Clonal Evolution In Patients Research Articles

Role of Telomere in Clonal Evolution of Acquired Aplastic Anemia--Review

Studies have found that 1/3 patients with acquired aplastic anemia have shortened telomere length, and the shorter the telomere, the longer the disease course, the more prone to relapse, the lower the overall survival rate, and the higher the probability of clonal evolution. The regulation of telomere length is affected by many factors, including telomerase activity, telomerase-related genes, telomere regulatory proteins and other related factors. Telomere shortening can lead to genetic instability and increases the probability of clonal evolution in patients with acquired aplastic anemia. This article reviews the role of telomere in the clonal evolution of acquired aplastic anemia and factors affecting telomere length.

Sequential Analysis of cfDNA Reveals Clonal Evolution in Patients with Neuroblastoma Receiving ALK-Targeted Therapy.

The study of cell-free DNA (cfDNA) enables sequential analysis of tumor cell-specific genetic alterations in patients with neuroblastoma. Eighteen patients with relapsing neuroblastoma having received lorlatinib, a third-generation ALK inhibitor, were identified (SACHA national registry and/or in the institution). cfDNA was analyzed at relapse for nine patients and sequentially for five patients (blood/bone marrow plasma) by performing whole-genome sequencing library construction followed by ALK-targeted ddPCR of the hotspot mutations [F1174L, R1275Q, and I1170N; variant allele fraction (VAF) detection limit 0.1%] and whole-exome sequencing (WES) to evaluate disease burden and clonal evolution, following comparison with tumor/germline WES. Overall response rate to lorlatinib was 33% (CI, 13%-59%), with response observed in 6/10 cases without versus 0/8 cases with MYCN amplification (MNA). ALK VAFs correlated with the overall clinical disease status, with a VAF < 0.1% in clinical remission, versus higher VAFs (>30%) at progression. Importantly, sequential ALK ddPCR detected relapse earlier than clinical imaging. cfDNA WES revealed new SNVs, not seen in the primary tumor, in all instances of disease progression after lorlatinib treatment, indicating clonal evolution, including alterations in genes linked to tumor aggressivity (TP53) or novel targets (EGFR). Gene pathway analysis revealed an enrichment for genes targeting cell differentiation in emerging clones, and cell adhesion in persistent clones. Evidence of clonal hematopoiesis could be observed in follow-up samples. We demonstrate the clinical utility of combining ALK cfDNA ddPCR for disease monitoring and cfDNA WES for the study of clonal evolution and resistance mechanisms in patients with neuroblastoma receiving ALK-targeted therapy.

Longitudinal Comparative Analysis of Circulating Tumor DNA and Matched Tumor Tissue DNA in Patients with Metastatic Colorectal Cancer Receiving Palliative First-Line Systemic Anti-Cancer Therapy.

This study aimed to compare tumor tissue DNA (ttDNA) and circulating tumor DNA (ctDNA) to explore the clinical applicability of ctDNA and to better understand clonal evolution in patients with metastatic colorectal cancer undergoing palliative first-line systemic therapy. We performed targeted sequencing analysis of 88 cancer-associated genes using germline DNA, ctDNA at baseline (baseline-ctDNA), and ctDNA at progressive disease (PD-ctDNA). The results were compared with ttDNA data. Among 208 consecutively enrolled patients, we selected 84 (41 males; median age, 59 years; range, 35 to 90 years) with all four sample types available. A total of 202 driver mutations were found in 34 genes. ttDNA exhibited the highest mutation frequency (n=232), followed by baseline-ctDNA (n=155) and PD-ctDNA (n=117). Sequencing ctDNA alongside ttDNA revealed additional mutations in 40 patients (47.6%). PD-ctDNA detected 13 novel mutations in 10 patients (11.9%) compared to ttDNA and baseline-ctDNA. Notably, seven mutations in five patients (6.0%) were missense or nonsense mutations in APC, TP53, SMAD4, and CDH1 genes. In baseline-ctDNA, higher maximal variant allele frequency (VAF) values (p=0.010) and higher VAF values of APC (p=0.012), TP53 (p=0.012), and KRAS (p=0.005) mutations were significantly associated with worse overall survival. While ttDNA remains more sensitive than ctDNA, our ctDNA platform demonstrated validity and potential value when ttDNA was unavailable. Post-treatment analysis of PD-ctDNA unveiled new pathogenic mutations, signifying cancer's clonal evolution. Additionally, baseline-ctDNA's VAF values were prognostic after treatment.

Abstract 966: Longitudinal comparative analysis of circulating tumor DNA and matched tumor tissue DNA in patients with metastatic colorectal cancer receiving palliative first-line systemic anti-cancer therapy

Abstract Background: Plasma circulating tumor DNA (ctDNA) analysis has become an attractive method for precision oncology. This study compared mutational landscapes of ctDNA with matched tumor tissue DNA (ttDNA) to explore clinical applicability and to better understand clonal evolution in patients with metastatic colorectal cancer receiving palliative first-line systemic anti-cancer therapy (SACT). Methods: We performed unique molecular identifier-based targeted sequencing of 88 cancer-associated genes using the following samples: ttDNA, germline DNA, ctDNA at baseline (baseline-ctDNA), and ctDNA at progressive disease (PD-ctDNA). Results: Of the 208 consecutively enrolled patients, 84 were selected (41 males; median age 59, ranging from 35 to 90) with access to all four samples. Excluding duplicated mutations, a total of 202 driver mutations were discovered in 34 genes. ttDNA exhibited the highest occurrence of mutations (N=232), followed by baseline-ctDNA (N=155) and PD-ctDNA (N=117). Genotype concordance for the ten most mutated genes was highest between baseline-ctDNA and PD-ctDNA, at 94.3%, while the concordance rates for ttDNA were 85.5% with baseline-ctDNA and 83.6% with PD-ctDNA. Overall, 40 of the 84 patients (47.6%) benefited from sequencing ctDNA in addition to ttDNA as it identified additional mutations. Compared to ttDNA and baseline-ctDNA, PD-ctDNA identified 13 novel mutations in ten patients (11.9%). Notably, 7 mutations in five patients (6.0%) were missense or nonsense mutations in APC, TP53, SMAD4, and CDH1 genes. In baseline-ctDNA, patients with maximal variant allele frequency (VAF) values of &amp;gt;0.059 showed significantly worse progression-free survival (median 10.5 vs. 17.1 months, P=0.036) and overall survival (median 18.1 vs. 40.3 months, P=0.010). Moreover, overall survival was significantly worse in those with higher VAF values of APC (median 18.1 vs. 36.8 months, P=0.012), TP53 (median 24.7 vs. 40.3 months, P=0.012), and KRAS (median 13.7 vs. 27.6 months, P=0.005) mutations. Conclusions: While ttDNA remains more sensitive than ctDNA, our unique molecular identifier-based ctDNA platform demonstrated the validity and potential value when ttDNA was unavailable. Furthermore, post-SACT analysis of PD-ctDNA revealed new pathogenic mutations, indicating the clonal evolution of cancer. In addition, the VAF values of baseline-ctDNA predicted prognosis after SACT. Citation Format: Ji-Won Kim, Seung-been Lee, Hong-Geun Kim, Sung-Hyun Hwang, Kui-Jin Kim, Ju Hyun Lee, Jeongmin Seo, Minsu Kang, Eun Hee Jung, Koung Jin Suh, Se Hyun Kim, Jin Won Kim, Yu Jung Kim, Jee Hyun Kim, Nak-Jung Kwon, Keun-Wook Lee. Longitudinal comparative analysis of circulating tumor DNA and matched tumor tissue DNA in patients with metastatic colorectal cancer receiving palliative first-line systemic anti-cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 966.

