Complex Clonal Evolution Research Articles

MPN-123 Complex Clonal Evolution in a Patient with Advanced Myelofibrosis Exhibiting Bone Marrow Hypercellularity and Chromosomal Anomalies

MPN-123 Complex Clonal Evolution in a Patient with Advanced Myelofibrosis Exhibiting Bone Marrow Hypercellularity and Chromosomal Anomalies

Single Cell Multi-Omic Correlation of Single Nucleotide Variants, Copy Number Variation and Surface Epitopes for Clonal Profiling of Myeloma

Introduction Multiple myeloma (MM) is a cancer of plasma cells with approximately 200,000 new diagnoses each year and a 54% 5-year overall survival rate. As myeloma cells expand, clonal genetic differences lead to relapse due to acquired resistance in 100% of patients, mandating regular, long-term surveillance. Improvements in precision medicine for MM have come from monoclonal antibodies and antibody-drug conjugates that specifically target the offending cells. However, while existing diagnostic modalities offer exquisite sensitivity, they are unable to correlate subclonal genetic changes and putative antibody targets on refractory myeloma cells, leaving the clinician to use their best judgment on salvage therapy which can lead to unnecessary expense and toxicity to patients due to ineffective treatment. Specifically knowing actual targets on refractory MM cells would better facilitate precision medicine and potentially improve outcomes. Methods Cryopreserved, human MM patient samples were processed on the Mission Bio Tapestri platform, enabling simultaneous single cell quantification of subclones by single nucleotide variants (SNV), copy number variants (CNV), and surface protein analysis. These single time point samples were thawed from frozen bone marrow mononuclear cells previously enriched for CD38, stained with a 45-plex antibody-oligo cocktail to label common heme-specific surface markers for sequencing analysis, and processed with a 733-plex DNA primer panel that combined whole-genome CNV coverage with MM gene hotspots. Sequencing was performed on an Illumina system with the raw data being analyzed using Mission Bio proprietary algorithms. Results We show complex clonal evolution of MM in individual samples as copy gains and losses that were sequentially acquired and correlated with expression changes of MM markers. Across the cases analyzed, complex branching phylogenetic trees were reconstructed with as many as five subclones and clear associated shifts in MM-marker expression. When averaged across subclones, each sample had CNV profiles that matched patient bulk genome-wide array records, ranging from a single gene-level copy gain to arm-level gains and losses across the majority. The progression of protein expression within different samples could be mapped together on a single plot and correlated with generally higher MM-markers as subclonal genetic variants were acquired, though occasional branches saw reversal. The fraction of other cell phenotypes, such as T-cells and those with low viability, decreased within subclones as mutational burden grew. Conclusion This high-resolution, single cell assay offers a potential new modality for the diagnosis and surveillance of patients with suspected MGUS, SGUS or high-risk MM. We have demonstrated: 1) exceptional results from cryopreserved human specimens, 2) the ability to use genetic lesion profiling to positively identify subclonal MM and, most importantly, 3) correlate cell surface protein expression of potential therapeutic targets with each clonal and subclonal population

B-lymphoblastic leukemia/lymphoma with MYC and BCL2 gene rearrangements shows evidence for clonal evolution and mitotic recombination

BackgroundB-lymphoblastic leukemia/lymphomas (B-ALL/LBL) are uncommon neoplasms that may be associated with a variety of cytogenetic and molecular changes. The mechanisms by which these changes arise have not been fully described.Aims/PurposeThis report describes an unusual case of B-ALL/LBL with complex clonal evolution that includes BCL2 and MYC gene rearrangements.MethodsImmunophenotyping was performed by immunohistochemistry and flow cytometry. Traditional G-band karyotyping was accompanied by fluorescence in-situ hybridization (FISH) using break-apart and dual fusion probes. Single nucleotide polymorphisms were assessed using a high-density DNA microarray.ResultsThe karyotype of the blasts showed reciprocal translocation of chromosomes 4 and 18, reciprocal translocation of chromosomes 8 and 14 with two copies of the oncogenic translocation derivative(14)t(8;14), and no normal chromosome 14. FISH studies showed complex IGH-BCL2 and IGH-MYC fusion signals.ConclusionsA clonal evolution model involving multiple chromosomal translocations and mitotic recombination is postulated to account for the karyotype, FISH, and microarray results but leaves unresolved the exact order of the evolutionary changes.

Molecular characteristics of multifocal esophageal squamous cell carcinomas to discriminate multicentric origin from intramural metastasis.

