ETV6 Mutations Research Articles

Testicular large B-cell lymphoma is genetically similar to PCNSL and distinct from nodal DLBCL.

Testicular large B-cell lymphoma (TLBCL) is an infrequent and aggressive lymphoma arising in an immune-privileged site and has recently been recognized as a distinct entity from diffuse large B-cell lymphoma (DLBCL). We describe the genetic features of TLBCL and compare them with published series of nodal DLBCL and primary large B-cell lymphomas of the CNS (PCNSL). We collected 61 patients with TLBCL. We performed targeted next-generation sequencing, copy number arrays, and fluorescent in situ hybridization to assess chromosomal rearrangements in 40 cases with available material. Seventy percent of the cases showed localized stages. BCL6 rearrangements were detected in 36% of cases, and no concomitant BCL2 and MYC rearrangements were found. TLBCL had fewer copy number alterations (p < 0.04) but more somatic variants (p < 0.02) than nodal DLBCL and had more frequent 18q21.32-q23 (BCL2) gains and 6q and 9p21.3 (CDKN2A/B) deletions. PIM1, MYD88 L265P , CD79B, TBL1XR1, MEF2B, CIITA, EP300, and ETV6 mutations were more frequent in TLBCL, and BCL10 mutations in nodal DLBCL. There were no major genetic differences between TLBCL and PCNSL. Localized or disseminated TLBCL displayed similar genomic profiles. Using LymphGen, the majority of cases were classified as MCD. However, we observed a subgroup of patients classified as BN2, both in localized and disseminated TLBCL, suggesting a degree of genetic heterogeneity in the TLBCL genetic profile. TLBCL has a distinctive genetic profile similar to PCNSL, supporting its recognition as a separate entity from DLBCL and might provide information to devise targeted therapeutic approaches.

Molecular Analysis of Renal/Adrenal Angiosarcomas Reveals High Frequency of Recurrent Genetic Alterations.

Angiosarcomas of the kidney and adrenal gland are rare, highly aggressive vascular neoplasms. Their genomic profile has not been systematically studied to date. We report the clinicopathologic and molecular features of six angiosarcomas centered in the kidney/adrenal gland. All patients were male adults, ranging from 58 to 77 years of age. Tumor sizes ranged from 2.5 to 22.5 cm. Half of the cases demonstrated hot spot mutations in the KDR gene, while one-third demonstrated mutations in the PIK3CA gene; both of these gene alterations being previously described, preferentially in breast angiosarcomas. In addition, two cases each demonstrated BRIP1 gene amplification, CTNNB1 and ETV6 mutations, which have not been previously reported in angiosarcoma. Notably, molecular studies were critical in establishing the correct diagnoses in three cases: one was an epithelioid angiosarcoma originally misdiagnosed as metastatic adenocarcinoma to the adrenal gland, the second was a vasoformative angiosarcoma that mimicked hemangioma, and the third was a collision tumor between a high-grade angiosarcoma and a chromophobe renal cell carcinoma which was originally diagnosed as a sarcomatoid renal cell carcinoma. In summary, angiosarcomas of the kidney and adrenal gland have a high frequency of recurrent genetic alterations, some of them being shared with other angiosarcoma subtypes, while other appear to be novel. In particular, activating hot spot KDR and PIK3CA mutations represent potential therapeutic targets for these highly aggressive cancers.

The Diverse Roles of ETV6 Alterations in B-Lymphoblastic Leukemia and Other Hematopoietic Cancers.

Genetic alterations of the repressive ETS family transcription factor gene ETV6 are recurrent in several categories of hematopoietic malignancy, including subsets of B-cell and T-cell acute lymphoblastic leukemias (B-ALL and T-ALL), myeloid neoplasms, and mature B-cell lymphomas. ETV6 is essential for adult hematopoietic stem cells (HSCs), contributes to specific functions of some mature immune cells, and plays a key role in thrombopoiesis as demonstrated by familial ETV6 mutations associated with thrombocytopenia and predisposition to hematopoietic cancers, particularly B-ALL. ETV6 appears to have a tumor suppressor role in several hematopoietic lineages, as demonstrated by recurrent somatic loss-of-function (LoF) and putative dominant-negative alterations in leukemias and lymphomas. ETV6 rearrangements contribute to recurrent fusion oncogenes such as the B-ALL-associated transcription factor (TF) fusions ETV6::RUNX1 and PAX5::ETV6, rare drivers such as ETV6::NCOA6, and a spectrum of tyrosine kinase gene fusions encoding hyperactive signaling proteins that self-associate via the ETV6 N-terminal pointed domain. Another subset of recurrent rearrangements involving the ETV6 gene locus appear to function primarily to drive overexpression of the partner gene. This review surveys what is known about the biochemical and genome regulatory properties of ETV6 as well as our current understanding of how alterations in these functions contribute to hematopoietic and nonhematopoietic cancers.