TCRαβ +/CD19 + - Depleted HLA-Haploidentical Hematopoietic Stem Cell Traansplantation in Pediatric Patient with Fanconi Anemia

Background Allogeneic hematopoietic stem cell transplantation (HSCT) currently represents the only proven treatment able to rescue bone marrow failure and prevent the occurrence of clonal evolution in patients with Fanconi Anemia (FA). If HSCT from HLA-identical related donor (MRD) is reported to be associated with better outcomes, this is not available for most patients. On the other hand, the identification of a fully matched unrelated donor (MUD) may be unsuccessful, or require times incompatible with a prompt treatment of the haematological condition. For patients who lack a MRD or MUD, the preferred donor choice is debated. HLA partially matched haploidentical donor (haplo) is virtually immediately available for all patients and haplo-HSCT has been reported over the last few years as a promising alternative for those patients. Following the favorable results already reported from our group of a cohort of pediatric and young adult FA patients underwent haplo-HSCT, based on the selective depletion of TCRαβ + and CD19 + cells graft manipulation, here we present the outcome of an enlarged cohort of patients who received HSCT in 3 different centers. Methods Patients diagnosed with FA and eligible for an allogeneic transplantation, but lacking a MRD or MUD, and with a suitable HLA-haploidentical donor were eligible to this study. The conditioning regimen included intravenous fludarabine, cyclophosphamide and single-dose total body irradiation for most patients. Pretransplant anti-T-lymphocyte globulin was administered in all patient to control in vivo bidirectional donor-recipient alloreactivity. Apheresis and graft manipulation were performed as previously reported (Li Pira, Biol Blood Marrow Transplant 2016). Results Thirty-five patients (19 males and 16 females) underwent haplo-HSCT between September 2011 and April 2023 in 3 different centers (Bambino Gesù Children's Hospital, Rome, Italy; Policlinico San Matteo, Pavia, Italy; Tokyo; National Center for Child Health and Development, Children's Cancer Center, Tokyo, Japan). Twenty-four patients have been previously reported (Strocchio, Blood Adv 2021). Details on patients and donor characteristics, graft composition and conditioning regimen are listed in table 1. One patient with clonal evolution and 1 with AML received fludarabine and AraC 3 weeks before the start of the conditioning. Primary engraftment was achieved in 33 patients (94.3%), with median time for neutrophil and platelet recovery of 12 days (range, 9-20 days) and 10 days (range, 7-14 days), respectively. Primary graft failure occurred in 2 patients and both were successfully transplanted from the other haploidentical parent. The monitoring of chimerism analysis confirmed a stable engraftment of donor hemopoiesis in all engrafted patients. Within 33 evaluable patients, 9 (27.3%) experienced grade 1-2 aGvHD (7 with stage I-II skin-only involvement, 1 with stage I lower gastrointestinal involvement) at a median time of 35.5 days (range, 16-67 days) after HSCT. One patient developed late-onset skin only grade 2 aGvHD at day +211 after HSCT. One patient (3%) experienced grade IV aGvHD (liver and gastrointestinal involvement) at day + 100 from HSCT, 4 weeks after the infusion of adenoviral-specific donor T cells; he is currently receiving ruxolitinib and the complete resolution of GvHD was obtained. Only one patient (3%), developed cGvHD with mild skin involvement. Thirteen patients (39.4%) experienced one or more viral infections or reactivations (6 cytomegalovirus, 4 herpesvirus-6, 2 adenovirus, 1 parainfluenzae); the specific antiviral treatment was administered with a complete resolution of infection in all cases. With a median follow up of 5.5 years (range, 0.6-11.4 years) all the patients are alive and with resolution of hematological complications. Except for the already reported vulvar intraepithelial neoplasia, no additional posttransplant malignancy was observed Conclusions Our data obtained from enlarged cohort of patients previously reported, confirm excellent results in terms of survival and a good rate of engraftment also in a multicenter setting. The low incidence of acute and chronic GvHD, a particularly detrimental complication in patients with DNA repair disorder, makes this approach attractive in this patient population. In FA patients lacking a standard donor, TCRab +/CD19 + haplo-HSCT is confirmed to be a promising strategy.

FLT3 Testing and Clonal Evolution in Patients with Acute Myeloid Leukemia: A Retrospective Cohort Study in Taiwan