Multifocal esophageal squamous cell carcinomas (ESCCs) can be diagnosed as of multicentric origin (MO) or intramural metastasis (IMM). We aimed here to accurately discriminate MO from IMM and explore the tumor immune microenvironment of multifocal ESCCs. Multifocal ESCCs were identified in 333 ESCC patients, and in 145 patients discrimination between MO and IMM was not possible by histopathological examination. Of the 145 patients, tissues of 14 were analyzed by whole-exome sequencing (WES) of 71 different tumor regions, and MO, IMM, and MO/IMM mixed groups were identified in three, ten, and one cases, respectively, based on the similarity of genomic architecture between or among different tumors from one patient. Further phylogenetic analyses revealed complex clonal evolution patterns in IMM cases, and tumor cells disseminated from the primary tumors to IMM tumors were independent of lymph node metastasis. The NanoString-based assay showed that immune cell infiltrates were significantly enriched, and that the immune and proliferation pathways were more activated, in large tumors than in small ones in MO but not IMM cases. Similarly, PD-L1 expression and the density of paratumoral CD8+ T cells were higher in large tumors than in small tumors in MO. Taken together, through analysis of the genomic and immune landscapes, our study has comprehensively characterized the heterogeneity and clonal relationship of multifocal ESCCs, which may be helpful in distinguishing MO from IMM, and for interpreting the immunotherapy responses for multifocal ESCC patients. © 2022 The Pathological Society of Great Britain and Ireland.

Abstract A009: Longitudinal monitoring of pediatric acute myeloid leukemia using duplex sequencing of patient-specific panels reveals ultra-low frequency MRD that marks persistent carcinogenesis and complex clonal evolution

Abstract Rationale: Accurate and sensitive detection of measurable residual disease (MRD) is critical for clinical management and the development of new therapies for pediatric acute myeloid leukemia (AML). The presence of MRD is a well-established predictor of disease relapse and mortality. Ideally, MRD detection would be both broadly applicable across patients and highly specific, thus enabling clinicians to make timely treatment decisions to improve outcomes. Background: In pediatric AML, unlike adult AML, there are few cross-patient recurrent somatic driver mutations. This makes it impractical to use a fixed gene panel for MRD monitoring. One solution is to perform disease tracking with patient-specific mutations that are present in individual AMLs at time of diagnosis (TOD). However, following modern therapies, should residual disease remain, the telltale mutations will be present in only a very small subpopulation of cells–far below the ~1% limit-of-detection of conventional NGS methods. Duplex sequencing (DS) is an ultra-accurate NGS error-correction method which increases the accuracy of base calls by more than 10,000-fold. Here we demonstrate the use of tumor-informed DS to detect patient-specific MRD in pediatric AML samples with unprecedented sensitivity and specificity. Methods: Marrow aspirates were collected from 13 pediatric AML patients at TOD, during treatment, remission, and at relapse. Among the cohort, 9/13 patients ultimately relapsed. Personalized hybrid capture panels were designed to target hundreds of somatic mutations that were present in each patient’s TOD sample, as identified by whole genome sequencing of tumor-normal pairs. DS was used for longitudinal monitoring of these mutations in blood or marrow at up to 5 time points following initial induction. Results: We detected MRD in one or more samples from all 9 patients who went on to relapse. However, we also observed high-confidence TOD variants in the last collected sample from all 5 patients who did not relapse during at least 24 months of clinical follow-up. As a technical control, we tested a subset of patient panels on a blood sample from a healthy subject and found no disease-specific mutations. Interestingly, we observed a marked degree of heterogeneity of response-to-therapy in the cohort. In some cases, all mutations logarithmically decreased uniformly, whereas in others there was clear dispersion of subclones over time, with some declining 100-times more quickly than others. Conclusions: While DS in conjunction with personalized panels represents a powerful approach for MRD tracking, simply the existence of very low frequency TOD mutations in pediatric AML is not specific enough for predicting relapse without additional interpretation. Lingering mutations in non-relapsers might represent preneoplastic field defects, pre-existing somatic mosaicism, or perhaps even true residual disease under immune suppression. Our study highlights an unappreciated degree of complexity that arises when using ultra-accurate mutation detection for cancer monitoring. Citation Format: Thomas H. Smith, Jake E. Higgins, Fang Y. Lo, Michael J. Hipp, Charles C. Valentine, Amanda R. Leonti, Rhonda E. Ries, Soheil Meshinchi, Benjamin J. Huang, Jesse J. Salk. Longitudinal monitoring of pediatric acute myeloid leukemia using duplex sequencing of patient-specific panels reveals ultra-low frequency MRD that marks persistent carcinogenesis and complex clonal evolution [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A009.

Synergistic cytotoxicity of dual PI3K/mTOR and FLT3 inhibition in FLT3-ITD AML cells.

Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy, characterized by a heterogeneous genetic landscape and complex clonal evolution, with poor outcomes. Mutation at the internal tandem duplication of FLT3 (FLT3-ITD) is one of the most common somatic alterations in AML, associated with high relapse rates and poor survival due to the constitutive activation of the FLT3 receptor tyrosine kinase and its downstream effectors, such as PI3K signaling. Thus, aberrantly activated FLT3-kinase is regarded as an attractive target for therapy for this AML subtype, and a number of small molecule inhibitors of this kinase have been identified, some of which are approved for clinical practice. Nevertheless, acquired resistance to these molecules is often observed, leading to severe clinical outcomes. Therapeutic strategies to tackle resistance include combining FLT3 inhibitors with other antileukemic agents. Here, we report on the preclinical activity of the combination of the FLT3 inhibitor quizartinib with the dual PI3K/mTOR inhibitor PF-04691502 in FLT3-ITD cells. Briefly, we show that the association of these two molecules displays synergistic cytotoxicity in vitro in FLT3-ITD AML cells, triggering 90% cell death at nanomolar concentrations after 48h.

Complex Clonal Evolution Can Occur Following Transplantation for Transfusion Dependent Thalassaemia in the Context of Mixed Myeloid Chimerism and Reduced Conditioning Regimens

Haemopoietic stem cell transplantation (HSCT) is a well-established treatment modality for the cure of transfusion dependent thalassaemia (TDT) and sickle cell disease (SCD). Clonal evolution has recently been identified as a concerning event in the setting of mixed chimerism and/or ineffective haemopoiesis following conventional bone marrow transplantation and gene therapy for haemoglobinopathies. This has so far been restricted to SCD only, with the presumption that despite both conditions sharing an ineffective erythropoietic marrow compartment, there may be inflammatory and hypoxic differences enabling clonal evolution, in addition to the different exposure to hydroxycarbamide as a therapeutic agent. However, there is a need to investigate whether this may also be an occurrence in TDT.From 2011 to 2021, over a ten-year period, sixty-five consecutive paediatric patients received a sibling HSCT (n=55) or a haploidentical HSCT (n=10) for TDT in our institution. Conditioning intensity was minimised at the start of this cohort in order to limit toxicity and late effects, abandoning the use of Bu/Cy, which resulted in approximately 50% of the patients having stable mixed chimerism long-term. Sibling HSCT was conditioned with fludarabine 160 mg/m 2, treosulfan 42 g/m 2, thiotepa 10 mg/kg and ATG (Thymoglobulin) or alemtuzumab, and received GvHD prophylaxis with ciclosporin and MMF. Haploidentical HSCT was conditioned with fludarabine 150 mg/m 2, cyclophosphamide 30 mg/kg, TBI 2 or 4 Gy, and ATG 4.5 mg/kg (thiotepa 10 mg/kg added if TBI 2 Gy only) with GvHD prophylaxis provided by two doses of post-transplantation cyclophosphamide 50 mg/kg, sirolimus and MMF. All patients had pre-transplantation endogenous haemopoiesis was suppressed pre-transplantation with hypertransfusions for a minimum of 8 weeks, and/or the use of hydroxycarbamide and azathioprine. GvHD prophylaxis was provided with ciclosporin and MMF. All patients were Pesaro class I or II at the time of transplantation. The median age was 5 years (2 - 19). The median survival was 26.8 months (2.6-101.8). The OS was 93.8% and DFS was 89.2%.Three patients in this cohort developed clonal evolution in the context of myeloid mixed chimerism identified due to the development of cytopenias and transfusion dependence. All patients had a complex karyotype and it involved deletion of chromosome 7: •Patient 1 had a sibling BMT at 3 years and 2 months. Day +28 chimerism was >95% in whole blood and 95% in T cells. The myeloid fraction had a progressive reduction from day +60 onwards. At 15 months post-transplantation clonal evolution was identified [18% ring sideroblasts, 46;XY, del (7) (q22 q34) [5]/46;XY [5], chimerism 13% donor in whole marrow and 41% marrow T cells. Two months later he became red cell transfusion dependence. A second BMT with busulfan based conditioning resulted in long-term cure.•Patient 2 had a sibling BMT at 3 years and 8 months of age. Day +28 chimerism was 99% donor in whole blood and 99% donor in T cells. Day +161 post-transplantation he started requiring erythropoietin support to maintain him transfusion independent and on day +217 we first identified in the bone marrow the appearance of myeloid mixed chimerism (75% donor in whole marrow and 91% marrow T cells) and complex clonal evolution involving -7 and FISH identified deletion of one copy of KMT2E (7q22) and MET (7q31) detected [16/200]. The patient is under monitoring at present with a progressive reduction of the size of the abnormal clones.•Patient 3 had a haplo BMT at 5 years and 8 months. Day +28 chimerism was 97% donor in whole blood and 99% donor in T cells. She developed mixed myeloid chimerism following cessation of immunosuppression on day +206: 86% donor whole blood and 99% donor in T cells. At 22 months post-BMT she started to require transfusion and a complex clonal evolution involving deletion 7 in her bone marrow when the chimerism was 42% donor whole blood and 81% donor marrow T cells. FISH identified deletion of one copy of KMT2E(7q22) and MET(7q31) detected[22/100]. She is being prepared for a second bone marrow transplant.In conclusion, complex clonal evolution also occurs post HSCT in TDT, at least in the context of reduction of conditioning intensity and development of mixed myeloid chimerism. This finding warrants further investigation and may have significant implications for the design of both conventional HSCT and gene therapy strategies. DisclosuresNo relevant conflicts of interest to declare.

