FOUND IN TRANSLATION Minimal nomenclature and maximum sensitivity complicate MRD measures

 

In hematologic malignancies, there is a deep and direct connection between each individual patient, that patient’s symptoms, the visible cells that cause the disease, and the direct measurements and assessments of those cells. The totality of these factors helps to determine the diagnosis and treatment plan. As a butterfly needle often is sufficient for obtaining a diagnostic tumor biopsy, it is not surprising that these same diagnostic techniques are now standardly being used to monitor disease response.

The techniques differ in their limits of detection, however. With sequencing depths able to reliably detect variant allele frequencies of less than 10%, even when patients’ overt leukemia may no longer be detectable, clinicians may be left to ponder what to do with persistent “preleukemic” or “rising clones.”^1-3

Clearly, minimal residual disease (MRD) status is prognostic and can be used to risk stratify patients for appropriate postremission therapy, as noted in the NCCN (National Comprehensive Cancer Network) clinical practice guidelines for postinduction assessment in acute lymphoblastic leukemia. Given the high risk of relapse in this population, consideration of upfront allogeneic stem cell transplant in MRD-positive ALL patients is recommended by the NCCN. Similarly, given the high risk of MRD-positive status in AML patients, clinical trials are examining agents such as SL-401 for consolidation therapy in MRD-positive AML in CR1 or CR2, as noted in work presented at the 2016 annual meeting of the American Society of Hematology (ASH 2016) by Andrew Lane, MD, PhD, of Dana-Farber Cancer Institute, Boston, and his colleagues.⁴

These patients, now more appropriately stratified for risk of recurrence, are in desperate need of better care algorithms. Standard MRD assessment by flow cytometric analysis is able to detect less than 1 x 10^-4 cells. While it can be applied to most patients, its sensitivity will likely be surpassed by new and emerging genomic assays. Real time quantitative polymerase chain reaction (RT-qPCR) and next generation sequencing (NGS) require a leukemia-specific abnormality but have the potential for far greater sensitivity with deeper sequencing techniques.

Long-term follow up data in acute promyelocytic leukemia (APL) provides the illustrative example where morphologic remission is not durable in the setting of a persistent PML-RARa transcript and therapeutic goals for PCR negativity irrespective of morphology are standard. Pathologic fusion proteins are ideal for marker-driven therapy, but are found in only about 50% of patients, mainly those with APL and Philadelphia chromosome-positive leukemias.

With driver mutations identified in the majority of patients, we can be hopeful that NGS negativity may be a useful clinical endpoint. In work presented at ASH 2016 by Bartlomiej M Getta, MBBS, of Memorial Sloan Kettering Cancer Center, New York, and his colleagues, patients with concordant MRD positivity by flow cytometry and NGS had inferior outcomes, even after allogeneic transplant, compared to patients with MRD positivity on one assay but not both.⁵ Nonetheless, caution should be taken in early adoption of NGS as a independent marker of MRD status for two main reasons: 1) False positives and lack of standardization make current interpretation difficult. 2) The presence of “preleukemic” clones remains enigmatic – and no matter the nomenclature used, can a DNMT3A or IDH-mutant clone really be deemed “clonal hematopoiesis of indeterminate potential” when a patient has already had clonal transformation?

Conversely, not all patients reported in the work by Klco² and Getta ultimately relapse. Thus, while it would be preferred to clear all mutant clones, as a therapeutic goal this likely would subject many patients to unnecessary toxicity. One half of the patients reported by Getta were disease free at a year with concordant flow and NGS positive MRD while patients with NGS positivity alone had outcomes equivalent to those of MRD-negative patients, highlighting that certain persistent clones in NGS-only, MRD-positive patients might be amenable to immunotherapy, either with checkpoint inhibitors or allogeneic transplant. Insight into which clones remain quiescent and which are more sinister will require more investigation, but there does seem to be an additive role to NGS-positivity, whereby all MRD is not created equal and the precision and clinical utility of MRD status will likely take on nuanced nomenclature.
 

References

1. Jan, M. et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Science Translational Medicine 4, 149ra118, doi: 10.1126/scitranslmed.3004315 (2012).

2. Klco, J. M. et al. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA 2015;314:811-22. doi: 10.1001/jama.2015.9643.

3. Wong, T. N. et al. Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood 2016;127:893-7. doi: 10.1182/blood-2015-10-677021 (2016).

4. Lane, A. A. et al. Results from Ongoing Phase II Trial of SL-401 As Consolidation Therapy in Patients with Acute Myeloid Leukemia (AML) in Remission with High Relapse Risk Including Minimal Residual Disease (MRD), Abstract 215, ASH 2016.

5. Getta, B. M. et al. Multicolor Flow Cytometry and Multi-Gene Next Generation Sequencing Are Complimentary and Highly Predictive for Relapse in Acute Myeloid Leukemia Following Allogeneic Hematopoietic Stem Cell Transplant, Abstract 834, ASH 2016.

 

Dr. Viny is with the Memorial Sloan-Kettering Cancer Center, New York, where he is a clinical instructor, on the staff of the leukemia service, and a clinical researcher in The Ross Levine Lab. Contact Dr. Viny at vinya@mskcc.org.