INTRODUCTION: Mutation of the FMS-like tyrosine kinase 3 ( FLT3) gene is one of the most common genetic alterations in acute myeloid leukemia (AML), while FLT3 internal tandem duplication (ITD) is a predictor of poor disease prognosis in patients. Timing of FLT3 mutation testing and the pattern of FLT3 clonal evolution are critical issues for ensuring that patients with FLT3 mutation-positive AML receive targeted therapy promptly, but data from real-world clinical practice are limited. AIM: This retrospective cohort study aimed to assess the turnaround time of FLT3 testing in two patient cohorts with non-M3 primary AML: newly diagnosed (ND) patients and those with relapsed or refractory disease (R/R). A further aim in the R/R cohort was to assess the pattern of FLT3 clonal evolution. METHODS: Eligible adult patients had evidence of new diagnosis of AML or R/R AML between 1 January 2009 and 31 December 2019 and had undergone at least one FLT3 test at National Taiwan University Hospital. Patients were followed up until either the end of the data period, loss to follow up (no records for 6 months), or death. We analyzed the time from the date of ordering FLT3 test to receipt of results (both cohorts) and the acquisition (negative at diagnosis, positive at R/R), loss (positive at diagnosis, negative at R/R), or maintenance (no change in status) of FLT3 mutation at R/R compared with status at diagnosis. We also explored the association between acquisition/loss/maintenance of FLT3 mutation at R/R and overall survival (OS) in the R/R cohort. RESULTS: From a total AML dataset of 1,789 patients, 659 and 223 were included in the ND and R/R cohorts, respectively ( Table 1). Demographics and clinical characteristics of the ND and R/R cohorts were similar. The most common type of AML was recurrent genetic abnormalities in both ND and R/R cohorts (50.7% and 67.7%, respectively); 45.8% and 48.0% of patients, respectively, had a normal karyotype; and NPM1 (21.1% and 16.6%, respectively), and IDH1/ IDH2 (18.5% and 15.2%, respectively) were the most common types of co-mutations detected. There was no difference in the turnaround time of FLT3 testing between the ND and R/R cohorts ( Table 1). Since 2020, FLT3 testing protocols have been further optimized to meet a 7-day turnaround time; additionally, almost all chemotherapy-fit patients with FLT3 mutation receive midostaurin in combination with 3+7 chemotherapy after reimbursement of midostaurin was implemented in Taiwan in February 2020. Of 164 patients with FLT3 tests at both diagnosis and R/R, most (75.6%, n=124) were FLT3 mutation-negative at diagnosis ( Table 1). At R/R, 27/124 (21.8%) acquired an FLT3 mutation and 12/40 (30.0%) patients lost their FLT3 mutation ( Table 1). Risk of mortality was increased in patients who acquired an FLT3 mutation (HR [95% CI] 1.59 [0.97, 2.62]), maintained their FLT3 mutation (1.52 [0.58, 2.56]), or lost their FLT3 mutation (1.22 [0.58, 2.56]), compared with those who were FLT3-mutation negative at both diagnosis and R/R ( Figure 1). CONCLUSIONS: This study provided information on the real-world landscape of FLT3 testing among patients with AML in Taiwan. The turnaround time of FLT3 testing in the current study was longer than the time reported in clinical trials, likely owing to different procedures in sampling arrangement and report delivery between real world and clinical trial settings. The distribution of FLT3 mutation and pattern of clonal evolution were largely consistent with previously published clinical studies. The higher prevalence of FLT3 mutation in the R/R cohort versus the ND cohort is in accordance with previous research showing that FLT3-ITD mutation is predictive of relapse. Patients with FLT3 mutation at R/R had a shorter OS, which indicates the importance of FLT3 testing at R/R diagnosis to optimize outcomes through targeted therapy.

Molecular-defined clonal evolution in patients with classical myeloproliferative neoplasms.

Classical myeloproliferative neoplasms (MPNs) are characterized by distinct clinical phenotypes. The discovery of driver mutations in JAK2, CALR and MPL genes provided new insights into their pathogenesis. Next-generation sequencing (NGS) identified additional somatic mutations, most frequently in epigenetic modulator genes. In this study, a cohort of 95 MPN patients was genetically characterized using targeted NGS. Clonal hierarchies of detected mutations were subsequently analysed using colony forming progenitor assays derived from single cells to study mutation acquisition. Further, the hierarchy of mutations within distinct cell lineages was evaluated. NGS revealed mutations in three epigenetic modulator genes (TET2, DNMT3A, ASXL1) as most common co-mutations to the classical driver mutations. JAK2V617F as well as DNMT3A and TET2 mutations were detected as primary events in disease formation and most cases presented with a linear mutation pattern. Mutations appear mostly in the myeloid lineages but can also appear in lymphoid subpopulations. In one case with a double mutant MPL gene, mutations exclusively appeared in the monocyte lineage. Overall, this study confirms the mutational heterogeneity of classical MPNs and highlights the role of JAK2V617F and epigenetic modifier genes as early events in hematologic disease formation.

The Role of Heterozygous Variants in SAMD9/9L and Recessive Bone Marrow Failure-Related Genes in Adults with Severe Aplastic Anemia

Background Genetic reports of patients with severe AA (SAA) often identify heterozygous variants of unknown significance in recessive genes associated with inherited bone marrow failure syndromes (IBMFS), such as Fanconi anemia (FA) and telomere biology diseases (TBD). More recently, heterozygous SAMD9 and SAMD9L (SAMD9/9L) variants have also been reported in children and young adults with BMF, but whether all variants are gain-of-function (GoF) and pathogenic is unknown. In a large cohort of SAA patients, we investigated the prevalence of heterozygous variants in SAMD9/9L and FA/TBD genes and correlated them to disease characteristics and clinical outcomes. Methods SAA patients (n=198; median age [range]: 32 [3-82]) enrolled on a phase II trial for treatment with horse anti-thymocyte globulin, cyclosporine, and eltrombopag (NCT01623167) at the National Institutes of Health from 2012 - 2022 were included (Table 1). All patients were screened for germline mutations in IBMFS related genes. SAMD9/9L variants were segregated by rarity according to frequency in the gnomAD database as common (<0.1% in overall population, including variants with maximum population frequency [MaxPopFreq] >1%), rare (MaxPopFreq <0.1%), very rare (MaxPopFreq <0.01%), ultra-rare (MaxPopFreq <0.005%), and novel (absent in gnomAD). Results We first investigated whether patients had an undiagnosed SAMD9/9L disorder. Although 40/198 patients (20%) had a heterozygous SAMD9/9L variant, including 8 (20%) with 2 variants, these were mostly classed as common (73%; n=35), followed by rare, very rare, ultra-rare and novel variants seen in 17% (n=8), 4% (n=2), 2% (n=1), and 4% (n=2), respectively. Most variants were missense (n=39; 81%), followed by nonsense (n=6; 13%) and frameshift mutations (n=3; 6%). Except for ultra-rare and novel, SAMD9/9L often co-occurred with typical features of immune AA (6p-LOH, PNH clones, HLA and PIGA mutations). None of the 40 patients with germline SAMD9/9L variants had primary somatic genetic reversions (SGR) such as somatic loss of function (LoF) mutations (VAF>0.5%) in SAMD9/9L or UPD7q. Since GoF SAMD9/9L variants are located on chr7 and they associate with development of monosomy 7, we investigated whether SAMD9/9L variants in our cohort were associated with clonal evolution after treatment. However, only 2/40 patients (5%) with chr7 abnormalities had these variants, both common. Patients with SAMD9/9L variants, both common and rare, were significantly younger (35 years vs. 24 years, p=0.026) and more frequently had VSAA (defined as absolute neutrophil count <0.2 K/uL) than those without these variants (62% vs. 41%, p=0.02); they had lower median neutrophil counts (p=0.038), reticulocyte counts (p=0.024), and platelet counts (p=0.047). The presence of rarer (MaxPopFreq<0.1%; n=11) or common SAMD9/9L variants (n=29) did not impact disease severity, or correlate with molecular characteristics of immune AA, response to immunosuppressive therapy, and overall survival (Figure 1). In addition to SAMD9/9L variants, 82 patients (41%) had 1 or more heterozygous variants in FA/TBD, but these were not associated with disease severity or with clinical outcomes, even when co-occurring with SAMD9/9L variants. Twenty five patients (13%) had co-occurring heterozygous mutations in both SAMD9/9L and FA/TBD genes, but these were not correlated with disease severity or response to therapy when compared to patients without co-occurring mutations. Conclusions As opposed to classical SAMD9/9L disorders in pediatric cohorts, SAMD9/9L variants found in our primarily adult patients with SAA are not disease-causing germline GoF mutations, even the rarest variants. Most patients with variants responded to immunosuppressive therapy, and the less rare variants were associated with molecular features of immune AA but not SGR, both findings suggestive of immune pathophysiology. Interpretation of genetic reports, including SAMD9/9L, in adults appears to be different from mostly pediatric cohorts with SAMD9/9L disorders. Heterozygous SAMD9/9L variants do affect AA severity but are not predictive of response to therapy or prognosis. FA/TBD heterozygous variants did not impact disease characteristics or outcomes. We did not observe a higher rate of clonal evolution in patients with SAMD9/9L after EPAG treatment compared to patients carrying FA/TBD variants and others without variants. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

