Cell-Free DNA for Minimal Residual Disease Monitoring in Multiple Myeloma Patients

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3423-3423 ◽  
Author(s):  
Lenka Kubiczkova-Besse ◽  
Daniela Drandi ◽  
Lenka Sedlarikova ◽  
Stefania Oliva ◽  
Manuela Gambella ◽  
...  

Abstract Background Circulating nucleic acids, such as cell-free DNA (cf-DNA), are becoming a promising minimally-invasive diagnostic tool for cancer detection. Recent studies demonstrated that tumor-derived cf-DNA can be used to monitor tumor burden and response to treatment in patients (pts) with solid tumors as well as hematological malignancies (Dawson et al, 2013, Armand et al, 2013). In this study we investigated the clinical utility of cf-DNA in the monitoring of minimal residual disease (MRD) of pts with multiple myeloma (MM) carrying the tumor specific immunoglobulin (IGH) rearrangement. Methods Cf-DNA was extracted from 1 ml of serum sample from 13 MM patients enrolled in Italian CRD/MEL-200 and EMN-02 protocols. The total amount of cf-DNA was estimated by fluorometric measurement (median 560 ng, range 15-5158 ng) and the length of fragments was evaluated by high sensitivity dsDNA chips (Agilent). Patient specific clonal IGH rearrangement was identified at the time of diagnosis from bone marrow (BM) genomic DNA (gDNA) as previously reported (Ladetto et al, 2000). For each patient, MRD in BM and peripheral blood (PB) was estimated by real time quantitative PCR (qPCR) using ASO-specific primers and the quantification was based on serial 10-fold dilution standard curves from plasmid carrying the patient specific IGH rearrangement. The amount of IGH rearrangement in cf-DNA (cf-IGH) was estimated by qPCR and droplet digital PCR (ddPCR) (Bio-Rad) on diagnostic and follow up samples and was expressed as the amount of copies per 1 µg of total cf-DNA. qPCR and ddPCR results were interpreted according to the Euro-MRD guidelines (van der Velden et al, 2003). Results Overall, 54 cf-DNA samples from MM serum (13 diagnostic, 41 follow-up samples) were analyzed for the presence of patient specific IGH rearrangement. The most abundant fraction of cf-DNA was 180-220bp, than 350-400bp and 700-10000bp (in 100%, 85% and 68% of samples respectively), whereas longer fragments more often appeared in follow-up samples. By qPCR, cf-IGH at diagnosis were observed in 11/13 diagnostic samples. Only 3/13 pts were quantifiable (116, 85, 187 copies/1 µg of cfDNA) and 8/13 pts were positive but not quantifiable (PNQ) cf-IGH. By ddPCR, levels of cf-IGH at diagnosis were observed in 9/13 pts. 6/13 pts were quantifiable (246, 195, 96, 88, 184, 25 copies/1µg of cfDNA), and only 3/13 pts were PNQ. In follow-up samples, levels of cf-IGH were undetectable by qRT-PCR; however in 5 samples they were PNQ by ddPCR. Interestingly, in one available relapse sample, cf-IGH reappeared again to quantifiable level (61 copies by qRT-PCR and 190 copies by ddPCR). The levels of cf-IGH are quantifiable in samples with higher amount of tumor specific IGH rearrangements in BM or PB; however, no association was observed between cf-IGH level at diagnosis and disease burden estimated by the PCs infiltration in BM or the monoclonal immunoglobulin concentration in blood/urine. Conclusions These data show the potential utility of cf-IGH monitoring in MM pts. Although by qPCR, cf-IGH were detected in 11/13 pts, they were quantifiable only in 3/13 pts and ddPCR was more precise as it was able to quantify cf-IGH in 6/13 pts. Since cf-IGH copies were quantifiable only in diagnostic samples and in 1 available sample at the relapse, we conclude that higher amounts of serum are necessary to overcome the limitation of assay sensitivity. Potential advantages and predictive value, for monitoring tumor marker in a non-invasive manner, need to be further validated on larger cohort of samples using increased amount of cf-DNA. Work was supported by IGA grants NT12130, NT14575. This work is funded by a Black Swan Research Initiative grant by the International Myeloma Foundation "Dynamics of microRNA and cell-free DNA profiles during multiple myeloma progression“. Disclosures Boccadoro: Celgene: Honoraria; Janssen: Honoraria; Onyx: Honoraria. Palumbo:Amgen: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria; Array BioPharma: Honoraria; Genmab A/S: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen-Cilag: Consultancy, Honoraria; Millennium Pharmaceuticals, Inc.: Consultancy, Honoraria; Onyx Pharmaceuticals: Consultancy, Honoraria; Sanofi Aventis: Honoraria.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 5128-5128 ◽  
Author(s):  
B. Bruno ◽  
M. Ladetto ◽  
M. Astolfi ◽  
L. Veneziano ◽  
L. Cimolin ◽  
...  

