Cancer Res Treat.  2022 Apr;54(2):597-612. 10.4143/crt.2021.752.

Plasma Circulating Tumor DNA in Patients with Primary Central Nervous System Lymphoma

• Yoon SE
• Kim YJ
• Shim JH
• Park D
• Cho J
• Ko YH
• Park WY
• Mun YC
• Lee KE
• Cho D
• Kim WS
• Kim SJ

• KMID: 2528229
• DOI: http://doi.org/10.4143/crt.2021.752

Abstract

Purpose
Analysis of circulating tumor DNA (ctDNA) in blood could allow noninvasive genetic analysis of primary tumors. Although there have been unmet needs for noninvasive methods in patients with primary central nervous system lymphoma (PCNSL), it is still not determined whether plasma ctDNA analysis could be useful for patients with PCNSL.
Materials and Methods
Targeted deep sequencing of 54 genes was performed in cell-free DNA isolated from plasma samples collected pretreatment, during treatment, and at the end of treatment in 42 consecutively diagnosed PCNSL patients between January 2017 and December 2018.
Results
Targeted sequencing of plasma cell-free DNA detected somatic mutations representing ctDNA in 11 cases (11/41, 27%). The detection of ctDNA was not related to the concentration of cell-free DNA or tumor volume. The mutation profiles of these 11 cases varied between patients. The most frequently mutated gene was PIM1 (4/11, 36.4%), whereas KMT2D, PIK3CA, and MYD88 were each observed in three patients (3/11, 27%). The mutations of 13 genes were concordantly found in primary tumor tissue and plasma ctDNA, giving a detection sensitivity of 45%. During the serial tracking of seven patients with complete response, the disappearance of ctDNA mutations was found in four patients, whereas three patients had detected ctDNA mutation at the end of treatment.
Conclusion
The plasma ctDNA mutation analysis still has limited value for surveillance and predicting treatment outcomes of PCNSL because the detection efficiency was lower than other systemic lymphomas. Thus, analytical platforms should be improved to overcome anatomical hurdles associated with PCNSL.

Keyword

Primary CNS lymphoma; Circulating tumor DNA; Prognosis

Figure

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  Fig. 1 Study scheme. (A) Forty-two patients suffering from newly diagnosed primary central nervous system lymphoma (PCNSL) (n=39) or relapsed PCNSL (n=3) were enrolled from January 2017 to December 2018. The plasma cell-free DNA of 41 PCNSL patients (except for one poor-quality DNA sample) was finally analyzed. a)Poor DNA quality. (B) We collected plasma samples sequentially from PCNSL patients at diagnosis, interim, and end of treatment. The obtained samples were interpreted based on high-depth targeted sequencing of 54 genes.

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  Fig. 2 Cell-free DNA (cfDNA) and treatment outcomes in patients with primary central nervous system lymphoma (PCNSL). (A) Overall Kaplan-Meier survival curve of the 42 patients. (B) The median cfDNA concentration of PCNSL (13.5 ng/mL; range, 2.6 to 121.60 ng/mL; orange bar) was significantly higher than diffuse large B-cell lymphoma (DLBCL) (median, 25.48 ng/mL; range, 4.8 to 427.6 ng/mL; blue bar). (C) The concentration of cfDNA was not significantly associated with tumor volume (R2 coefficient=0.02, p=0.90). (D) The concentration of cfDNA was not different according to the tumor location, either. (E, F) Patients were dichotomized into high and low cfDNA groups according to the median value (13.5 ng/mL), and they did not show significant differences of progression-free and overall survival. (G) The sequential changes of cfDNA were not associated with therapeutic response and relapse.

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  Fig. 3 Mutation profiles of plasma circulating tumor DNA (ctDNA) in patients with primary central nervous system lymphoma. (A) The concentration of cell-free DNA (cfDNA) did not differ between patients in whom mutations in plasma ctDNA were detected (blue bar) and not detected (red bar). (B) The detection of mutations was not related to the concentration of cfDNA within the intermediate- and poor-risk groups of International Extranodal Lymphoma Study Group. (C) The progression-free survival did not differ significantly according to the detection of ctDNA mutations (p=0.297). (D) The overall survival did not differ significantly according to the detection of ctDNA mutations (p=0.941). (E) The maximum genome equivalents was not significantly associated with the tumor volume in the 11 patients in whom ctDNA mutations were detected (R2 coefficient=0.210, p=0.450). (F) The mutation profiles of 11 cases showed somatic mutations with variable variant allele fraction detected by targeted sequencing of plasma ctDNA. (G) A comparison of the mutation profiles of plasma ctDNA and primary tumor tissue represented with orange (plasma) and green (tissue).

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  Fig. 4 Pretreatment mutations detected by plasma circulating tumor DNA (ctDNA) and treatment outcomes. (A) A patient (P596) with a high number of mutations at diagnosis experienced early progression during treatment. (B) A patient (P764) with mutations of plasma ctDNA at pretreatment showed disease progression within 10 months after the end of treatment. (C) The summary of 11 patients’ progression-free survival and plasma ctDNA mutation burden at diagnosis.

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  Fig. 5 Serial monitoring of mutation profiles of plasma circulating tumor DNA (ctDNA) in primary central nervous system lymphoma (PCNSL). The ctDNA diversity and levels assessed by targeted deep sequencing are indicated on the y-axis. The time course of diagnosis, interim, and final analysis are indicated on the x-axis. The therapeutic response of patients at the time of analysis was estimated from their International PCNSL Collaborative Group (IPCG). (A) Four patients showing the complete disappearance of ctDNA mutations at the final response evaluation achieved complete response at the end of treatment and maintained their response without any evidence of relapse (P205, P543, P582, and P586). However, one patient obtaining a complete response with a detected DNMT3A mutation at the end of treatment eventually relapsed during follow-up (P297). CR, complete response; PD, progressive disease; PR, partial response. (B) Three patients (P152, P309, and P223) who achieved a complete response assessed by brain magnetic resonance imaging showed the persistence of mutations in plasma ctDNA after treatment. One patient showed a new mutation in the interim analysis but did not show any evidence of relapse at the time of analysis (P152), and another patient receiving hemodialysis showed the persistence of mutations (P309). The other patient harboring a persistent TET2 mutation at the interim and end of treatment analyses showed a late relapse during follow-up (P223). (C) Limitations of ctDNA-based mutation analysis in patients with PCNSL. The plasma ctDNA mutation analysis still has limited value for surveillance and predicting treatment outcomes of PCNSL because the detection efficiency was lower than other systemic lymphomas. CNS, central nervous system.

Reference

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