HLA Class I Allele-Specific Pathology Defines Clinical Manifestations of Immune Aplastic Anemia

Leukocytes that have lost the cell surface expression of an HLA class I allele due to somatic HLA gene mutations or 6p loss of heterozygosity (LOH) are often present in patients with immune aplastic anemia (AA), consistent with T cell-mediated bone marrow cell destruction. A recent NIH study suggested that the clinical significance and underlying pathology of HLA loss may differ according to the type of HLA allele affected (Zaimoku et al. Blood 2021) because (1) the significant correlation of HLA loss with clonal evolution was primarily attributed to patients who lost HLA-B*14:02 and A*02:01; (2) all patients who lost B*40:02 and A*02:06 achieved a hematologic response to immunosuppressive therapy (IST), though HLA loss in general was not correlated with the IST response; (3) loss of B*07:02 and B*40:01 was associated with older age of onset; (4) patients who retained B*14:02, B*07:02, and B*40:01 also showed clinical features of patients who lost respective HLA alleles. We aimed to confirm the HLA class I allele-related clinical manifestations in Japanese AA patients. HLA loss was assessed by SNP array, HLA flow cytometry, digital PCR, or deep nucleotide sequencing. An HLA allele was classified as "affected by loss" in individual patients when the single allele was lost or inactivated by somatic mutations or when both HLA-A and HLA-B alleles in a haplotype were lost due to 6p LOH with no evidence of loss or inactivation of a single HLA allele. Clinical characteristics were compared according to the affected HLA alleles. In 496 Japanese patients with AA (severe, n = 368; non-severe, n = 128; median age, 59 [range, 1-89] years), there were 146 (29%) patients with HLA loss. HLA-B*40:02, A*02:06, A*31:01, and B*54:01 were more frequently affected in our cohort than in the NIH cohort, where B*14:02, A*02:01, B*08:01, and B*07:02 held the majority of lost alleles (Figure 1). The median age of patients with B*40:01 loss (75 years) was highest among the groups of patients with HLA allele loss, consistent with the NIH study. The prevalence of ≥0.003% paroxysmal nocturnal hemoglobinuria (PNH) clones was significantly reduced in patients with B*40:02 loss but not in others. Sex and severity of AA were not markedly different across the groups of patients with HLA allele loss. Outcomes after anti-thymocyte globulin (ATG)-based IST were evaluable in 263 of the 496 patients. Although HLA loss was correlated with the IST response at 6 months (as reported by our group), loss of HLA-A*02:01 did not contribute to the high response, consistent with the NIH study. Loss of frequently affected HLA alleles in Japanese patients (B*40:02, A*02:06, B*54:01, etc.) was generally correlated with the IST-response. Further, patients who carried 5 HLA-B alleles (B*40:01, B*40:02, B*44:03, B*54:01, and B*56:01) without loss still displayed higher response rates than other patients. In contrast, the favorable effect of A*02:06 loss was not seen in patients who carried A*02:06 without loss. A*02:06 loss, the presence of the 5 HLA-B alleles (irrespective of loss), and previously reported HLA class II alleles (DRB1*13 and DRB1*15) were independently correlated with the IST response. The incidence of clonal evolution to myeloid neoplasms after ATG-based IST was significantly higher in patients with HLA-A*02:01 loss than other patients (Figure 2), as observed in the NIH study; A*02:01 was affected in 4 of 7 patients showing both HLA loss and clonal evolution in our cohort; B*40:02, B*44:02, and B*52:01 were affected in other 3 patients. In summary, our study in Japanese AA patients broadly confirmed the associations of loss of specific HLA alleles with clinical manifestations observed in American patients, including older age of onset in patients with HLA-B*40:01 loss, high IST response rates in patients who lost B*40:02 and A*02:06 but not in patients with A*02:01 loss, and frequent clonal evolution in patients with A*02:01 loss. We also revealed the correlation of 5 HLA-B alleles with IST response, irrespective of loss, similar to the relationship of B*14:02 to clonal evolution in the United States, and the reduced prevalence of PNH clones in patients with B*40:02 loss. These findings strongly suggest that the heterogeneous pathology of AA can be classified by affected HLA alleles. This should be useful for studies to unravel the pathophysiology and improve the outcomes of patients with immune AA. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Clonal Evolution in Patients with Hormone Receptor Positive, HER-2 Negative Breast Cancer Treated with Chemotherapy or CDK4/6 Inhibitors

Introduction: Somatic evolution of the cancer genome resulting in genetically different subclones is thought to be involved in the development of treatment resistance but might also offer new therapeutic opportunities in metastatic breast cancer. No data are available if clonal evolution differs in patients treated with chemotherapy (chemo) or CDK4/6 inhibitors given with endocrine treatment (CE treatment). Methods: We performed a prospective analysis of circulating tumor DNA (ctDNA) by targeted next-generation sequencing in 46 patients before the beginning of a systemic first-line (n = 37) or second-line (n = 9) treatment. Ct DNA was analyzed again upon disease progression. Results: New mutations in ctDNA of patients with progressive disease were detected in 1/11 patients who started chemo, in 4/9 patients treated with chemo followed by CE maintenance treatment, and in 9/26 patients receiving CE therapy. The number of acquired new mutations did not differ significantly between the three therapy cohorts (all p values >0.05). However, in patients classified as secondary resistant (n = 37), occurrence of new mutations significantly differed between patients who started chemo (0/9) compared to patients treated with chemo followed by CE (4/11; p = 0.041) and patients receiving CE therapy (8/19; p = 0.024), respectively. Conclusion: Clonal evolution might differ significantly between metastatic breast cancer patients with hormone receptor positive and HER-2 negative disease treated with chemo or CDK4/6 inhibitors. These results should be confirmed in larger patient cohorts.