Abstract New allogeneic transplant protocols with non myeloablative conditioning regimens for treatment of multiple myeloma (MM) have been developed in the attempt to reduce the transplant related toxicity associated with myeloablation. Preliminary data have been encouraging with remarkable clinical response rates (Maloney et al, Blood 2003). However, data on the achievement of molecular remission, prerequisite for eventual cure, are still lacking. We implemented a tandem transplant approach consisting of high dose melphalan (200 mg/sqm) with autografting followed by non myeloablative low dose (2.0 Gy) total body irradiation and G-CSF mobilized PBSC infusion from HLA-identical siblings. The curative potential relies exclusively upon a potent graft versus myeloma (GVM) effect through donor T cells. At diagnosis, patient specific clonal markers were generated based upon the rearrangement of the immunoglobulin heavy chain (IgH) genes and used for nested polymerase chain reaction (PCR) detection of minimal residual disease after transplant. Molecular remission was defined as the disappearance of the molecular marker post transplant in both bone marrow and blood. The sensitivity of the nested PCR-based assay was 1 in 100000 cells. A patient specific marker was generated in 11/15 (73%) patients who entered the study. After a median follow up of 16 months (range 5–50), molecular follow up post transplant showed that 3/11 (27%) reached molecular remission at 1, 3 and 7 months post allografting, respectively. Of the remaining 8 patients, 3/8 and 5/8 reached clinical complete remission, defined as the disappearance of the monoclonal paraprotein by immunofixation, and partial remission, respectively. However, minimal residual disease by nested PCR could be detected at all timepoints. The molecular remissions have been durable at 7, 30, and 48 months post transplant, respectively. In 1 case the remission was achieved and sustained in the absence of graft versus host disease (GVHD) which is consistent with the notion that GVHD is not essential for GVM. Furthermore, in 4/11 patients real-time quantification of IgH rearrangements was performed on genomic DNA samples using tumor specific primers and consensus probes. All patients showed a considerable tumor burden reduction post autografting. Samples from two patients became negative by real time PCR at 3 months post allografting, but became PCR-negative by nested PCR at 3 and 7 months, respectively. This discrepancy is explained by the greater sensitivity of nested PCR and the larger amount of IgH copies which are expected in cDNA compared to genomic DNA. The remaining two patients only obtained a clinical partial response throughout the study period. This report indicates that the tandem auto-allo transplant approach can lead to molecular remission in MM. Prospective quantitative monitoring of disease response may be helpful to design individual additional immunotherapeutic manoeuvres, such as donor lymphocyte infusions, to enhance GVM. Longer follow up on a larger series of patients is needed to determine the frequency and durability of molecular remissions.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 29-29
Author(s):  
Juan Du ◽  
Baoan Chen ◽  
Wanting Qiang ◽  
Yanchun Jia ◽  
Jing Lu ◽  
...  