Single-Cell Transcriptomics for Residual Disease Detection in Acute Myelogenous Leukemia Post Allogeneic Hematopoietic Cell Transplantation

Detection of residual disease is a critical component of modern, risk-adapted therapy for Acute Myeloid Leukemia (AML). However, the genetic and phenotypic diversity of AML has made the development of a universal assay for disease assessment particularly challenging. While purely mutation-based tests promise high sensitivity, they are not broadly applicable given molecular heterogeneity and complex clonal evolution. Single-cell approaches, such as multiparameter flow cytometry (MFC), are more broadly applicable and increasingly accepted as the standard in clinical care. However, the limited number of leukemia-specific cell-surface markers and high numbers of shared markers between malignant myeloid blasts and healthy progenitors make MFC data extremely challenging to interpret. Motivated to develop a broadly applicable assay that can provide a more confident assessment of residual disease, we developed a platform using droplet-partitioned single-cell RNA sequencing accompanied by a computational pipeline specifically tailored to quantify residual disease after allogeneic HCT (alloHCT).With bone marrow samples from an 11-year-old patient with suspected post-alloHCT relapse of AML, we interrogated three methods of sample processing, 1) RBC lysis, 2) Ficoll-centrifugation, and 3) Ficoll-centrifugation combined with CD34+ immunomagnetic selection. The samples were further split to separately capture the 3' or 5' end of polyadenylated transcripts. The six resulting libraries were sequenced using standard short-read sequencing, and reads were demultiplexed and counted using common workflows. Data from the samples were combined, and sub-populations were visualized using UMAP (see Figure).This study demonstrated the feasibility of real-time single-cell sequencing for clinical utility. It is possible to process, capture, and sequence a patient's sample in approximately three working days (A). By integrating our data with single-cell expression profiles from an atlas of healthy human bone marrow, we were able to identify cells with gene-expression programs distinct from those of normal hematopoietic cells (B). With these integrated data, we could clearly identify populations of cells that embed away from healthy atlas cells (yellow circle, B), defining a different than normal single-cell profile. This “malignant” profile also included several genes whose expression is usually restricted to healthy hematopoietic progenitors (Panel C), suggesting these cells had a severely dysregulated transcriptome. As this patient was post-alloHCT, we interrogated the abundance of single-nucleotide-polymorphisms (SNPs) in the sequence data. We quantified these SNPs in single cells to distinguish each cell as either of donor or recipient origin using a method we have previously validated for genotyping RNA sequence in single cells. We clearly demonstrate that those cells identified as “different than normal” have a distinct SNP profile suggesting they are of recipient origin. Further analysis revealed that this malignant population was highly enriched for a population of cells expressing a previously described set of “AML-restricted genes” (Huang, B. et al., ASH 2021). (Panel E). Finally, from the Ficoll-processed sample, we quantified a level of 9.8% residual disease (243 malignant cells from a total of 2487). Notably, the number of abnormal myeloid progenitors determined by MFC was 2.0% which increased to 13% on a subsequent marrow sample drawn one week later. Incidentally, we observed only minimal differences across the two single-cell sequencing chemistries (3' vs. 5').Taken together, our data strongly argue that droplet-based, single-cell RNA sequencing is a feasible and powerful tool for the ascertainment of residual disease in AML. Given the robust nature of the platform and the ability to incorporate SNP integration into the analytic pipeline, it allows confident detection of residual disease in the post-alloHCT setting. By combining genomic quantification of transcripts with the power of SNP-based genotyping all at the level of the single cells, we believe this technology can substantially improve our diagnosis of post-alloHCT AML relapse. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Single-Cell Multi-Omics Reveals the Genetic, Cellular and Molecular Landscape of TP53 Mutated Leukemic Transformation in MPN

Single-Cell Multi-Omics Reveals the Genetic, Cellular and Molecular Landscape of TP53 Mutated Leukemic Transformation in MPN

