzler KW, Papadopoulos N, Bettegowda C, Venkatesan A, Brahmer JR, Grossman SA. Pembrolizumab for patients with leptomeningeal metastasis from solid tumors: efficacy, safety, and cerebrospinal fluid biomarkers. Journal for immunotherapy of cancer. 2021 Aug;9. (8). PMID: 34380662
  • Mattox AK, Douville C, Silliman N, Ptak J, Dobbyn L, Schaefer J, Popoli M, Blair C, Judge K, Pollard K, Pratilas C, Blakeley J, Rodriguez F, Papadopoulos N, Belzberg A, Bettegowda C. Detection of malignant peripheral nerve sheath tumors in patients with neurofibromatosis using aneuploidy and mutation identification in plasma. eLife. 2022 Mar 4;11. PMID: 35244537
  • Downs BM, Ding W, Cope LM, Umbricht CB, Li W, He H, Ke X, Holdhoff M, Bettegowda C, Tao W, Sukumar S. Methylated markers accurately distinguish primary central nervous system lymphomas (PCNSL) from other CNS tumors. Clinical epigenetics. 2021 May 5;13(1):104. PMID: 33952317
  • Douville C, Moinova HR, Thota PN, Shaheen NJ, Iyer PG, Canto MI, Wang JS, Dumot JA, Faulx A, Kinzler KW, Papadopoulos N, Vogelstein B, Markowitz SD, Bettegowda C, Willis JE, Chak A. Massively Parallel Sequencing of Esophageal Brushings Enables an Aneuploidy-Based Classification of Patients With Barrett's Esophagus. Gastroenterology. 2021 May;160(6):2043-2054.e2. Epub 2021 Jan 22. PMID: 33493502
  • Bettegowda C, Upadhayaya M, Evans DG, Kim A, Mathios D, Hanemann CO, REiNS International Collaboration. Genotype-Phenotype Correlations in Neurofibromatosis and Their Potential Clinical Use. Neurology. 2021 Aug 17;97(7 Suppl 1):S91-S98. Epub 2021 Jul 6. PMID: 34230207