Background: Minimal residual disease (MRD) is becoming standard diagnostic care for multiple myeloma. Here we investigate cell-free DNA chromosomal instability as minimal invasive biomarker for minimal residual disease monitoring. Methods: 55 patients were recruited, including 47 newly diagnosed and 8 relapsed multiple myelomas. Plasma samples were collected before treatments, end of 2 cycle and 4 cycle of treatments. Treatment response was assessed by using IMWG criteria. Cell-free DNA was analyzed by illumine HiSeq X10, followed by chromosomal instability analyses by a customized bioinformatics workflow, ultrasensitive chromosomal aneuploidy detector (UCAD), and cfDNA CIN responding to treatment was summarized as cfDNA MRD INDEX. Results: In this cohort study, 53 (96.3%) patients were found with treatment responses after 4 cycle of treatments, including 16 (29.1%) complete, 13 (23.6%) very good partial, 17 (30.9%) partial and 6 (10.9%) marginal responses. The other 2 (3.64%) recurrent MM experiences disease progression. At baseline, plasma cfDNA chromosomal aberrations were found in 14/17(82.3%) multiple myeloma patients. Less patients were found with detectable chromosomal changes after treatments (58.8% after C2, 41.2% after C4, versus 82.3% before treatments, P<0.01). The treatment responses identified in plasma cfDNA were summarized as cfDNA MRD INDEX. Low cfDNA MRD INDEX predicts better treatment responses (Fisher exact test, Odds ratio=7.3, P=4.69e-05). And it predicts complete response with sensitivity 100% and specificity 83.3%, with cutoff value 0.044. Furthermore, cfDNA CIN MRD index were found linearly correlated with percentage of malignant plasma cells from bone marrow aspiration as examined by flow cytometry assay (R-square=0.883, P<0.01). Cutoff -0.06 predicts 100% MRD negatives at specificity 100%. Conclusions: Plasma cfDNA CIN might be used for monitoring multiple myeloma patients treatment responses, especially for predicting minimal residual diseases. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 72 (1) ◽  
pp. 399-413
Author(s):  
Van K. Morris ◽  
John H. Strickler

Patient-specific biomarkers form the foundation of precision medicine strategies. To realize the promise of precision medicine in patients with colorectal cancer (CRC), access to cost-effective, convenient, and safe assays is critical. Improvements in diagnostic technology have enabled ultrasensitive and specific assays to identify cell-free DNA (cfDNA) from a routine blood draw. Clinicians are already employing these minimally invasive assays to identify drivers of therapeutic resistance and measure genomic heterogeneity, particularly when tumor tissue is difficult to access or serial sampling is necessary. As cfDNA diagnostic technology continues to improve, more innovative applications are anticipated. In this review, we focus on four clinical applications for cfDNA analysis in the management of CRC: detecting minimal residual disease, monitoring treatment response in the metastatic setting, identifying drivers of treatment sensitivity and resistance, and guiding therapeutic strategies to overcome resistance.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8001-8001
Author(s):  
Martin F. Kaiser ◽  
Andrew Hall ◽  
Katrina Walker ◽  
Ruth De Tute ◽  
Sadie Roberts ◽  
...  