Features of 18F-fluorodeoxyglucose uptake in multiple myeloma

Background. Multiple myeloma (MM) is a kind of malignancy from malignant plasma cells with high intra- and interpatient variability, because of complex clonal evolution of tumor cells. Positron emission tomography combined with computed tomography with 18F-fluorodeoxyglucose (18F-FDG-PET/CT) plays a major role in MM visualization, but there are evidences of non-FDG-avid cases of MM. Taking into account the increasing role of 18F-FDG-PET/CT in MM, special criteria for risk-group stratification was elaborated. These criteria are based on comparison of radiotracer uptake in tumor tissue, mediastinal blood pool and liver.Objective: the study of 18F-FDG uptake in MM and solitary plasmacytoma before antitumor treatment to assess the applicability of criteria based on the ratio of activity in tumor tissue and liver.Materials and methods. We reviewed 65 18F-FDG-PET/CT scans of patients with MM and solitary plasmacytoma before treatment.Results. In our cohort we identified 2 tumor cases of a plasma cell nature, which amounted to 2 % among all B-NHLs. In one case, the process was located in the nasal cavity and clinically manifested itself with nosebleeds. The second case is a lesion of the mouth floor, primarily with the ulcer formation. In the first cases, at diagnosis, the immunohistochemistry (IHC) test was performed after patient’s chemotherapy and radiation treatment, which distorted the tumor immunophenotype. In the second cases with extensive process in maxillary sinuses, a complete and very detailed IHC test was carried out; however the data did not allow for a definitive diagnosis. Difficulties apparently arose in the interpretation of CD38 expression – main marker of plasmacytic line cells, as well as due to the unusual morphology.Conclusion. Therefore, 5-point scale is eligible for MM tumor assessment in 52 % of patients and feasible in 32 % of patients, but in 16 % patients alternative criteria are required.

Genomic and Transcriptomic Characterization of Relapsed SCLC Through Rapid Research Autopsy

IntroductionRelapsed SCLC is characterized by therapeutic resistance and high mortality rate. Despite decades of research, mechanisms responsible for therapeutic resistance have remained elusive owing to limited tissues available for molecular studies. Thus, an unmet need remains for molecular characterization of relapsed SCLC to facilitate development of effective therapies. MethodsWe performed whole-exome and transcriptome sequencing of metastatic tumor samples procured from research autopsies of five patients with relapsed SCLC. We implemented bioinformatics tools to infer subclonal phylogeny and identify recurrent genomic alterations. We implemented immune cell signature and single-sample gene set enrichment analyses on tumor and normal transcriptome data from autopsy and additional primary and relapsed SCLC data sets. Furthermore, we evaluated T cell-inflamed gene expression profiles in neuroendocrine (ASCL1, NEUROD1) and non-neuroendocrine (YAP1, POU2F3) SCLC subtypes. ResultsExome sequencing revealed clonal heterogeneity (intertumor and intratumor) arising from branched evolution and identified resistance-associated truncal and subclonal alterations in relapsed SCLC. Transcriptome analyses further revealed a noninflamed phenotype in neuroendocrine SCLC subtypes (ASCL1, NEUROD1) associated with decreased expression of genes involved in adaptive antitumor immunity whereas non-neuroendocrine subtypes (YAP1, POU2F3) revealed a more inflamed phenotype. ConclusionsOur results reveal substantial tumor heterogeneity and complex clonal evolution in relapsed SCLC. Furthermore, we report that neuroendocrine SCLC subtypes are immunologically cold, thus explaining decreased responsiveness to immune checkpoint blockade. These results suggest that the mechanisms of innate and acquired therapeutic resistances are subtype-specific in SCLC and highlight the need for continued investigation to bolster therapy selection and development for this cancer.

3033 – SINGLE-CELL MULTI-OMIC ANALYSIS UNRAVELS GENETIC AND MOLECULAR HETEROGENEITY IN TRANSFORMED MYELOPROLIFERATIVE NEOPLASMS

One out of five patients with myeloproliferative neoplasms (MPN) will progress to an aggressive and largely untreatable form of Acute Myeloid Leukaemia (post-MPN secondary AML, or sAML). Transformation is associated with acquisition of TP53 missense mutations in approximately 50% of cases, and markedly increased genetic and molecular heterogeneity. This makes it challenging to effectively eliminate all subpopulations of tumour cells, and likely underlies the mostly universal treatment failure in sAML. Characterizing the complex genetic and cellular hierarchies associated with TP53 transformation is crucial for the development of effective targeted therapies. To resolve these multiple layers of intratumoral heterogeneity, we recently developed TARGET-seq (Rodriguez-Meira et al, 2019), a single-cell multi-omic method that correlates genetic, transcriptional and cell-surface proteomic readouts from the same single cell with extremely high resolution. TARGET-seq analysis of over 7000 Lineage-CD34+ cells (indexed for CD38/90/45RA/123) from TP53-mutant sAML patients revealed striking patterns of clonal evolution in different immunophenotypically defined stem/progenitor cell types, and identified preleukemic and leukemic subclones with markedly distinct molecular signatures. Acquisition of TP53 mutations was invariably associated with highly complex clonal evolution, enrichment of cell-cycle associated transcription and downregulation of key stem cell regulators. Interestingly, preleukemic subclones from patients undergoing transformation were highly enriched in WNT-beta catenin signaling and depleted in DNA-repair genes, as compared to non-transformed MPN patients. This suggests that preleukemic clones could be primed for disease transformation, and could potentially be targeted to prevent disease progression. Ultimately, single-cell multi-omic analysis identified key molecular regulators of TP53 mediated transformation, providing unique insights into the evolution of these tumors and how they might be therapeutically targeted.

