15 research outputs found
ALK-positive histiocytosis: a new clinicopathologic spectrum highlighting neurologic involvement and responses to ALK inhibition
ALK-positive histiocytosis is a rare subtype of histiocytic neoplasm first described in 2008 in three infants with multisystemic disease involving the liver and hematopoietic system. This entity has subsequently been documented in case reports and series to occupy a wider clinicopathologic spectrum with recurrent KIF5B-ALK fusions. The full clinicopathologic and molecular spectra of ALK-positive histiocytosis remain, however, poorly characterized. Here, we describe the largest study of ALK-positive histiocytosis to date, with detailed clinicopathologic data of 39 cases, including 37 cases with confirmed ALKrearrangements. The clinical spectrum comprised distinct clinical phenotypic groups: infants with multisystemic disease with liver and hematopoietic involvement, as originally described (Group 1A: 6/39), other patients with multisystemic disease (Group 1B: 10/39), and patients with single-system disease (Group 2: 23/39). Nineteen patients of the entire cohort (49%) had neurologic involvement (seven and twelve from Groups 1B and 2, respectively). Histology included classic xanthogranuloma features in almost one third of cases, whereas the majority displayed a more densely cellular, monomorphic appearance without lipidized histiocytes but sometimes more spindled or epithelioid morphology. Neoplastic histiocytes were positive for macrophage markers and often conferred strong expression of phosphorylated-ERK, confirming MAPK pathway activation. KIF5B-ALK fusions were detected in 27 patients, while CLTC-ALK, TPM3-ALK, TFG-ALK, EML4-ALK and DCTN1-ALK fusions were identified in single cases. Robust and durable responses were observed in 11/11 patients treated with ALK inhibition, ten with neurologic involvement. This study presents the existing clinicopathologic and molecular landscape of ALK-positive histiocytosis, and provides guidance for the clinical management of this emerging histiocytic entity.Molecular tumour pathology - and tumour genetic
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Next-Generation Sequencing-Based Assay Shows High Clonal Characterization Success Rate for Plasma Cell Neoplasms, and Concordance with Flow Cytometry in Minimal Residual Disease Detection
Abstract
Introduction
After therapy or stem cell transplantation, multiple myeloma patients achieving complete response (CR) or stringent complete response (sCR) can still have a significant risk of disease relapse, illustrating the importance of using highly sensitive methods for minimal residual disease (MRD) detection and prognostication. Two techniques used clinically for MRD detection include multiparametric flow cytometry (FC), which has a sensitivity down to 2-6 X 10-6 of cells, and next-generation sequencing (NGS)-based assay for detection of patient-specific clonal IGH VDJ gene sequences associated with the neoplastic plasma cells (PC). We determined the clonal characterization success rate of plasma cell neoplasm samples from a single institution in a clinical lab, using a commercially available NGS-based assay, Lymphotrack® (Invivoscribe, San Diego, CA). The characterized clonal sequences were used for MRD detection in subsequent monitoring samples, and the results were compared to concurrent FC findings.
Methods
DNA was extracted from fresh marrow or formalin-fixed paraffin-embedded (FFPE) tissue, and amplified by PCR reactions using primers sets for IGH Leader, FR1, FR2, FR3 regions, and IGK. Sequencing was performed on the Illumina MiSeqTM Platform, and sequence analyses were performed using the Lymphotrack® software, and MSK-Lymphoclone, a software developed at our institution. Disease-associated clonal sequences were characterized based on predefined clonal calling criteria and stored. In subsequent samples sent for disease monitoring, a search for sequencing reads with high homology (>99%) to the patient-specific sequences was performed for MRD detection. 10-color FC for PC analyses were also performed on the same samples at our institution (Roshal M, et al. Blood Adv 2017;1(12):728-32), with a target minimum of 3 million cells for MRD analyses.