Clonal evolution in patients developing therapy-related myeloid neoplasms following autologous stem cell transplantation.

Clonal hematopoiesis (CH) denotes somatic mutations in genes related to myeloid neoplasms present at any variant allele frequency (VAF). Clonal hematopoiesis is associated with increasing age and with a factor 6 increase in the risk of developing therapy-related myeloid neoplasms (tMNs) following autologous stem cell transplantation (ASCT). However, the impact of specific mutations on progression from CH to tMN has yet to be unraveled, and it remains unclear whether mutations directly impact or even drive the development of tMN. We performed deep sequencing in longitudinal samples from a cohort of 12 patients with either multiple myeloma or lymphoma who developed tMN following ASCT. Nine patients had one or more mutations that could be tracked longitudinally. Seven patients had clonal expansion from time of ASCT to diagnosis of tMN. Of these, six patients had CH at VAF < 2% at baseline. The median VAF of non-DNMT3A clones increased from 1% (IQR 0.7%-10.0%) at time of ASCT to 37% (IQR 17%-47%) at tMN diagnosis (P = 0.002), while DNMT3A clones showed quiescent trajectories (P = 0.625). Our data provide evidence to support the hypothesis that the development of tMN following ASCT is likely instigated by CH present at VAFs as low as 0.5%, detectable years before tMN onset.

Strong Predictors of Chromosomal Aberrations and Myeloid Neoplasia Following Immunosuppression Therapy for Severe Aplastic Anemia: A Retrospective Cohort Study

Introduction: Immune aplastic anemia (AA) is effectively treated with either immunosuppressive treatment (IST) or allogeneic hematopoietic stem cell transplant (HSCT). Clonal evolution remains the most feared long-term complication after IST. We investigated predictor factors, genetic characteristics, and long-term outcomes of patients who developed either secondary myeloid neoplasia or isolated chromosomal abnormalities without morphologic dysplasia after immunosuppression.Methods: All patients with severe AA treated at the NIH Clinical Center with IST from 1989-2020 who underwent clonal evolution were categorized as “high-risk” (overt myeloid neoplasia, or isolated chromosome 7 abnormality / complex cytogenetics) or “low-risk” (isolated chromosome abnormalities without overt myeloid neoplasia or dysplasia; isolated chromosome 7 abnormality or complex cytogenetics were characterized as high-risk). Univariable analysis was performed using the Fine-Gray competing risk regression model using death as a competing risk to determine predictors of clonal evolution. Classification and regression tree analysis of time to clonal evolution was performed on continuous baseline variables to partition the data based on the best categorical cutoff. Long term outcomes assessed included overall survival (OS) and HSCT. Error corrected next-generation sequencing (ECS) was used to assess for pathogenic somatic variants in known myeloid cancer genes in clonal evolvers both at time of evolution and in serial samples prior when available.Results: Of 659 patients with severe AA included in this study, 95 developed clonal evolution: 59 high-risk and 36 low-risk. Age >48 years at diagnosis and pre-treatment ANC >0.87x10 9/L were strong predictors of high-risk clonal evolution. High-risk clonal evolution was increased in patients aged >48 years, with cumulative incidence (CI) of 13.9% by 5 years compared to patients aged <48 years of 3.8% by 5 years (p<0.001). Baseline ANC >0.87 x10 9/L (independent of age) predicted an even higher risk of evolution; CI for high-risk evolution was 17% by 5 years (p<0.001). Combined high ANC and older age (>48 years) were prognostic of the greatest risk of high-risk evolution, with a hazard ratio (HR) of 5.51; conversely, ANC <0.87 x10 9/L and age <48 years was protective, with HR 0.32. High-risk clonal evolution was not significantly increased by use of eltrombopag with IST versus IST only (p=0.3), but there was an increase when all clonal evolution was considered (p=0.02). Overall survival in high-risk evolution was 35% at 5 years and in low-risk evolution was 84% (p<0.001). Patients with high-risk evolution who underwent HSCT (n=26) had better OS compared to those treated with chemotherapy or supportive care (p=0.005).RUNX1 (13 variants in 8 [35%] patients) and ASXL1 (13 variants in 10 [43%] patients) were the most frequent mutated genes at time of clonal evolution in high-risk patients, and BCOR/L1 (14 variants in 8 [32%] patients) was the most frequently mutated in the low-risk group. Longitudinal data were available in five high-risk and eight low-risk patients. Three of five high-risk patients had acquisition or expansion of RUNX1 clones at evolution. Small RUNX1 variants were present in two patients as early as three years prior to high-risk evolution. Splicing factor genes and RUNX1 somatic variants were detected exclusively in the high-risk group; DNMT3A, BCOR/L1 and ASXL1 gene mutations were present in both groups.Conclusion: Age and pre-treatment ANC strongly predict high-risk clonal evolution in AA patients after IST and may be used determine at-risk patients for long term follow-up. Outcomes in patients with low-risk evolution are favorable but poor in high-risk evolution without HSCT. The clonal landscape differs between high-risk and low-risk evolution; MDS-associated genetic mutations are enriched in high-risk evolution, in particular RUNX1. Further study of the role of RUNX1 in high-risk clonal evolvers may give insight into leukemogenesis in AA.Figure 1: Cumulative incidence (CI) of clonal evolution since immunosuppression with death treated as competing risk. (A) CI for development of all clonal evolution in patients >37 years (B) and high-risk clonal evolution in patients >48 years (C) CI for development of all clonal evolution when baseline ANC >0.87x10 9/L and (D) high-risk clonal evolution when baseline ANC >0.87x10 9/L. [Display omitted] DisclosuresYoung: Novartis: Research Funding.