Clonal evolution of esophageal squamous cell carcinoma from normal mucosa to primary tumor and metastases.

The clonal evolution which drives esophageal squamous cell carcinoma (ESCC) from initiation in normal cell to primary carcinoma and metastases is poorly understood. In this study, multi-region whole-exome sequencing (WES) (284X) and whole-genome single nucleotide polymorphism genotyping were performed on a total of 109 samples of ESCC from 10 patients. This included 42 apparently normal samples of esophageal mucosa at increasing distances from the upper or lower boundaries of the primary tumor to the surgical margins of resection, 43 spatially separated tissue samples within primary tumor and 24 regional lymph node metastases. Phylogenetic analysis was performed to reconstruct ancestor-descendant relationships of clones and the clonal composition of multi-region samples. Mutations of cancer-related genes were validated by deep targeted sequencing (1,168X). Both inter- and intra-tumoral genetic heterogeneity were obvious across multi-region samples among ESCC patients. Clones varying in number from one to seven were discovered within each regional tumor or metastatic sample. Phylogenetic analysis demonstrated complex clonal evolution patterns. Regional lymph node metastases had characteristics of early initiation and polyclonal spreading, and could be derived from carcinoma in situ (CIS) directly. TP53 was the only gene harboring non-silent mutations identified across all multi-region tumor samples of all ten patients. Mutations of TP53 were also found in histologically normal mucosa in sites away from primary tumor.

Specific clonal expansion at disease progression (PD) in solid cancers pinpointed by cell free DNA analysis.

e13144 Background: More than 50% of solid cancers sooner or later escape control of standard treatments. Detection and analysis of cell free circulating DNA (cfDNA) now offer the possibility to detect key mutations of cancer driver genes which may play a major role in the therapy escaping mechanism. We sought to identify clones of solid tumors escaping standard treatments in order to assess personalized treatment at PD. Methods: A cohort of patients with 10 different solid tumors progressing after standard therapy were selected. CfDNA analysis was performed using PAXgene blood ccfDNA tubes (QIAGEN), MagMAX cell-free total nucleic acid isolation kit, and ION PROTON platform (ThermoFisher Scientific). Results: Next generation sequencing analysis of 52 cancer-driver genes of cfDNA samples of 39 patients allowed for picking up clones plausibly involved in the PD mechanism in 60% of cases. A mean of 1.3 mutated genes (range 1-3) for each tumor was found. Point mutations in TP53, PIK3CA, and CNV in FGFR3 were the most commonly observed, with a rate of 41%, 16%, and 13%, respectively. Increased copy number variations of FGF receptors were identified in patients with non-small cell lung, pancreatic, and gastric cancer, and cholangiocarcinoma. Other clones had mutations in ESR1 (breast), CTNNB1 (uterus), KRAS and CCND2 (pancreas), EGFR and BRAF (lung). Interestingly, retinoblastomas resistant to Melphalan showed expanding mutated clones in PTEN or SMAD4. Increased levels of cfDNA were observed in the plasma of all patients. Conclusions: The results presented here show that irrespective of the primary tumor mutational burden and subsequent complex clonal evolution, a simplified mutational load is present at PD. One or few “sniper” clones drive progression and the molecular profile has a weak correlation with the primary tumor. Single driver mutations in TP53 remain the main target of a not yet developed specific therapy in most tumors such as breast, ovarian, uterine, lung, gastric cancers and glioblastoma. Among the actionable mutations, PIK3CA were found, not only in breast cancers, but also in uterine carcinoma, Sezary syndrome and glioblastoma, pinpointing the needs of specific trials in these tumors.

Plasma cell-free DNA chromosomal instability score as early predictor to monitor tumor burden in response to therapeutic in multiple myeloma patients.