Results
Overall, clonal characterization was successful in 235/251 cases (93.6%), with no difference in number of sequencing reads between the successful and unsuccessful cases (p=0.24). Higher success rate was observed among cases with higher aspirate PC counts: ≥5% (95.6% success rate) and ≥10% (98.1% success rate). IGH FR1 and Leader primers together characterized 214/251 cases (85.3%), while the remaining cases required additional primers. The characterized clones showed high median somatic hypermutation (SHM) rate of 8.1% (range: 0.0-29.0%), as well as IGH V and J segment usage bias: V3 (50.2%), followed by V4 (20.3%); J4 (43.4%), followed by J6 (27.5%), concordant with prior literature. 187 samples from 124 unique patients were tested by the Lymphotrack® assay for monitoring purposes, of which the diagnostic clones were detected in 147/187 samples (78.6%), with no difference in number of sequencing reads between cases with and without detectable clone (p=0.35). Within the short median time interval of 9.5 months between the characterization and monitoring samples, most clonal sequences remained stable. In 2 cases, new clonal sequences emerged in subsequent samples. Overall, FC and Lymphotrack® showed high concordance rate for MRD detection (92.9%) (See figures). All discordant cases showed <5% PC by aspirate differential counts and CD138 immunostains. FC+/NGS- cases (9/184, 4.9%) showed abnormal PC comprising a median of 0.00095% of WBC by FC, while FC-/NGS+ cases (4/184, 2.2%) showed detectable clone at a median of 0.0405% of sequencing reads. Sampling differences might have contributed to the discrepancies. Additionally, in the FC+/NGS- cases, neoplastic subclones might be present at very low level in the characterization samples, below threshold for clonal calling, and therefore could not be specifically tracked in subsequent samples.
Conclusions
Our study demonstrated high clonal characterization success rate for plasma cell neoplasms using the Lymphotrack® assay when multiple primers sets were used, and the assay showed concordance with FC in MRD detection for the majority of cases. MRD detection sensitivity can be limited by low sample concentration/volume. Furthermore, the presence of very low level neoplastic subclones in the characterization samples might hamper clonal calling and detection in subsequent samples.
Disclosures
Ho: Invivoscribe, Inc.: Honoraria. Landgren:Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy; Karyopharm: Consultancy. Arcila:Invivoscribe, Inc.: Consultancy, Honoraria
Successful treatment and integrated genomic analysis of an infant with FIP1L1-RARA fusion-associated myeloid neoplasm.
FIP1L1-RARA-a ssociated neoplasm is a very rare and aggressive disease, with only 3 previously reported cases in the literature. Here, we describe a 9-month-old boy who presented with a FIP1L1-RARA fusion-associated myelodysplastic/myeloproliferative neoplasm-like overlap syndrome, with similarities and distinct features to both acute promyelocytic leukemia and juvenile myelomonocytic leukemia. Using a combined approach of chemotherapy, differentiating agents, and allogeneic hematopoietic stem cell transplant (allo-HCT), this patient remains in remission 20 months after allo-HCT. To our knowledge, this is only the second published pediatric case involving this condition and the only case with a favorable long-term outcome. Given the aggressive disease described in the previously published case report, as well as the successful treatment course described, the combinatorial use of chemotherapy, differentiation therapy, and allo-HCT for treatment of FIP1L1-RARA fusion-associated myeloid neoplasms should be considered
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Plasma Cell Myeloma Residual Disease Quantitation Using a Next-Generation Sequencing-Based IGH Clonal Rearrangement Assay with the Aid of a "Spike-in" Clonal Sequence
Introduction: Next-generation sequencing (NGS)-based IGH clonal rearrangement assays can characterize and subsequently track disease-associated clonal sequences for lymphoid and plasma cell neoplasms, even at very low levels. As IGH PCR primers are used, the detected clonal sequences are usually reported as % of sequencing reads, roughly corresponding to % of B and plasma cells (PC) in samples, rather than % of total cellularity, hampering accurate disease burden assessment. In this study, we evaluated a method for calculating residual disease burden as % of total cellularity, with the aid of adding a known quantity of "spike-in" clonal sequence to the samples, and compared to concurrent 10-color flow cytometry (FC) quantitation of abnormal PC.