Clinical Correlates and Outcomes of Bone Marrow Failure and Myeloid Clonal Evolution in Patients with Germline GATA2 Haploinsufficiency

BackgroundGATA2 is a zinc finger transcription factor that plays a critical role in lymphatic development and hematopoiesis. Germline mutations in GATA2 are highly penetrant, resulting in an autosomal dominant spectrum of disorders characterized by familial MDS (myelodysplastic syndrome)/ AML (acute myeloid leukemia), B/NK/dendritic cell immunodeficiency, lymphedema, and HPV-driven warts (Mir, Cancer Medicine, 2015). Myeloid clonal evolution is seen in approximately 75% of individuals with GATA2 haploinsufficiency and is associated with the acquisition of somatic mutations. We conducted this study to assess clinical correlates and outcomes of bone marrow (BM) failure and myeloid clonal evolution in patients with germline GATA2 haploinsufficiency .MethodsSuccessive patients with germline GATA2 haploinsufficiency were identified from our institutional database. GATA2 mutations and deletions were confirmed using next generation (NGS) and Sanger sequencing (Mir, Cancer Medicine 2015). Time to clonal evolution was calculated from the time of earliest reported GATA2 -related clinical manifestation, to the development of clonal cytopenias of undetermined significance (CCUS), BM failure, or frank MDS/AML. In most patients, a myeloid relevant NGS panel was performed at the time of clonal evolution to identify the acquisition of somatic mutations. GVHD-free, relapse-free survival (GRFS) was calculated for hematopoietic stem cell transplant (HSCT) recipients (Holtan, Blood, 2015). Standard statistical measures were utilized.Clinical Features:Thirteen patients with GATA2 haploinsufficiency were identified, median age 31 years (range, 0.5 to 57), of which 39% (5) were male. Median follow-up time was 46.1 months. Seven individuals comprised a kinship with a c.1339A>C, p.S447R mutation in the C-terminal domain of GATA2 . Three individuals had mutations within the zinc-finger 2 (ZF2) domain, specifically c.1192C>T, p.R398W, c.1186C>G, p.R396G, and c.1187G>A, p.R396Q, which interfere with DNA binding (Chong, Leukemia, 2017). Three individuals had larger deletions of chromosome 3q involving GATA2 (Table 1, Figure 1). Of the 13 individuals, two were asymptomatic and without clinical manifestations (Table 1). The remaining individuals' earliest symptoms included recurrent infections or immunodeficiency (n=5), warts (n=3), and cytopenias (n=2), with 3 cases of MDS/AML at the time of diagnosis.Myeloid Clonal Evolution:Nine (69%) of 13 patients developed myeloid clonal evolution; CCUS -1, bone marrow failure - 2, MDS- 3, JAK2/CALR/MPL negative, accelerated myeloproliferation- 1, and AML - 2. Of the cases that did not present with clonal evolution, the median time to clonal evolution was approximately 144 months (range, 96 to 168) from the earliest manifestations of GATA2 haploinsufficiency. At the time of clonal evolution, NGS was performed in 6 out of 9 patients, with all 6 (100%) demonstrating truncating ASXL1 mutations. In the 2 AML patients, additional somatic mutations included; DNMT3A, ETV6, SRSF2, and SETBP1 . Karyotypic abnormalities were seen in 4 (44%) of 9 cases (table 1).Transplant Outcomes:Seven patients underwent allogeneic HSCT for MDS, AML, or refractory immunodeficiency; 5 with myeloablative and 2 with reduced-intensity conditioning. Two (29%) were from 9/10 HLA mismatched unrelated donors (M-MUD), 3 (43%) were from MUD, and 1 (14%) each was from a matched related donor and a haploidentical source, respectively. 86% developed acute GVHD, mostly grade I-II, with the exception of one patient who developed grade 4 GI GVHD resulting in death. Transplant outcomes were favorable, with a GFRS of 88.3% at one year, and a 3 year relapse free survival of 66.7%. The 6 patients who have not undergone HSCT are alive and are being closely observed, or are in the planning phase for HSCT (Table 1).ConclusionsGermline GATA2 haploinsufficiency is characterized by variable B/NK/dendritic cell immunodeficiency with an enhanced predisposition to myeloid neoplasms. Myeloid clonal evolution is seen >70% of cases, with almost all patients acquiring somatic truncating ASXL1 mutations at the time of evolution. In patients with AML, additional epigenetic regulator mutations are often seen. In our series, early allogeneic stem cell transplantation was associated with favorable outcomes. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A Moderate Increase in the WT1 mRNA Copy Number in Peripheral Blood of Patients with Long-Standing Acquired Aplastic Anemia without Apparent Signs of Myelodysplastic Syndrome

Background: The copy number of Wilms tumor 1 mRNA (WT1) correlates well with the acute myeloid leukemia (AML) cell burden and is being used as a reliable marker of residual AML cells. WT1 has also been shown to be useful for distinguishing high-risk myelodysplastic syndrome from low-risk myelodysplastic syndrome (MDS) as well as diagnosing disease progression with time in patients with low-risk MDS. However, few studies have so far focused on the role of measuring WT1 in diagnosing clonal evolution in patients with acquired aplastic anemia (AA). Although normal values of WT1 are defined as <50 copies/µgRNA, the reference values in AA patients without a propensity toward progression to MDS also remain unclear. To address these issues, we retrospectively studied 36 patients with bone marrow failure whose WT1 copy numbers in peripheral blood (PB) were serially measured to determine their correlation with the clinical picture and prognosis of the patients. Patients & Methods: PB samples of 36 patients (male/female, 19/17; a median age, 53.5 [range, 23-85] years) were subjected to WT1 measurement using a quantitative PCR method. The diagnoses of the patients were acquired AA in 29, MDS-multilineage dysplasia (MLD) evolved from AA in 4, and hemolytic paroxysmal nocturnal hemoglobinuria (PNH) in 3. Among 29 AA patients, 2 was untreated, and 22 were in convalescence while 5 were refractory after 0.5-457 months of immunosuppressive therapy (IST) and/or androgen therapy. WT1 was serially measured over time for all the patients except 5 whose initial examination produced negative (<50 copies/µgRNA) results. Myeloid malignancy-related gene abnormalities were screened in 11 patients showing an increase in the WT1 copy number. Results: WT1 at the initial examination was negative in 12 and positive in 17 (59%) patients with AA ranging from 59 to 520 copies. The 17 patients with increased WT1 had a disease duration of 122 months (11-495) but did not shown any signs of progression to MDS. The WT1 levels in patients possessing PNH-type cells (<50-330, median 62) were comparable to those without PNH-type cells (<67-520, median 89. There was a significant difference in the WT1 level between the 10 patients with a disease duration <3 years (<50-190, median <50) and the 19 patients with a disease duration ≥3 years (<50-520, median, 110, P=0.032). All 6 patients with WT1>200 had a disease duration ≥3 years. In contrast, the WT1 levels in the 4 patients who relapsed with cytopenia due to progression to MDS were as high as 690-5,700 (median, 2,400). Deep sequencing revealed somatic mutations of myeloid malignancy-related genes in 4 of 11 patients studied, which included EZH2 in an MDS patient (WT1 2,000), BCOR and DNMT3A in another MDS patient (WT1 2,800), and ASXL1 in a PNH patients (WT1 96). Conclusions: The WT1 copy numbers in PB of AA patients were higher than in AML patients with minimal residual diseases, and the cut-off value that helps diagnose MDS evolving from AA was considered to be around 600 copies. The high WT1 levels in long-standing AA patients without any signs of progression to MDS may represent an increased proliferative potential of hematopoietic stem/progenitor cells that support sustained hematopoiesis with their limited numbers. An increase in the WT1 copy number was associated with somatic mutations in some MDS patients but not in AA patients. Although AA patients with increased WT1 copy numbers need to be carefully followed, a moderate increase in the WT1 copy number does not portend myeloid malignancies unless the number steadily increases. DisclosuresIshiyama:Alexion Pharma GK: Research Funding.