Genomic Correlates of Radiosensitivity in Diffuse Large B Cell Lymphoma

Introduction Radiotherapy (RT) is beneficial for select patients with localized diffuse large B cell lymphoma (DLBCL), in both the early stage and relapsed/refractory settings. Although molecular subtyping plays a key role in classification of DLBCL, genomic predictors of local response to RT have yet to be adequately explored. To our knowledge, there are no existing studies investigating the genomic landscape of DLBCL patients treated with RT. Therefore, we sought to identify genomic signatures of radiosensitivity in localized DLBCL patients. Methods We analyzed an institutional database of DLBCL patients treated with RT for localized measurable disease treated between 2007-2022. All patients underwent next-generation sequencing using an institutional 505-gene panel (MSK-Impact). Clinical and radiographic characteristics were obtained from chart and imaging review. All patients had measurable disease on CT scan at time of RT and included both Ann Arbor stage I/II patients referred for consolidative radiotherapy and those with isolated sites of relapsed/refractory disease. Patients did not receive any systemic therapy between RT start and time of response assessment. The public NCI LymphGen algorithm was used to further classify genomic subgroups. Using Fisher's exact test and logistic regression, we tested for univariable correlation between specific gene alterations and LymphGen subgroups with initial radiation response, defined by Lugano criteria and decrease in maximum SUV. Results We identified 46 patients including 15 (33%) tumors treated in the early-stage setting (13% definitively without prior chemotherapy, 87% as consolidation), while 31 (60%) were treated in the localized relapsed/refractory setting. The majority were GCB subtype (57%) while 28% were non-GCB and 15% had missing immunohistochemistry data. The median number of prior lines of systemic therapy was 1 (0-2) in early stage and 1 (1-7) in localized relapsed/refractory diseases. The median RT dose was 36 Gy (4-54), with 38 (83%) tumors receiving at least 30Gy. The median lesion SUV at the time of RT was 4.11 (1.1-46.0). Complete response (CR) was achieved in 41% of tumors at the time of first imaging assessment (median 3.1 months) with a median of 90.3% (42-100%) decrease in SUV. The most commonly altered individual genes were KMT2D (35%), MYD88 (28%), and TP53 (35%). LymphGen classified 22% of cases as EZB subtype, 13% as MCD, 2% as BN2, 2% as ST2, and the remaining 61% were unclassified. Mutations in ETV6 (13% of tumors) were associated with a higher CR rate in response to RT (83% mutated vs 35% wildtype, p=0.068). Lesions from ETV6 mutated cases had similar SUVs (p=0.74) and sizes (p=0.92) as wildtype cases. Alterations in genes from the LymphGen MCD subgroup were associated with greater reductions in SUV (ETV6 p&amp;lt;0.0001, PIM1 p&amp;lt;0.0001, MYD88 p&amp;lt;0.001, and TNFAIP3 p=0.02) The MCD subgroup trended towards increased odds of CR post-RT (log odds 1.9, p=0.08) and greater reduction of SUV (p=0.07) compared to the EZB subgroup. Conclusions To our knowledge this is the first study evaluating the role of LymphGen subgrouping on radiotherapy response, and the first study to examine genomic alterations in DLBCL patients treated with radiation. Genomic biomarkers of radiosensitivity are needed to identify radioresponsive tumors which may benefit from better integration of RT into existing salvage paradigms such as CAR T cells. Our data suggest that alterations in MCD LymphGen subgroup genes (ETV6, PIM1, MYD88, TNFAIP3) may be associated with better response to radiotherapy. ETV6 is a strong hematopoietic transcription factor known to be altered in many human leukemias and myelodysplastic syndromes. Its role in DLBCL is not well defined, with preclinical studies suggesting a distinct role compared to leukemias. Due to the limited sample size, these findings are hypothesis generating and warrant further study with larger, prospective cohorts to validate the ability of genomic signatures to predict RT response.