8036 Background: Multiple myeloma (MM) is a plasma cell malignancy characterized by chromosomal instabilities (CIN). Here we investigate the potential of cell-free DNA CIN as non-invasive biomarker to predict early response for MM treatments. Methods: In this prospective study, we recruited 11 relapsed/refractory (RRMM) and 19 newly diagnosed (NDMM) patients at Changzheng Hospital. Plasma samples were collected after finished two cycles or one month (RRMM) of therapy, with matched ones before the current regimen. cfDNA was extracted, followed by CIN analyses by using a customized bioinformatics workflow, ultrasensitive chromosomal aneuploidy detector (UCAD). Criteria for response and progression were according to the IMWG (Durie BG et al. 2006). Results: 7 (23%) patients (5 RRMM and 2 NDMM) showed high cfDNA CIN regard as strong positive after two cycles of treatment. Plasma cfDNA CIN profiling found complex clonal evolution compared two cycles to baseline. Multiple genomic regions, including chr7, 17p (TP53), 12q and 3p, were involved in clonal evolution. The degree of cfDNA CIN correlated with myeloma stage and overall survival. Remarkably, of the 5 heavily treated RRMM patients and 1 primary refractory newly diagnosed patient, 3 died within 60 days after the last time of cfDNA detection. Nine patients (30%) of patients showed positive cfDNA CIN after two cycles of treatment, which response rate was 11% (n=1) with SD, 33% (n=3) with MR, and 56% with PR, respectively. Fourteen patients with 5 RRMM and 9 NDMM were detected marginal or negative cfDNA CIN after two cycle’s treatment. The overall response rate in 14 patients was 100%, including 14.3% with a complete response, 14.3% with a very good partial response (VGPR), 57.1% with a PR, and 14.3% with a MR. Of these patients, 3 RRMM who received with more than six lines of therapy, showed positive cfDNA CIN. Subsequently, these three heavily treated RRMM patients have chance to enroll the chimeric antigen receptor T-Cell immunotherapy (CAR-T) therapy (enrolled NCT03093168). Surprisedly, all of them benefit from the CAR-T therapy to improve responses dramatically, meanwhile, the dynamics of total cfDNA concentration correlated with tumor burden to negative. Conclusions: We provide evidence that cfDNA level correlates with tumor burden and response rate in MM. For heavily pre-treated advanced RRMM patients with cfDNA CIN positive were benefit from the CAR-T therapy. Therefore, serial plasma cfDNA analysis is a robust and sensitive tool for monitoring response to therapy.

A novel PAX5 rearrangement in TCF3-PBX1 acute lymphoblastic leukemia: a case report

BackgroundChromosome translocations are a hallmark of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Additional genomic aberrations are also crucial in both BCP-ALL leukemogenesis and treatment management. Herein, we report the phenotypic and molecular cytogenetic characterization of an extremely rare case of BCP-ALL harboring two concomitant leukemia-associated chromosome translocations: t(1;19)(q23;q13.3) and t(9;17)(p13;q11.2). Of note, we described a new rearrangement between exon 6 of PAX5 and a 17q11.2 region, where intron 3 of SPECC1 is located. This rearrangement seems to disrupt PAX5 similarly to a PAX5 deletion. Furthermore, a distinct karyotype between diagnosis and relapse samples was observed, disclosing a complex clonal evolution during leukemia progression.Case presentationA 16-year-old boy was admitted febrile with abdominal and joint pain. At clinical investigation, he presented with anemia, splenomegaly, low white blood cell count and 92% lymphoblast. He was diagnosed with pre-B ALL and treated according to high risk GBTLI-ALL2009. Twelve months after complete remission, he developed a relapse in consequence of a high central nervous system and bone marrow infiltration, and unfortunately died.ConclusionsTo our knowledge, this is the first report of a rearrangement between PAX5 and SPECC1. The presence of TCF3-PBX1 and PAX5-rearrangement at diagnosis and relapse indicates that both might have participated in the malignant transformation disease maintenance and dismal outcome.

High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics.

To enable the characterization of genetic heterogeneity in tumor cell populations, we developed a novel microfluidic approach that barcodes amplified genomic DNA from thousands of individual cancer cells confined to droplets. The barcodes are then used to reassemble the genetic profiles of cells from next-generation sequencing data. By using this approach, we sequenced longitudinally collected acute myeloid leukemia (AML) tumor populations from two patients and genotyped up to 62 disease relevant loci across more than 16,000 individual cells. Targeted single-cell sequencing was able to sensitively identify cells harboring pathogenic mutations during complete remission and uncovered complex clonal evolution within AML tumors that was not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of AML heterogeneity, leading to improved stratification and therapy selection for the disease.

PDGFRB mutation and tyrosine kinase inhibitor resistance in Ph-like acute lymphoblastic leukemia

AbstractPhiladelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) comprises ∼10% to 15% of childhood ALL cases, many of which respond exquisitely to tyrosine kinase inhibitors (TKIs), for example, imatinib in PDGFRB-rearranged ALL. However, some cases developed drug resistance to TKIs and the mechanisms are poorly understood. In this study, we identified a novel PDGFRB fusion gene, namely AGGF1-PDGFRB, and functionally characterized its oncogenic potential in vitro. Further genomic profiling of longitudinally collected samples during treatment revealed the emergence of a mutation, PDGFRBC843G, which directly conferred resistance to all generations of ABL TKIs, including imatinib, dasatinib, nilotinib, and ponatinib. PDGFRB-mutant leukemia cells are highly sensitive to multitarget kinase inhibitor CHZ868, suggesting potential therapeutic options for some patients resistant to ABL TKIs. In summary, we describe a complex clonal evolution pattern in Ph-like ALL and identified a novel PDGFRB point mutation that drives leukemia relapse after ABL TKI treatment.