Comprehensive CRISPR-Cas9 screens identify genetic determinants of drug responsiveness in multiple myeloma

The introduction of new drugs in the past years has substantially improved outcome in multiple myeloma (MM). However, the majority of patients eventually relapse and become resistant to one or multiple drugs. While the genetic landscape of relapsed/ resistant multiple myeloma has been elucidated, the causal relationship between relapse-specific gene mutations and the sensitivity to a given drug in MM has not systematically been evaluated. To determine the functional impact of gene mutations, we performed combined whole-exome sequencing (WES) of longitudinal patient samples with CRISPR-Cas9 drug resistance screens for lenalidomide, bortezomib, dexamethasone, and melphalan. WES of longitudinal samples from 16 MM patients identified a large number of mutations in each patient that were newly acquired or evolved from a small subclone (median 9, range 1-55), including recurrent mutations in TP53, DNAH5, and WSCD2. Focused CRISPR-Cas9 resistance screens against 170 relapse-specific mutations functionally linked 15 of them to drug resistance. These included cereblon E3 ligase complex members for lenalidomide, structural genes PCDHA5 and ANKMY2 for dexamethasone, RB1 and CDK2NC for bortezomib, and TP53 for melphalan. In contrast, inactivation of genes involved in the DNA damage repair pathway, including ATM, FANCA, RAD54B, and BRCC3, enhanced susceptibility to cytotoxic chemotherapy. Resistance patterns were highly drug specific with low overlap and highly correlated with the treatment-dependent clonal evolution in patients. The functional association of specific genetic alterations with drug sensitivity will help to personalize treatment of MM in the future.

Clonal evolution of acute myeloid leukemia with FLT3-ITD mutation under treatment with midostaurin

In the international randomized phase 3 RATIFY (Randomized AML Trial In FLT3 in patients less than 60 Years old) trial, the multikinase inhibitor midostaurin significantly improved overall and event-free survival in patients 18 to 59 years of age with FLT3-mutated acute myeloid leukemia (AML). However, only 59% of patients in the midostaurin arm achieved protocol-specified complete remission (CR), and almost half of patients achieving CR relapsed. To explore underlying mechanisms of resistance, we studied patterns of clonal evolution in patients with FLT3-internal tandem duplications (ITD)-positive AML who were entered in the RATIFY or German-Austrian Acute Myeloid Leukemia Study Group 16-10 trial and received treatment with midostaurin. To this end, paired samples from 54 patients obtained at time of diagnosis and at time of either relapsed or refractory disease were analyzed using conventional Genescan-based testing for FLT3-ITD and whole exome sequencing. At the time of disease resistance or progression, almost half of the patients (46%) became FLT3-ITD negative but acquired mutations in signaling pathways (eg, MAPK), thereby providing a new proliferative advantage. In cases with FLT3-ITD persistence, the selection of resistant ITD clones was found in 11% as potential drivers of disease. In 32% of cases, no FLT3-ITD mutational change was observed, suggesting either resistance mechanisms bypassing FLT3 inhibition or loss of midostaurin inhibitory activity because of inadequate drug levels. In summary, our study provides novel insights into the clonal evolution and resistance mechanisms of FLT3-ITD–mutated AML under treatment with midostaurin in combination with intensive chemotherapy.

Next-generation sequencing reveals gene mutations landscape and clonal evolution in patients with acute myeloid leukemia

ABSTRACT Objectives The study aims to understand geneome diversification and complexity that developed in Acute myeloid leukemia (AML). Methods Next-generation sequencing (NGS) was used to identify the genetic profiles of 22 genes relevant to hematological malignancy in 204 patients with de novo non-M3 AML. Results At time of initial diagnosis, at least one mutation was identified in 80.9% of patients (165/204). The most commonly mutated gene was NPM1 (22.1%), followed by ASXL1 (18.1%), TET2 (18.1%), IDH2 (15.7%), CEBPA (14.7%), FLT3-ITD (13.2%) and DNMT3A (11.8%). Mutations landscape analysis indicated several patterns of co-occurring and mutual exclusive gene mutations. Some correlation was observed between gene mutations and clinicohematological features. Multivariate analysis showed that age >60 years, karyotypes, IDH2 and KIT mutations were the independent unfavorable prognostic factors for OS; NPM1-mut/ FLT3-ITD-wt was independently correlated with prolonged OS; whereas the independent poor risk factors for RFS were karyotypes, high WBC and RUNX1 mutation. According to different genotype demonstrated by multivariate analysis, 163 patients with intermediate-risk cytogenetics were classified into three subgroups: patients with NPM1-mut/ FLT3-ITD-wt or biallelic CEBPA mutation as favorable risk, patients with KIT, IDH2, TP53 or NRAS mutations as unfavorable risk, and the remaining was the intermediate risk. We also obtain information of clonal evolution during leukemia progression by observing five patients who underwent repeat NGS at relapse in our cohort. Conclusion NGS techniques is a useful tool for discovering related gene mutations and clonal evolution in AML genomes, leading to novel targeted therapeutic approaches that could improve patients outcomes.