Familial Thrombocytopenia-Associated Germline ETV6 P214L Mutation Results in XPO1-Mediated Nuclear Export

In recent years, a number of heterozygous germline mutations in ETV6 have been associated with familial thrombocytopenia and predisposition to hematologic malignancies. While most of these missense mutations occur in the DNA-binding-domain of ETV6, the recurrent P214L mutation is unique in that it occurs in the central disordered region of the protein. The ETV6 P214L mutation has previously been shown to disrupt the nuclear localization of ETV6 and the ability of ETV6 to act as a transcriptional repressor. Unexpectedly, we have found that the P214L missense mutation creates a recognition motif for the nuclear export protein XPO1. We have demonstrated in cellular and protein reconstitution assays that XPO1 directly engages the P214L but not the wild-type ETV6 construct. Consistent with this mechanism, we are able to fully rescue the nuclear localization of ETV6 P214L in mammalian cells with small molecule XPO1 inhibitors. We have also found that once localized to the nucleus, the P214L mutant construct exhibits functional consequences indistinguishable from wild-type ETV6 in Ba/F3 transformation assays. When looking at the evolutionary conservation of the ETV6 amino acid sequence involved in the XPO1 recognition motif, we observed that the synonymous P216L mutation in the mouse ETV6 ortholog does not create a nuclear export signal. In order to study XPO1-mediated export of ETV6 P214L and its impact on hematopoiesis, we have generated a mouse model in which two point mutations (P216L and S211I) have been introduced into a single endogenous ETV6 allele, which precisely matches the sequence of this region in human P214L carriers. Using CRISPR-Cas9, we generated 3 transgenic mouse lines: Etv6 P216L, Etv6 S211I, and Etv6 S211IP216L. Immunofluorescence of fixed bone marrow shows that ETV6 is only mislocalized in megakaryocytes from ETV6 S211I P216L mice. Complete blood counts revealed a significant decrease in platelet counts in ETV6 S211I P216L heterozygotes (485 x 10 3/µL) compared to ETV6 S211I heterozygotes (1140 x 10 3/µL, p&amp;lt;0.0001), ETV6 P216L heterozygotes (1065 x 10 3/µL, p&amp;lt;0.0006), and wild-type littermates (1254 x 10 3/µL, p&amp;lt;0.0001). Flow cytometry phenotyping of bone marrow from the three transgenic lines and wild-type littermates shows a significant decrease in the absolute numbers of hematopoietic stem cells (HSCs) and megakaryocyte precursors (MkPs) in ETV6 S211I P216L mice. In summary, we have determined that XPO1-mediated nuclear export is the mechanistic basis for ETV6 P214L mislocalization. We developed a mouse model that recapitulates this export signal in the endogenous ETV6 allele and found that this model demonstrates a thrombocytopenic phenotype as seen in human patients. Reductions in HSCs and MkPs suggest both a decreased fitness of HSCs, as well as dysregulated megakaryopoiesis in this model.

Impact of Mutational Status on Clinical Response to Imetelstat in Patients with Lower-Risk Myelodysplastic Syndromes in the IMerge Phase 3 Study