Methods: DNA was extracted from 40 plasma cell myeloma patient marrow biopsies sent for disease monitoring purposes at Memorial Sloan Kettering Cancer Center (MSKCC), with previously-characterized clonal sequences specific to the patients' myelomas. All samples had concurrent FC analyses and aspirate differential counts performed. 100 cell equivalent of DNA with a known clonal sequence (LymphoQuant®, LQ) was added to 700ng of patient DNA (~100,000 cell equivalent), and testing was performed using LymphotrackTM, a NGS-based assay. Following PCR amplification using IGH FR1 primers, sequencing was performed on the Illumina MiSeqTM instruments at the molecular laboratory of MSKCC. Reproducibility studies were conducted on a subset of samples at the laboratory of Invivoscribe, Inc. using identical methodology. LymphoTrack MRD data analysis tool (MRDDAT) v.1.0.3 was used to search for both the myeloma-specific and LQ clonal sequences. Disease as # of cell equivalent was calculated as: (% reads for myeloma clonal sequence/% reads for LQ) X 100 cells. Disease as % of total cellularity was calculated as: (# of cell equivalent/100,000 cells) X 100%.
Results: Disease as % of total cellularity calculated by LQ showed a median of 0.7576% cells (range: 0.000614% to 39.89%), compared to abnormal PC as % of total WBC by FC with a median of 0.355% cells (range: 0.00061% to 44.70%). Overall, a good correlation between disease quantitation by LQ and FC could be observed for cases with ≤10% total PC by aspirate count (r=0.79), while the correlation is lower for cases with >10% total PC (r=0.51). 12/40 samples were tested in two different laboratories, and showed excellent correlation in disease quantitation by LQ (r=0.94). As expected, detectable clonal sequences as % of sequencing reads (rather than as % of total cellularity) showed poor correlation with FC quantitation (r=0.32), due to variability of total B and plasma cell content in different samples.
Conclusions: Disease as % of total cellularity calculated with the aid of a known "spike-in" sequence in the NGS-based assay showed good correlation with the quantitation of abnormal PC by FC, when total PC was ≤10% by aspirate count. The correlation between the two declines when total PC was >10%. When patient samples contain a high number of B and/or plasma cells, the PCR amplification efficiency of the very small amount of the admixed "spike-in" clonal sequence may be hampered, affecting accurate quantitation. Furthermore, FR1 primers may not anneal optimally to some patients' clonal sequences due to somatic hypermutations in binding sites, underestimating the % of disease clone. Utilization of a second "spike-in" sequence and other primer sets (FR2, FR3) may improve disease % calculations in some cases.
Disclosures
Ho: Invivoscribe, Inc.: Honoraria. Roshal:Celgene: Other: Provision of Services; Auron Therapeutics: Equity Ownership, Other: Provision of services; Physicians' Education Resource: Other: Provision of services. Huang:Invivoscribe, Inc.: Employment. Hutt:Invivoscribe, Inc.: Employment. Miller:Invivoscribe, Inc.: Employment. Landgren:Theradex: Other: IDMC; Abbvie: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Merck: Other: IDMC; Adaptive: Honoraria, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Arcila:Invivoscribe, Inc.: Consultancy, Honoraria
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Germ cell tumors and associated hematologic malignancies evolve from a common shared precursor
Germ cell tumors (GCTs) are the most common cancer in men between the ages of 15 and 40. Although most patients are cured, those with disease arising in the mediastinum have distinctly poor outcomes. One in every 17 patients with primary mediastinal nonseminomatous GCTs develop an incurable hematologic malignancy and prior data intriguingly suggest a clonal relationship exists between hematologic malignancies and GCTs in these cases. To date, however, the precise clonal relationship between GCTs and the diverse additional somatic malignancies arising in such individuals have not been determined. Here, we traced the clonal evolution and characterized the genetic features of each neoplasm from a cohort of 15 patients with GCTs and associated hematologic malignancies. We discovered that GCTs and hematologic malignancies developing in such individuals evolved from a common shared precursor, nearly all of which harbored allelically imbalanced p53 and/or RAS pathway mutations. Hematologic malignancies arising in this setting genetically resembled mediastinal GCTs rather than de novo myeloid neoplasms. Our findings argue that this scenario represents a unique clinical syndrome, distinct from de novo GCTs or hematologic malignancies, initiated by an ancestral precursor that gives rise to the parallel evolution of GCTs and blood cancers in these patients
Assessing clonal haematopoiesis: clinical burdens and benefits of diagnosing myelodysplastic syndrome precursor states
Activating mutations in CSF1R and additional receptor tyrosine kinases in histiocytic neoplasms
Histiocytoses are clonal hematopoietic disorders frequently driven by mutations mapping to the BRAF and MEK1 and MEK2 kinases. Currently, however, the developmental origins of histiocytoses in patients are not well understood, and clinically meaningful therapeutic targets outside of BRAF and MEK are undefined. In this study, we uncovered activating mutations in CSF1R and rearrangements in RET and ALK that conferred dramatic responses to selective inhibition of RET (selpercatinib) and crizotinib, respectively, in patients with histiocytosis
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Non-Relapse Mortality in TP53 -Mutated MDS/AML - a Multi-Center Collaborative Study
Abstract
Background:
Patients with TP53 MUT MDS/AML experience poor clinical outcomes with high rates of disease recurrence and short overall survival (OS). Characterization of these individuals' post-HCT mortality is uniquely challenging due to competing risks from disease relapse and treatment toxicity. Transplant registries contain high-level outcomes data, however, there is a lack of detailed data in molecularly defined subsets of diease. This analysis was undertaken to bridge this gap.