Late Appearance of 14q32/IGH Translocation in Chronic Lumphocytic Leukemia

AbstractAbstract 2429Up to 80% of Chronic Lymphocytic Leukemia (CLL) harbour clonal chromosome aberrations having important clinical implications (i.e. 13q deletion, +12, 11q/ATM and 17p/TP53 deletions). 14q32/IGH rearrangements were recently found in 6–19% of CLL patients and were associated with therapy-demanding disease and inferior outcome. Whereas evidence was provided that some of the classical aberrations, such as 11q-, 17p-, may appear late in CLL clinical history, no information is presently available concerning 14q32/IGH translocations. The aim of this study was i) to analyze the incidence of 14q32/IGH translocations occurring at clonal evolution in CLL, ii) to analyze the clinicobiologic significance of late-appearing 14q32/IGH translocations. One hundred-five CLL cases seen at our institution in a 10-year period were submitted to FISH analysis at diagnosis or before 1st line treatment as part of routine diagnostic workup. In 47 patients with indolent disease (untreated or treated with 1 line without relapse, group 1) FISH analysis was repeated after 48–96 months (median 72). In 58 relapsed patients who started 2nd line treatment (group 2), FISH was performed sequentially before administration of the 2nd line and before each subsequent line of therapy. These 105 patients fulfilled the following criteria: a) diagnosis of bona fide CLL based on morphology and immunophenotyping (CD5/CD19+, CD23+ as minimal requirement), b) clinical records available for review, c) successful FISH analysis at diagnosis and during follow-up. Those cases with t (11;14)(q13;q32)/CCND1-IGH or other 14q32/IGH translocations present at diagnosis were excluded from this study. Sequential FISH studies were performed in all patients on peripheral blood (PB) samples using commercially available probes for the identification of deletions at 13q14, 11q22/ATM, 17p13/TP53, of trisomy 12 and of 14q32/IGH translocations. In 10 patients bone marrow (BM) aspiration and/or lymph node (LN) biopsy were studied by FISH as well. The patients were treated at disease progression as defined by NCI criteria. Refractory disease was defined by stable disease or progressive disease during treatment or disease progression within 6 months of from antileukemic treatment using fludarabine alone or in combination with other agents. Time to chemorefractoriness was measured from date of first line treatment to date of refractoriness to fludarabine containing regimen or date of last follow-up. Overall survival was measured from diagnosis to date of last follow-up or death and from initiation of first line treatment to the date of death or last follow-up. At diagnosis 39% of the cases had 13q-, 14% had +12, 7% had 11q- and 3% had 17p-. A late-appearing 14q32/IGH rearrangement was not detected among 47 patients in group 1, whereas 7/58 cases (12,1%) in group 2 showed a 14q32/IGH break in 16–25% of the cells. These 7 patients had the following aberrations at diagnosis: 13q- and 11q- in 1 case, 13q- in 2 cases; 11q- in 1 case, +12 in 2 cases, no aberrations 1 case. The 14q32 translocation appeared after a median time of 64 months (range 51–91). It was associated with the appearance of 17p- in 3/7 cases with one of these presenting also biallelic del13q. In two cases paired BM or LN sample and PB samples were available for FISH studies and the appearance of IgH translocation in the BM or in the LN sample preceded its appearance in PB by 13–58 months. All 7 cases with late appearing 14q32/IGH translocation developed chemorefractoriness to fludarabine regimen with a median TTC of 27 months (range 12–40 months), as compared with a TTC of 67 months (range 1–143 months) in 51 treated patients who did not develop the 14q32 translocation (p=0.0002). Overall survival did not differ significantly either when measured from diagnosis or from 1st line treatment in 7 patients with 14q32 translocation as compared with the appropriate control. We arrived at the following conclusions: i) a late-appearing 14q32/IGH translocation occurred at a relatively high incidence (12,1%) in patients with relapsing disease and not in patients with stable disease, ii) this aberration involved a minority of cells and, in approximately half of the cases, it was associated with other aberrations, reflecting complex clonal evolution, iii) in 2 assessable cases it first appeared first in the BM or LN; iv) the appearance of 14q32/IGH translocation was associated with shorter TTC. Disclosures:No relevant conflicts of interest to declare.

CML clonal evolution with resistance to single agent imatinib therapy

We describe a 58-year-old male diagnosed with chronic myeloid leukaemia (CML) who failed to have a cytogenetic response to interferon-alpha and hydroxyurea. On subsequent therapy with imatinib mesylate he failed to have any cytogenetic response but also developed a complex clonal evolution with an additional Philadelphia (Ph) chromosome and trisomy 8 respectively in two Ph-positive subclones. The addition of cytosine arabinoside to imatinib resulted in reversion to single Ph-chromosome positivity with the disappearance of the previous additional clonal abnormalities. The case demonstrates the efficacy of combined treatment with imatinib and cytarabine in the management of CML resistant to single agent imatinib.