CONCLUSIONS Imetelstat, a first-in-class telomerase inhibitor, showed higher rates of red blood cell (RBC) transfusion independence (TI) for ≥8 weeks, ≥24 weeks, and ≥1 year (39.8%, 28.0%, and 17.8%) than placebo (15.0%, 3.3%, and 1.7%) in the IMerge (NCT02598661) phase 3 study of patients with RBC transfusion-dependent non-del(5q) lower-risk myelodysplastic syndromes (LR-MDS) relapsed/refractory to erythropoiesis-stimulating agents (Platzbecker et al. EHA 2023. Abstr S165). To evaluate the impact of MDS-associated mutations on clinical efficacy of imetelstat, we performed next-generation sequencing of a panel of 36 genes, recurrently mutated in MDS, using DNA samples from peripheral blood collected at study entry. Further analysis of TI responses to imetelstat was performed across different mutation subgroups, defined based on genes involved in different biological functions, including the splicing process, epigenetic modifiers, transcription regulation, and receptors/kinases. Baseline mutation data were available in 165 of 178 patients (imetelstat, n = 110; placebo, n = 55; 93.2% and 91.7% of total in each group, respectively). Of patients with mutation data, 161 (97.6%) had ≥1 mutation detected, among whom, 75 (70.1%), 33 (30.8%), and 9 (8.4%) patients in the imetelstat group and 38 (70.4%), 15 (27.8%), and 7 (13%) patients in the placebo group had &amp;gt;1, &amp;gt;2, and &amp;gt;3 mutations, respectively. The ≥8-week TI rates in the imetelstat vs placebo groups were 42.7% vs 15.8% ( P = .006) for patients with &amp;gt;1 mutation, 45.5% vs 6.7% ( P = .012) for patients with &amp;gt;2 mutations, and 55.6% vs 14.3% ( P = .089) for patients with &amp;gt;3 mutations, respectively. The ≥24-week TI rates were 26.7% vs 2.6% ( P = .003), 33.3% vs 0% ( P = .014), and 33.3% vs 0% ( P = .117), respectively. In patients with mutations associated with poor prognosis ( TP53, ETV6, RUNX1, ASXL1 or EZH2), 31.8% and 9.1% of patients in the imetelstat group achieved ≥8-week and ≥24-week TI vs 0 of those in the placebo group. TP53 mutations were detected in 2 patients in each group; both patients in the imetelstat group and none in the placebo group had ≥8-week TI. Among patients with ASXL1 mutations, 5 of 18 patients (27.8%) in the imetelstat and 0 of 6 (0) in placebo group had ≥8-week TI. Among patients with ETV6 mutations, 1 of 2 (50%) in the imetelstat group and 0 of 1 patients in the placebo group had ≥8-week TI. Two patients in each group had RUNX1 mutations; none achieved TI. Imetelstat ≥8-week TI rates were 43.8%, 37.7%, 40.0%, and 80.0% for patients harboring mutated genes in the RNA spliceosome, epigenetic modifiers, transcription regulation, and receptors/kinases, respectively; ≥24-week TI was 30.2%, 27.5%, 20.0%, and 80.0%, respectively. The most frequently mutated gene was SF3B1 (125 of 165; 75.8%), the ≥8-week and ≥24-week TI rates were 48.8% vs 16.3% ( P = .001) and 35.4% vs 2.3% ( P &amp;lt; .001) with imetelstat vs placebo. In the imetelstat group, ≥8-week TI was achieved in patients with different spectrum of SF3B1 hot-spot mutations: 2 of 8 patients (25.0%) with E622D, 4 of 7 (57.1%) with R625C/L/G, 7 of 12 (58.3%) with H662Q/N/D/Y, 2 of 2 (100%) with T663P, 2 of 6 (33.3%) with K666R/T/Q/N, 18 of 41 (43.9%) with K700E, 2 of 2 (100%) with A744P, and 1 of 2 patients (50.0%) with E783K. Durable ≥24-week TI was also observed in patients with these hot-spot mutations. Other genes with mutation frequency &amp;gt;10% were TET2 (32.7%), DNMT3A (17.0%), ASXL1 (14.5%), and CUX1 (12.7%). The ≥8-week TI rates in the imetelstat group vs placebo group were 50% vs 21.4% for TET2 mutations; 31.6% vs 22.2% for DNMT3A mutations; 27.8% vs 0 for ASXL1 mutations; 35.7% vs 14.3% for CUX1 mutations (Figure). The ≥24-week TI rates were 40% vs 0, 26.3% vs 11.1%, 11.1% vs 0, and 14.3% vs 0, respectively, for those mutations (Figure). Higher RBC-TI rates were observed in patients with various baseline mutational profiles treated with imetelstat compared with placebo in IMerge. While the sample size for specific mutations was small, consistent with the observation that patients with LR-MDS have a low number of specific mutations, TI responses in patients receiving imetelstat occurred regardless of the presence of mutations associated with poor prognosis or the number of mutations. Imetelstat showed comparable TI rates across different molecularly defined subgroups, suggesting that clinical benefit of imetelstat in patients with LR-MDS is independent of the underlying molecular pattern.