Methods:
Allogeneic HCT recipients between 1/2014 and 12/2018 were retrospectively studied. Key inclusion criteria were TP53 MUT by NGS or deletion of chromosome 17/17p by FISH/cytogenetics. The primary outcome of non-relapse mortality (NRM) was defined as death from any cause other than disease with relapse as competing risk. Secondary outcomes for this analysis were OS, cumulative incidence of relapse (CIR), and relapse free survival (RFS). Relapse was defined as relapse/progression with NRM as competing risk.
Results:
384 TP53 MUT MDS/AML patients were analyzed. 55% of patients were transplanted for AML, 41% received myeloablative conditioning (MAC), 39% had secondary MDS/AML, and 26% received prior chemo and/or radiation therapy (XRT). Median time from HCT to last follow-up was 321 days (range 8-2,385 days). Mutational data was available in 264 patients and cytogenetic data was available in 368 patients; 78% of patients had a complex karyotype (CK), 82% had TP53 missense mutations, and 74% had bi-allelic targeting of the TP53 gene. The incidence of all-grade acute and chronic GVHD (cGVHD) was 52% and 31%, respectively. One and 2 year OS was 48.5% and 30.9%, respectively. Estimated CIR at 1 and 2 years was 49% and 54.9%, respectively. The 1 year NRM was 13.7% and 2 year NRM was 18.1%.
In multivariate analysis (MVA), there was no association between NRM and the clinical, molecular, or genetic features of TP53 MUT MDS/AML. HCT diagnosis of MDS (HR: 0.67, 95% CI: 0.46-0.97, p: 0.036), mono-allelic TP53 MUT (HR: 0.6, 95% CI: 0.39-0.94, p: 0.023), achievement of full donor PB chimerism (HR: 0.33, 95% CI: 0.14-0.85, p: 0.022), BM chimerism (HR: 0.33, 95% CI: 0.18-0.60, p: 0.003), and cGVHD (HR: 0.35, 95% CI: 0.23-0.51, p: <0.001) correlated with lower rates of relapse while CK predicted for increased relapse (HR: 2.5, 95% CI: 1.49-4.19, p: 0.001). Inferior OS was associated with CK (HR: 1.84, 95% CI: 1.19-2.85, p: 0.006) and history of prior chemo/XRT (HR: 1.84, 95% CI: 1.01-1.93, p: 0.006) whereas high KPS (HR: 0.98, 95% CI: 0.97-1, p: 0.046), mono-allelic TP53 mutations (HR: 0.52, HR: 0.36-0.77, p: 0.001), full donor PB chimerism (HR: 0.36, 95% CI: 0.19-0.68, p: 0.002), BM chimerism (HR: 0.3, 95% CI: 0.19-0.49, p: <0.001), and cGVHD (HR: 0.36, 95% CI: 0.18-0.36, p: <0.001) were associated with improved OS.