8001 Background: Patients with ultra high-risk (UHiR) newly diagnosed multiple myeloma (NDMM) and patients with plasma cell leukemia (PCL) continue to have dismal outcomes and are underrepresented in clinical trials. Recently, improved responses with anti-CD38 monoclonal antibody combination therapy have been reported for NDMM patients. We report here outcomes for NDMM UHiR and PCL patients treated in the OPTIMUM/MUKnine (NCT03188172) trial with daratumumab, cyclophosphamide, bortezomib, lenalidomide, dexamethasone (Dara-CVRd) induction, augmented high-dose melphalan (HDMEL) and ASCT. With final analysis follow-up surpassed in Feb 2021, we report here early protocol defined endpoints from induction to day 100 post ASCT. Methods: Between Sep 2017 and Jul 2019, 107 patients with UHiR NDMM by central trial genetic (≥2 high risk lesions: t(4;14), t(14;16), t(14;20), gain(1q), del(1p), del(17p)) or gene expression SKY92 (SkylineDx) profiling, or with PCL (circulating plasmablasts > 20%) were included in OPTIMUM across 39 UK hospitals. Patients received up to 6 cycles of Dara-CVRd induction, HDMEL and ASCT augmented with bortezomib, followed by Dara-VR(d) consolidation for 18 cycles and Dara-R maintenance. Primary trial endpoints are minimal residual disease (MRD) status post ASCT and progression-free survival. Secondary endpoints include response, safety and quality of life. Data is complete but subject to further data cleaning prior to conference. Results: Median follow-up for the 107 patients in the safety population was 22.2 months (95% CI: 20.6 – 23.9). Two patients died during induction due to infection. Bone marrow aspirates suitable for MRD assessment by flow cytometry (10-5 sensitivity) were available for 81% of patients at end of induction and 78% at D100 post ASCT. Responses in the intention to treat population at end of induction were 94% ORR with 22% CR, 58% VGPR, 15% PR, 1% PD, 5% timepoint not reached (TNR; withdrew, became ineligible or died) and at D100 post ASCT 83% ORR with 47% CR, 32% VGPR, 5% PR, 7% PD, 10% TNR. MRD status was 41% MRDneg, 40% MRDpos and 19% not evaluable post induction and 64% MRDneg, 14% MRDpos and 22% not evaluable at D100 post ASCT. Responses at D100 post ASCT were lower in PCL with 22% CR, 22% VGPR, 22% PR, 22% PD, 12% TNR. Most frequent grade 3/4 AEs during induction were neutropenia (21%), thrombocytopenia (12%) and infection (12%). Grade 3 neuropathy rate was 3.7%. Conclusions: This is to our knowledge the first report on a trial for UHiR NDMM and PCL investigating Dara-CVRd induction and augmented ASCT. Response rates were high in this difficult-to-treat patient population, with toxicity comparable to other induction regimens. However, some early progressions highlight the need for innovative approaches to UHiR NDMM. Clinical trial information: NCT03188172.


Author(s):  
Amrita Krishnan ◽  
Ravi Vij ◽  
Jesse Keller ◽  
Binod Dhakal ◽  
Parameswaran Hari

For multiple myeloma, introduction of novel agents as part of the front-line treatment followed by high-dose chemotherapy and autologous hematopoietic stem cell transplantation (ASCT) induces deep responses in a majority of patients with this disease. However, disease relapse is inevitable, and, with each relapse, the remission duration becomes shorter, ultimately leading to a refractory disease. Consolidation and maintenance strategy after ASCT is one route to provide sustained disease control and prevent repeated relapses. Though the consolidation strategy remains largely confined to clinical trials, significant data support the efficacy of consolidation in improving the depth of response and outcomes. There are also increasing rates of minimal residual disease–negativity with additional consolidation therapy. On the other hand, maintenance with novel agents post-transplant is well established and has been shown to improve both progression-free and overall survival. Evolving paradigms in maintenance include the use of newer proteasome inhibitors, immunotherapy maintenance, and patient-specific maintenance—a concept that utilizes minimal residual disease as the primary driver of decisions regarding starting or continuing maintenance therapy. The other approach to overcome residual disease is immune therapeutic strategies. The demonstration of myeloma-specific alloimmunity from allogeneic transplantation is well established. More sophisticated and promising immune approaches include adoptive cellular therapies, tumor vaccines, and immune checkpoint manipulations. In the future, personalized minimal residual disease–driven treatment strategies following ASCT will help overcome the residual disease, restore multiple myeloma–specific immunity, and achieve sustained disease control while minimizing the risk of overtreatment.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1093-1093
Author(s):  
Gareth Gerrard ◽  
Wayne Mitchell ◽  
Anthony Goldstone ◽  
Raj Chopra ◽  
Georgina Buck ◽  
...  