Clonal Evolution of Der(1;7)(q10;p10) Myeloid Neoplasms

Background der(1;7)(q10;p10) (der(1;7)) is a recurrent unbalanced translocation found in 1.5~6% of MDS and AML patients. It is caused by rearrangement of centromere alpha satellites in chromosomes 1 and 7 resulting in an amplification of 1q and a deletion of 7q. Previous studies comparing der(1;7)(+) cases to those with other lesions of 7q loss (-7/del(7q)) demonstrated a higher frequency of RUNX1 mutations, no TP53 mutations and a better prognosis for der(1;7) cases suggesting that der(1;7)(+) may define a unique entity of myeloid neoplasms (MN). However, with the lack of comprehensive molecular characterization using unbiased platforms such as whole genome/exome sequencing, the entire picture of der(1;7)(+) MN still remains unclear. Methods We enrolled a total of 148 MN cases harboring der(1;7) and an additional 3,238 der(1;7)(−) MN cases: -7/del(7q), +1q and ‘OTHER’. We first analyzed paired tumor/normal DNA from 26 der(1;7) cases using whole exome sequencing (WES), followed by targeted-capture sequencing of 329 genes, including those commonly mutated in MN and others newly identified in der(1;7) cases in WES. To investigate the origin of der(1;7)(+) MN, we also enrolled 11,234 healthy individuals to evaluate der(1;7) in clonal hematopoiesis, in which der(1;7) was detected on based on SNP array-based karyotyping. Results In accordance with previous reports, der(1;7) MDS cases showed an improved overall survival (OS) compared to -7/del(7q) MDS cases (Hazard Ratio (HR) =0.71, p=0.098), which however, was shorter than OS in +1q (HR=1.36, p=0.11) and ‘OTHER’ (HR=1.8, p&amp;lt;0.001) MDS cases. der(1;7)(+) cases were characterized by very high mortality from infection (45.5%), while mortality from disease progression was less common (36.4%), showing a sharp contrast to -7/del(7q) and ‘OTHER’ MDS cases which had 13.9% and 10.8% infection-related deaths, and 72.3% and 76.9% disease progression, respectively (Figure 1A.). WES in 26 der(1;7)(+) cases revealed a novel transcription factor, MYB in 2 cases, which was found in 18 (12%) of 148 der(1;7) cases using targeted-capture sequencing. der(1;7)(+) cases were characterized by high frequency of mutations in transcription factors, including RUNX1 (37.8%), GATA2 (12%), ETV6 (13%), and BCOR (14%) (Figure 1B.), which were significantly more frequent in der(1;7) cases than other sub-types (Odds Ratio (OR)&amp;lt;6)(Figure 1B.). Very high frequency of ETNK1 mutations is highly unique to der(1;7)(+) cases (18.9%) compared to that in other cases (&amp;lt;10%). High frequency of mutations in transcription factors seems to be a unique feature of der(1;7)(+) cases. Trisomy 8 and del(20q) CNAs were also common in der(1;7) cases (16% and 21%, respectively). Together with DNMT3A and del(20q), der(1;7) showed the highest variant allele frequency (VAF), suggesting the early origin of these lesions. Additionally, we identified der(1;7) in 6 out of 11,234 healthy individuals using SNP array-based highly sensitive copy number detection, of which 4 died from MDS, suggesting that der(1;7)(+) clonal hematopoiesis might be the origin of MDS in these cases. Moreover, we also analyzed longitudinal samples from 9 der(1;7)(+) cases using duplex-sequencing, der(1;7) showed consistently high VAF, further supporting that der(1;7) tended to represent the major clone. Conclusion Showing a unique set of co-mutation pattern and clinical features, der(1;7) MN defines a distinct subset of myeloid neoplasms, which may originate from der(1;7)(+) clonal hematopoiesis. der(1;7)(+) patients were at higher risk of life-threatening infection, which needs to be carefully prevented and monitored during their clinical course.

TL-895, a Highly Selective, Covalent Inhibitor of Bruton's Tyrosine Kinase (BTK), Sensitizes Myeloproliferative Neoplasm (MPN)-Blast Phase Stem Cells to Navtemadlin By Targeting Intrinsic Dysregulated MDM2/p53 and NF-Κb Pathways and Disrupting the Protective Tumor Microenvironment (TME)