 

In hematologic malignancies, there is a deep and direct connection between each individual patient, that patient’s symptoms, the visible cells that cause the disease, and the direct measurements and assessments of those cells. The totality of these factors helps to determine the diagnosis and treatment plan. As a butterfly needle often is sufficient for obtaining a diagnostic tumor biopsy, it is not surprising that these same diagnostic techniques are now standardly being used to monitor disease response.

The techniques differ in their limits of detection, however. With sequencing depths able to reliably detect variant allele frequencies of less than 10%, even when patients’ overt leukemia may no longer be detectable, clinicians may be left to ponder what to do with persistent “preleukemic” or “rising clones.”^1-3

Clearly, minimal residual disease (MRD) status is prognostic and can be used to risk stratify patients for appropriate postremission therapy, as noted in the NCCN (National Comprehensive Cancer Network) clinical practice guidelines for postinduction assessment in acute lymphoblastic leukemia. Given the high risk of relapse in this population, consideration of upfront allogeneic stem cell transplant in MRD-positive ALL patients is recommended by the NCCN. Similarly, given the high risk of MRD-positive status in AML patients, clinical trials are examining agents such as SL-401 for consolidation therapy in MRD-positive AML in CR1 or CR2, as noted in work presented at the 2016 annual meeting of the American Society of Hematology (ASH 2016) by Andrew Lane, MD, PhD, of Dana-Farber Cancer Institute, Boston, and his colleagues.⁴

These patients, now more appropriately stratified for risk of recurrence, are in desperate need of better care algorithms. Standard MRD assessment by flow cytometric analysis is able to detect less than 1 x 10^-4 cells. While it can be applied to most patients, its sensitivity will likely be surpassed by new and emerging genomic assays. Real time quantitative polymerase chain reaction (RT-qPCR) and next generation sequencing (NGS) require a leukemia-specific abnormality but have the potential for far greater sensitivity with deeper sequencing techniques.

Long-term follow up data in acute promyelocytic leukemia (APL) provides the illustrative example where morphologic remission is not durable in the setting of a persistent PML-RARa transcript and therapeutic goals for PCR negativity irrespective of morphology are standard. Pathologic fusion proteins are ideal for marker-driven therapy, but are found in only about 50% of patients, mainly those with APL and Philadelphia chromosome-positive leukemias.

With driver mutations identified in the majority of patients, we can be hopeful that NGS negativity may be a useful clinical endpoint. In work presented at ASH 2016 by Bartlomiej M Getta, MBBS, of Memorial Sloan Kettering Cancer Center, New York, and his colleagues, patients with concordant MRD positivity by flow cytometry and NGS had inferior outcomes, even after allogeneic transplant, compared to patients with MRD positivity on one assay but not both.⁵ Nonetheless, caution should be taken in early adoption of NGS as a independent marker of MRD status for two main reasons: 1) False positives and lack of standardization make current interpretation difficult. 2) The presence of “preleukemic” clones remains enigmatic – and no matter the nomenclature used, can a DNMT3A or IDH-mutant clone really be deemed “clonal hematopoiesis of indeterminate potential” when a patient has already had clonal transformation?

Conversely, not all patients reported in the work by Klco² and Getta ultimately relapse. Thus, while it would be preferred to clear all mutant clones, as a therapeutic goal this likely would subject many patients to unnecessary toxicity. One half of the patients reported by Getta were disease free at a year with concordant flow and NGS positive MRD while patients with NGS positivity alone had outcomes equivalent to those of MRD-negative patients, highlighting that certain persistent clones in NGS-only, MRD-positive patients might be amenable to immunotherapy, either with checkpoint inhibitors or allogeneic transplant. Insight into which clones remain quiescent and which are more sinister will require more investigation, but there does seem to be an additive role to NGS-positivity, whereby all MRD is not created equal and the precision and clinical utility of MRD status will likely take on nuanced nomenclature.
 

References

1. Jan, M. et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Science Translational Medicine 4, 149ra118, doi: 10.1126/scitranslmed.3004315 (2012).

2. Klco, J. M. et al. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA 2015;314:811-22. doi: 10.1001/jama.2015.9643.

3. Wong, T. N. et al. Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood 2016;127:893-7. doi: 10.1182/blood-2015-10-677021 (2016).

4. Lane, A. A. et al. Results from Ongoing Phase II Trial of SL-401 As Consolidation Therapy in Patients with Acute Myeloid Leukemia (AML) in Remission with High Relapse Risk Including Minimal Residual Disease (MRD), Abstract 215, ASH 2016.

5. Getta, B. M. et al. Multicolor Flow Cytometry and Multi-Gene Next Generation Sequencing Are Complimentary and Highly Predictive for Relapse in Acute Myeloid Leukemia Following Allogeneic Hematopoietic Stem Cell Transplant, Abstract 834, ASH 2016.

 

Dr. Viny is with the Memorial Sloan-Kettering Cancer Center, New York, where he is a clinical instructor, on the staff of the leukemia service, and a clinical researcher in The Ross Levine Lab. Contact Dr. Viny at vinya@mskcc.org.