Abstract Background: Minimal Residual Disease (MRD) monitoring in BCR-ABL+ acute lymphoblastic leukaemia (ALL) is a valuable tool in the management of Philadelphia positive adult ALL due to the markedly poor prognosis engendered by this leukemia subtype. As part of the UKALLXII trial we received samples from 104 de novo adult ALL patients, 26 of which (25%) were found to be BCR-ABL+. BM and PB received at presentation and during chemotherapy or post SCT were tested for MRD as part of a modified UKALLXII trial protocol which aimed at assessing the efficacy of combined chemotherapy and Imatinib treatment and SCT. Aims: 1) To establish which sample source offers the highest level of sensitivity; 2) To determine if differences in disease level is associated with the BCR-Abl rearrangement exhibited. Methods: BM and/or PB samples were received at presentation and at monthly follow-up points and were tested by quantitative real-time PCR (QRT-PCR) using a Roche LightCycler 1.3 with the SYBR-green fluorescent detection system. The BCR-ABL transcript levels were normalised as a ratio against Abl levels. Operating procedures were adapted from the recommendations of the European Study Group for MRD in ALL. Results: 138 samples (65 PB, 73 BM) were analysed from 26 BCR-ABL+ patients: 15M, 11F; median age 43y (range 17y to 58y). 17 (65%) were found to be minor and nine (35%) were major. Ten patients have received Imatinib and nine have undergone transplant (7 allo-SCT, 2 autograft). 2 patients have relapsed and 2 have died (1 following relapse). Paired t-tests between PB and BM sample BCR-Abl transcript levels show that BM offers a significantly higher level of sensitivity with a median BCR-ABL level of 2.93 x 10−4 against 1.8 x 10−4 for PB (p= 0.0056, n=46). Baseline ABL levels show the converse (1.49 x 104 BM against 1.77 x 104 PB, p= 0.016, n=46) suggesting that the generally greater quantity of material associated with PB samples may result in higher quality RNA. BCR-Abl levels between major and minor patients show that patients exhibiting the major form have significantly higher levels of disease in both PB (median 3.1 x 10−2 major (n= 24) against 3.3x10−4 in patients exhibiting minor BCR-Abl (n=41), (p< 0.0001) and BM samples (median 2.0 x 10−2 major (n= 28) against 3.3 x 10−4 minor (n=45), (p= 0.0009). Paired sequential analysis for 11 patients with 2 or more follow-up samples confirms this observation (median 3.5 x 10−2 major (n=4) against 3.5 x 10−4 minor (n=7), (p= 0.008). Conclusions: In the QRT-PCR MRD monitoring of adult ALL BM samples offer a small but significantly higher level of sensitivity than PB samples. Patients exhibiting the major BCR-ABL rearrangement have significantly higher levels of disease than patients with the minor form. These data describing differential disease status within the BCR-ABL+ subgroup and variance due to sample type may be important in providing guidelines for patient management.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2418-2418 ◽  
Author(s):  
M. E. Sarasquete ◽  
R. García-Sanz ◽  
A. Balanzategui ◽  
P. Martínez-Sánchez ◽  
J. Martínez-López ◽  
...  