We recently reported that navtemadlin (nvtm), a potent, orally available, selective inhibitor of MDM2 (MDM2i), can deplete/eliminate TP53WT MPN-blast phase (BP) stem cells (SC) in an MPN-BP patient (pt)-derived xenograft (PDX) model (Wang EHA 2023). Single agent nvtm has demonstrated significant clinical activity in pts with advanced myelofibrosis (MF) (Vachhani EHA 2023, Verstovsek Future Oncology 2022). We hypothesized that effects of nvtm on MPN-BP, which is characterized by multiple SC subclones, could be enhanced by combination with agents that target additional MPN-BP SC vulnerabilities, such as hyperactivation of p65 subunit of NF-κB (Fisher Leukemia 2017; our unpublished data) and dependence on TME support. BTK and bone marrow (BM) kinase X-linked (BMX) are key Tec family members expressed in cells of myeloid origin. Here, we show BTK is constitutively activated in MPN-BP SC subpopulations relative to normal donor (ND) hematopoietic SCs (HSC) and progenitors [phospho (p)-BTK Y233 mean fluorescence intensity fold change (FC)]: CD34 +CD38 - cells: 1.34±0.18, HSC/multipotent progenitor (MPP): 1.50±0.23, multi-lymphoid progenitor (MLP): 1.59±0.59, megakaryocyte-erythroid progenitor (MEP): 1.56±0.49; p &amp;lt;0.05]. TL-895 is a highly selective, potent, orally available, second-generation covalent inhibitor of BTK and BMX, currently under clinical evaluation for treatment of pts with CLL (NCT02825836) and MF (NCT04655118). We used multi-modal single-cell analysis to study mechanistic effects of combination TL-895 + nvtm on dysregulated intracellular signaling pathways in primary MPN-BP SC, and investigated the combination in a PDX model of MPN-BP. In vitro treatment with TL-895 alone (100 nM-5 µM) did not affect growth of ND CD34 + cells [FC (TL-895 vs. vehicle, veh): 2.5 µM: 1.27±0.11, 5 µM: 0.97±0.14, n=3)] but modestly decreased growth of primary TP53WT MPN-BP CD34 + cells, in a dose dependent fashion [FC (TL-895 vs. veh): 2.5 µM: 0.88±0.11, 5 µM: 0.62±0.12, n=4. p&amp;lt;0.05). Addition of TL-895 (5 µM) to nvtm (400 nM) resulted in much greater reductions in MPN-BP CD34 + and CD34 +CD38 - cell numbers, along with increased apoptosis (n=6, p&amp;lt;0.05, TL-895 + nvtm vs. veh, TL-895, or nvtm alone). By contrast, at these doses, combination TL-895 + nvtm did not affect ND HSC subpopulations (n=3). We previously demonstrated that, multiple MPN-BP SC subclones contribute to the development of MPN-BP irrespective of clone size, and minor subclones may be responsible for clonal evolution and disease progression in most cases (Wang JCI insight 2022). Strikingly, single cell mutational profiling and epitope analysis of primary MPN-BP CD34 + cells treated with TL-895 + nvtm showed depletion of all 8 distinct MPN-BP SC subclones with differing variant allele frequencies, each containing 2-3 oncogenic mutations in WT1, ETV6 and/or KRAS. Combination TL-895 + nvtm treatment depleted 7 of 8 subclones to a greater degree than either agent alone (Fig. 1). Bulk RNA-seq and gene set enrichment analysis showed that combination TL-895 + nvtm synergistically upregulated p53 pathway gene transcription ( CDKN1 HDM2, DDB2, BTG2, GADD45A, FAS, FUCA1, S100A10, ATF3) in primary MPN-BP CD34 + cells. Mass cytometry analysis and intracellular flow cytometry of MPN-BP CD34 + cells treated with combination TL-895 + nvtm further revealed significant (p&amp;lt;0.05) upregulation of p53 and BAX proteins and decreases in the anti-apoptotic factors BCL-xL and activated NF-κB (p-p65), as well as significant reductions in DNA synthesis and protein markers associated with glycolysis (p-AMPK, MCT1). Downregulation of NF-κB activation might result from decreases in the upstream modulators p-S6 and p-4EBP1 (p&amp;lt;0.05, TL-895 + nvtm vs. veh). Treatment in vivo withTL-895 promoted dose-dependent egress of hCD45 +CD34 + cells from BM into the spleen and peripheral blood (PB) of MPN-BP PDX mice (Fig. 2). Furthermore, a limited course of combination TL-895 + nvtm treatment for 3 cycles led to clearance of hCD45 +CD34 + cells from the BM, spleen and PB of MPN-BP PDX mice (Fig. 2); neither treatment had this effect when administered alone. Our results indicate that BTKi therapy might increase susceptibility of MPN-BP SC to MDM2i therapy, by upregulating p53 activity and dampening NF-κB signaling, and also by disrupting protective TME interactions that sustain MPN-BP SC. This novel combination merits further clinical investigation in advanced phase MPN.