In subgroup analysis, history of chemo and/or XRT increased NRM in AML (HR: 4.24, 95% CI: 1.35-13.39, p: 0.014). Pre-HCT TP53 MUT persistence by NGS (HR: 3.59, 95% CI: 1.43-9, p: 0.007) predicted for post-HCT relapse whereas pre-HCT CR (HR: 2.93, 95% CI: 1.54-5.59, p: 0.001) and full donor BM chimerism (HR: 0.14, 95% CI: 0.05-0.38, p: <0.001) were associated with lower rates of relapse. High KPS (HR: 0.96, 95% CI: 0.98-0.99, p: 0.021) and cGVHD (HR: 0.3, 95% CI: 0.16-0.56, p: <0.001) corresponded with improved OS. Prior chemo/XRT was associated with shorter OS (HR: 2.11, 95% CI: 1.06-4.18, p: 0.033)
No significant NRM associations were identified in MDS. CK (HR: 5.04, 95% CI: 1.95-13.01, p: <0.001) and RIC/NMA conditioning intensity (HR: 2.54, 95% CI: 1.26-5.1, p: 0.009) increased risk of post-HCT relapse while full donor BM chimerism (HR: 0.15 95% CI: 0.08-0.31, p: <0.001), full donor PB chimerism (HR: 0.17, 95% CI: 0.17, p: <0.001), and cGVHD (HR: 0.17, 95% CI: 0.07-0.42, p:<0.001) reduced this risk. OS was improved with mono-allelic mutations (HR: 0.54, 95% CI: 0.32-0.96, p: 0.034), full donor BM (HR: 0.24, 95% CI: 0.12-0.71, p: <0.001), PB (HR: 0.29, 95% CI: 0.09-0.3, p: 0.007) chimerism, and cGVHD (HR: 0.16, 95% CI: 0.09-0.3, p: <0.001).
Conclusions:
From this large multi-institutional cohort of TP53 MUT myeloid neoplasms, we report a low NRM rate, likely due to high rates of post-HCT relapse/progression. These data demonstrate associations between bi-allelic TP53m/CK and post-HCT outcomes. Our work highlights the importance donor chimerism after HCT and provides new understanding of the importance of chronic GVHD in TP53 MUT MDS/AML.
Figure 1 Figure 1.
Disclosures
Byrne: Karyopharm: Research Funding. Logan: Amgen, Pfizer, AbbVie: Consultancy; Pharmacyclics, Astellas, Jazz, Kite, Kadmon, Autolus, Amphivena: Research Funding. Lee: CareDx: Membership on an entity's Board of Directors or advisory committees; Kadmon: Membership on an entity's Board of Directors or advisory committees; Kite: Membership on an entity's Board of Directors or advisory committees; Fresensius Kabi: Consultancy; Jazz,: Consultancy; Incyte: Research Funding. Goodman: Seattle Genetics: Consultancy, Speakers Bureau; EUSA Pharma: Consultancy, Honoraria. Gill: Interius Biotherapeutics: Current holder of stock options in a privately-held company, Research Funding; Novartis: Other: licensed intellectual property, Research Funding; Carisma Therapeutics: Current holder of stock options in a privately-held company, Research Funding. Jimenez: Takeda: Research Funding; AbbVie: Research Funding. Metheny: Pharmacosmos: Honoraria; Incyte: Speakers Bureau. Bhatnagar: Pfizer: Honoraria; Celgene: Honoraria; Novartis: Honoraria; Astellas: Honoraria; Cell Therapeutics: Honoraria, Research Funding; Kite: Honoraria; Karyopharm: Honoraria, Research Funding; Sumitomo Dainippon Pharma: Research Funding. Hamilton: Syndax: Membership on an entity's Board of Directors or advisory committees; Equilium: Membership on an entity's Board of Directors or advisory committees. Mishra: Novartis: Research Funding. Savona: BMS-Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; CTI: Consultancy, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy, Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Geron: Consultancy, Membership on an entity's Board of Directors or advisory committees; NOVARTIS: Consultancy, Membership on an entity's Board of Directors or advisory committees; Ryvu: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sierra Oncology: Consultancy, Membership on an entity's Board of Directors or advisory committees; Taiho: Consultancy, Membership on an entity's Board of Directors or advisory committees; TG Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; ALX Oncology: Research Funding; Astex: Research Funding; Incyte: Research Funding