Cytogenetic Clonal Evolution in Myeloproliferative Neoplasms: Contexts and Prognostic Impact Among 650 Patients with Serial Bone Marrow Biopsies

Background:Cytogenetic abnormalities occur in approximately a third of patients with primary myelofibrosis (PMF) and 5-20% of those with essential thrombocythemia (ET) or polycythemia vera (PV). Abnormal karyotype in PV and specific cytogenetic abnormalities in PMF have been shown to adversely affect survival (Leukemia. 2018;32:1189; Br J Haematol. 2017 Jun 9. doi: 10.1111/bjh.14798). In the current retrospective study, we considered 650 Mayo Clinic patients with myeloproliferative neoplasms (MPN), including ET, PV and PMF, with at least two documented bone marrow (BM) biopsies, in order to examine the incidence and pattern of changes in karyotype and their clinical correlates.Methods:Study patients were recruited from the Mayo Clinic, Rochester, MN, USA, based on documentation of at least two serial BM biopsies. Diagnoses were according to the 2016 World Health Organization criteria (Blood. 2016;127:2391). BM biopsy #1 referred to the baseline karyotype at time of initial diagnosis/referral and BM biopsy #2 to the first repeat BM biopsy after diagnosis. In addition to documenting the presence or absence of changes in karyotype, a notation was made regarding disease phase, at the time of the repeat biopsy, in order to allow accurate interpretation of the data and evaluation of survival impact.Results:650 patients with MPN, including 153 ET, 105 PV and 392 PMF, were included in the current study and had undergone at least two BM biopsies; 227 patients had three, 108 four, 48 five, 19 six, and 4 seven repeat BM biopsies during their clinical course.Cytogenetic clonal evolution in patients with normal karyotype at baseline:Baseline karyotype was normal in 466 (72%) patients, including 139 (91%) ET, 91 (87%) PV and 236 (60%) PMF. Clonal evolution, which constituted a change from “normal” to “abnormal” karyotype, was documented in 16 (12%) patients with ET, 22 (24%) with PV and 75 (33%) with PMF; the latter included favorable karyotype in 11% of the cases, unfavorable in 12% and very high risk (VHR) in 10%. 11 (69%) of the 16 documented cases of clonal evolution in ET, 10 (45%) of 22 in PV and 11 (15%) of 75 in PMF were accompanied by clinically evident progression to blast or fibrotic phase disease, at the time of the repeat BM biopsy.Cytogenetic clonal evolution in patients with abnormal karyotype at baseline:Baseline karyotype was abnormal in 187 (28%) patients, including 17 (9%) ET, 14 (13%) PV and 156 (40%) PMF. Additional changes in karyotype, during serial BM biopsies, were documented in 6 (35%) ET, 5 (36%) PV and 71 (46%) PMF patients. In PMF, the pattern of changes in karyotype included “favorable” to “favorable” in 7%; “favorable” to “unfavorable” in 13%; “favorable” to “VHR” in 5%; “unfavorable” to “unfavorable” in 13%; “unfavorable” to “VHR” in 3%; and “VHR” to “VHR” in 6%. All 11 (100%) patients with ET or PV who underwent clonal evolution displayed clinically overt disease transformation into leukemic or fibrotic phase disease, at the time of the repeat BM biopsy. Leukemic transformation at the time of the repeat BM biopsy was evident in 13 (18%) of the 71 PMF cases with clonal evolution.Survival impact of cytogenetic clonal evolution without change in disease phase:The survival impact of cytogenetic clonal evolution was examined under the following provisions: i) analysis was limited to events occurring at BM biopsy #2 with survival calculated from the date of BM biopsy #2; ii) patients with leukemic or fibrotic transformation at time of BM biopsy #2 were excluded from analysis; and iii) clonal evolution for the purposes of survival analysis constituted changes from “normal” to “abnormal”, for ET and PV, while the type of changes were taken under consideration for PMF. Under these stipulations, clonal evolution appeared to affect survival in general, although statistical significance was apparent for only ET and PMF (Figures 1a, 1b and 1c).Conclusions: Cytogenetic clonal evolution in ET and PV is infrequent, in the absence of clinically overt disease transformation, and is more likely to occur in PMF. Such events, when documented in chronic phase disease, appeared to predict shortened survival in all three MPNs, which was most apparent in ET and with emergence of VHR or unfavorable abnormalities in PMF. These observations warrant prospective studies that account for indication bias. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Circulating tumor DNA reveals genetics, clonal evolution, and residual disease in classical Hodgkin lymphoma

AbstractThe rarity of neoplastic cells in the biopsy imposes major technical hurdles that have so far limited genomic studies in classical Hodgkin lymphoma (cHL). By using a highly sensitive and robust deep next-generation sequencing approach for circulating tumor DNA (ctDNA), we aimed to identify the genetics of cHL in different clinical phases, as well as its modifications on treatment. The analysis was based on specimens collected from 80 newly diagnosed and 32 refractory patients with cHL, including longitudinal samples collected under ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) chemotherapy and longitudinal samples from relapsing patients treated with chemotherapy and immunotherapy. ctDNA mirrored Hodgkin and Reed-Sternberg cell genetics, thus establishing ctDNA as an easily accessible source of tumor DNA for cHL genotyping. By identifying STAT6 as the most frequently mutated gene in ∼40% of cases, we refined the current knowledge of cHL genetics. Longitudinal ctDNA profiling identified treatment-dependent patterns of clonal evolution in patients relapsing after chemotherapy and patients maintained in partial remission under immunotherapy. By measuring ctDNA changes during therapy, we propose ctDNA as a radiation-free tool to track residual disease that may integrate positron emission tomography imaging for the early identification of chemorefractory patients with cHL. Collectively, our results provide the proof of concept that ctDNA may serve as a novel precision medicine biomarker in cHL.

Monitoring of clonal evolution of double C-KIT exon 17 mutations by Droplet Digital PCR in patients with core-binding factor acute myeloid leukemia

C-KIT gene mutations result in the constitutive activation of tyrosine kinase activity, and greatly affect the pathogenesis and prognosis of core-binding factor acute myeloid leukemia (CBF-AML). C-KIT mutations are often found as single point mutations. However, the rate of double mutations has recently increased in AML patients. In this study, we detected six cases (18.8%) harboring double C-KIT exon17 mutations in 75 patients with CBF-AML. The clone composition and dynamic evolution were analyzed by sequencing and droplet digital PCR (ddPCR). Results revealed that these double mutations can be occurred in either the same or different clones. Different clones of double mutations may result in different sensitivity to the treatment of CBF-AML. The clones with N822 mutation responded better to treatment as compared to those with D816 mutation. Moreover, D816 clone was readily transformed into a predominant clone at relapse. Meanwhile, the predominant clones in the same patient may change during the progression of disease. The emerging mutation can originate from a small quantity of clones at diagnosis or newly acquired during the course of disease. Furthermore, patients with double mutations had better overall survival (OS) and event-free survival (EFS) than those with single mutation, but the differences did not reach statistical significance (P > 0.05). The ddPCR is an effective method for monitoring clonal evolution in patients with CBF-AML.