Abstract Multiple myeloma (MM) remains as an incurable disease although new therapies can achieve a high rate of complete remissions (CR). Unfortunately, most patients ultimately relapse due to the persistence of minimal residual disease (MRD), and only a minority could be cured. Detection and quantification of these cells is an important tool for monitoring these patients and predicting a potential relapse. Here we analyze by RQ-PCR the MRD in MM patients achieving CR in order to classify them into different risk categories. MATERIAL AND METHODS: 38 MM patients uniformly treated according to the GEM-2000 (Spanish group for Myeloma) protocol, and that have achieved CR following PBSCT were included in the study. 22 were IgG, 9 IgA, 6 B-J and 1 non-secretory (κ/λ 21/16). 27 were male & 11 female with a median age of 58 (range 48–65). Bone marrow samples obtained at diagnosis and 3 months after transplant were analyzed. Complete (VDJH) and incomplete (DJH) Ig rearrangements were amplified with the Biomed-2 strategy (Leukemia2003;17:2257). PCR clonal products were sequenced on an ABI Prism 377 Sequence detector. VH, DH and JH segments were identified by comparing with germinal sequences on V-Base and BLAST databases. An ASO primer at the N-region was designed for each patient with the OLIGO 6.0 software. RQ-PCR was then performed on an ABI Prism 7700 using the ASO specific forward primer, a JH reverse intronic primer (JH1–6) and a TaqMan probe (JH1,2,4,5, JH3 or JH6) to amplify the patient specific rearrangement. Sample quality and quantity was controlled evaluating the standard curve of the albumin gene amplification. MRD was calculated according to ΔCT method. RESULTS: In 14 out of the cases included in the study, MRD investigation was not possible because the N-region was not longer enough to design the ASO primer (n=3), poor quality in the diagnostic sample to obtain the standard curve (n=8) or low plasma cell infiltration at diagnosis to obtain correct dilutions (n=3). The remaining 24 patients were classified into different risk groups according to the MRD level obtained 3 months after transplantation with a cut-off point of 0.01% tumor cells. Thus, progression free survival (PFS) was longer in those patients with MRD< 10−4 (p=0.03, figure 1A). By contrast, upon comparing the impact on PFS of immofixation (IFX) in these 24 patients that were in CR (defined by conventional electrophoresis criteria), it was observed that patients with IFX (−) didn’t showed a different outcome from those IFX (+) (figure 1B). CONCLUSION: In summary, although RQ-PCR is a labor and time-consuming technique, it is an useful tool for monitoring MRD in MM. The level of 10−4 can contribute to classify patients into 2 groups (high and low MRD) with different risk of relapse that can be used to design specific therapies.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4871-4871
Author(s):  
Roland Fenk ◽  
Mark Korthals ◽  
Guido Kobbe ◽  
Ulrich Steidl ◽  
Thorsten Graef ◽  
...  

Abstract Background: High-dose chemotherapy with autologous stem cell transplantation has improved outcome and survival of patients with multiple myeloma. However, the majority of patients suffer from relapse. Using real-time quantitative (RQ) PCR we have shown before (Haematologica 89,2004) that the amount of residual tumor cells in the bone marrow of patients before transplantation is of prognostic relevance. In this study we evaluated in a larger group of patients with multiple myeloma whether a pre-transplantation level of clonotypic cells in the bone marrow is predictive for time-to-progression (TTP) and overall survival (OS). Further, we compared results with known prognostic factors. Patients and Methods: Bone marrow samples of 19 patients with stage II/III multiple myeloma were obtained after induction therapy but before transplantation. Immunoglobulin heavy chain (IgH) RQ-PCR using patient-specific Taqman probes was performed to quantify pre-transplantation tumor levels. The proportion of clonotypic cells was assessed as IgH/2 beta-actin ratio in percent. Medical records of patients were reviewed for prognostic factors and outcome. Results: The median level of residual tumor cells in bone marrow of all patients at the time before transplantation was 0.3 %. At 23 month median follow-up after transplantation the median TTP and OS in our study were 14 and 36 month, respectively. The threshold level of 0.03% clonotypic cells identified two prognostic groups (p&lt;0.0001, log rank). Twelve patients in the bad prognostic group had an early relapse with a median TTP of 9 month (range: 3 – 17 month). All patients in the good prognostic group (n=7) had ongoing remissions after a median follow-up of 24 month (range: 13–44 month). Univariat analysis was performed including other prognostic factors at the time before transplantation such as cytogenetic abnormalities, beta2-microglobulin, hemoglobulin, platelet count, LDH, CRP, serum albumine and age. Besides the pre-transplant level of minimal residual disease, CRP level was predictive for TTP. In multivariat analysis using a step-wise cox regression model grouping by pre-transplantation tumor level was the only prognostic factor for TTP (p = 0.05). Moreover, low pre-transplantation tumor levels also showed a trend for a better OS, but in multivariat analysis only normal cytogenetics were predictive for a superior outcome (p = 0.03). Conclusion: Quantitative molecular assessment of pre-transplantation tumor level in the bone marrow is an independent prognostic parameter for the progression-free survival of patients with multiple myeloma and thus helps to guide therapeutic interventions


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