 

In hematologic malignancies, there is a deep and direct connection between each individual patient, that patient’s symptoms, the visible cells that cause the disease, and the direct measurements and assessments of those cells. The totality of these factors helps to determine the diagnosis and treatment plan. As a butterfly needle often is sufficient for obtaining a diagnostic tumor biopsy, it is not surprising that these same diagnostic techniques are now standardly being used to monitor disease response.

The techniques differ in their limits of detection, however. With sequencing depths able to reliably detect variant allele frequencies of less than 10%, even when patients’ overt leukemia may no longer be detectable, clinicians may be left to ponder what to do with persistent “preleukemic” or “rising clones.”^1-3

Clearly, minimal residual disease (MRD) status is prognostic and can be used to risk stratify patients for appropriate postremission therapy, as noted in the NCCN (National Comprehensive Cancer Network) clinical practice guidelines for postinduction assessment in acute lymphoblastic leukemia. Given the high risk of relapse in this population, consideration of upfront allogeneic stem cell transplant in MRD-positive ALL patients is recommended by the NCCN. Similarly, given the high risk of MRD-positive status in AML patients, clinical trials are examining agents such as SL-401 for consolidation therapy in MRD-positive AML in CR1 or CR2, as noted in work presented at the 2016 annual meeting of the American Society of Hematology (ASH 2016) by Andrew Lane, MD, PhD, of Dana-Farber Cancer Institute, Boston, and his colleagues.⁴

These patients, now more appropriately stratified for risk of recurrence, are in desperate need of better care algorithms. Standard MRD assessment by flow cytometric analysis is able to detect less than 1 x 10^-4 cells. While it can be applied to most patients, its sensitivity will likely be surpassed by new and emerging genomic assays. Real time quantitative polymerase chain reaction (RT-qPCR) and next generation sequencing (NGS) require a leukemia-specific abnormality but have the potential for far greater sensitivity with deeper sequencing techniques.

Long-term follow up data in acute promyelocytic leukemia (APL) provides the illustrative example where morphologic remission is not durable in the setting of a persistent PML-RARa transcript and therapeutic goals for PCR negativity irrespective of morphology are standard. Pathologic fusion proteins are ideal for marker-driven therapy, but are found in only about 50% of patients, mainly those with APL and Philadelphia chromosome-positive leukemias.

With driver mutations identified in the majority of patients, we can be hopeful that NGS negativity may be a useful clinical endpoint. In work presented at ASH 2016 by Bartlomiej M Getta, MBBS, of Memorial Sloan Kettering Cancer Center, New York, and his colleagues, patients with concordant MRD positivity by flow cytometry and NGS had inferior outcomes, even after allogeneic transplant, compared to patients with MRD positivity on one assay but not both.⁵ Nonetheless, caution should be taken in early adoption of NGS as a independent marker of MRD status for two main reasons: 1) False positives and lack of standardization make current interpretation difficult. 2) The presence of “preleukemic” clones remains enigmatic – and no matter the nomenclature used, can a DNMT3A or IDH-mutant clone really be deemed “clonal hematopoiesis of indeterminate potential” when a patient has already had clonal transformation?

Conversely, not all patients reported in the work by Klco² and Getta ultimately relapse. Thus, while it would be preferred to clear all mutant clones, as a therapeutic goal this likely would subject many patients to unnecessary toxicity. One half of the patients reported by Getta were disease free at a year with concordant flow and NGS positive MRD while patients with NGS positivity alone had outcomes equivalent to those of MRD-negative patients, highlighting that certain persistent clones in NGS-only, MRD-positive patients might be amenable to immunotherapy, either with checkpoint inhibitors or allogeneic transplant. Insight into which clones remain quiescent and which are more sinister will require more investigation, but there does seem to be an additive role to NGS-positivity, whereby all MRD is not created equal and the precision and clinical utility of MRD status will likely take on nuanced nomenclature.
 

References

1. Jan, M. et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Science Translational Medicine 4, 149ra118, doi: 10.1126/scitranslmed.3004315 (2012).

2. Klco, J. M. et al. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA 2015;314:811-22. doi: 10.1001/jama.2015.9643.

3. Wong, T. N. et al. Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood 2016;127:893-7. doi: 10.1182/blood-2015-10-677021 (2016).

4. Lane, A. A. et al. Results from Ongoing Phase II Trial of SL-401 As Consolidation Therapy in Patients with Acute Myeloid Leukemia (AML) in Remission with High Relapse Risk Including Minimal Residual Disease (MRD), Abstract 215, ASH 2016.

5. Getta, B. M. et al. Multicolor Flow Cytometry and Multi-Gene Next Generation Sequencing Are Complimentary and Highly Predictive for Relapse in Acute Myeloid Leukemia Following Allogeneic Hematopoietic Stem Cell Transplant, Abstract 834, ASH 2016.

 

Dr. Viny is with the Memorial Sloan-Kettering Cancer Center, New York, where he is a clinical instructor, on the staff of the leukemia service, and a clinical researcher in The Ross Levine Lab. Contact Dr. Viny at vinya@mskcc.org.