In Vivo Modeling of T-Cell Acute Lymphoblastic Leukemia Reveals Synergistic Oncogenic Pathways and Bcl11b Haploinsufficiency As a Potential Therapeutic Vulnerability

For decades, T-ALL models were based on retroviral overexpression of NOTCH1 in murine hematopoietic stem cells (HSCs). This induces aggressive T-ALL but does not reflect the genetic and clinical heterogeneity of the disease. Large-scale genomic analyses have mapped the detailed landscape of T-ALL driver events over recent years, but how these diverse oncogenic events interact in T-ALL pathogenesis and which vulnerabilities this creates remains incompletely explored. This is in part due to the lack of appropriate mouse models that recapitulate the complex disease biology and are suitable to identify and study potential therapeutic targets and interventions in a more realistic context. We modeled the genetic heterogeneity of T-ALL through in vivo multiplexing of gain-of-function and loss-of-function oncogenic events known to drive the disease. We developed a novel mouse strain that expresses Cre-recombinase and an inducible Cas9 only in the thymus ( LSL.Cas9 x Lck-cre) along with a lentiviral vector system into which T-ALL specific oncogenes are cloned in antisense flanked by LOX66/71 sites. Gain-of-function events, such as the overexpression of transcriptional regulators ( Tlx1, Tal1, or Lmo2) and signal transducers ( NRAS G12D, PIK3CD E1021K) were induced in developing thymocytes by Cre-mediated inversion together CRISPR-Cas9 editing of recurrent T-ALL loss-of-function drivers. This combinatorial approach allowed to probe more than 2000 possible oncogenic mutational combinations in vivo. Transplantation of HSCs from LSL.Cas9 x Lck-cre mice transduced with our vector system into sublethally irradiated mice led to T-ALL development with different morphology and disease phenotypes. Developing leukemia harbored reproducible phenotypes, covering very immature CD4-CD8-CD25+CD44+ T-ALL in the Tlx1_NRAS subgroup, in contrast to the classical cortical CD4+CD8+CD3- phenotype (Tlx1_PIK3CD subgroup), as well as mature single-positive CD4+CD3+ or CD8+CD3+ blasts (Tal1_Lmo2 subgroup). We identified Tlx1, Tal1, Lmo2, NRAS G12Dand PIK3CD E1021Kas the main driver of disease phenotype and gene expression profile, whereas the loss-of-function mutations contributed to and accelerated the onset of the disease. Tumor-derived cell lines could be easily established and kept their phenotypic characteristics and mutation patterns. The resulting T-ALL tumors contained up to eight different disease-relevant genetic alterations, thus recapitulating the genetic complexity in humans and overcoming the long latency for spontaneous mutations in less complex mouse models. Among these, co-evolution of insertions and deletions in Notch1, Cdkn2a, Bcl11b, and Pten were among the most frequently observed mutations in definitive T-ALL, whereas others, e.g., in Dnm2, Phf6, Etv6, and Lef1, occurred more randomly. While gene editing by CRISPR-Cas9 mostly resulted in frame-shift mutations in both alleles, Bcl11b exhibited a strong haploinsufficient phenotype with exactly one knock-out and one intact allele in each case examined. Following this observation, further suppression of Bcl11b by shRNAs in Bcl11b +/- cell lines derived from our tumor models demonstrated rapid induction of cell death, which was more intense in T-ALL cells compared to non-malignant thymocytes. In addition, re-analysis of CRISPR-based loss-of-function screens of human hematopoietic cell lines retrieved from the Cancer Dependency Map confirmed BCLL11B as a strong selective dependency in human T-ALL. In summary, we model subgroup-specific T-ALL transformation through conditional and multiplexed in vivo gene editing and oncogene overexpression, thus creating a resource of novel mouse models that recapitulate the genetic and biological heterogeneity of the disease. Using our resource, we identified Bcl11b as a strong and selective context-specific dependency in T-ALL. Although Bcl11b is a transcription factor, our results could serve as an starting point for novel therapies that interfere with Bcl11b function, such as molecular glue degraders or protein interaction inhibitors.

Biallelic Landscape of DNMT3A Mutant Myeloid Neoplasia

The structure of DNMT3A comprises an N-terminal regulatory part promoting nuclear localization and targeting chromatin and a C-terminal domain, mainly involved in DNA binding and methylation catalysis. 1DNMT3A mutations in myeloid neoplasia (MN) and clonal hematopoiesis are mostly heterozygous. Homozygous null Dnmt3amice are born runted and Dnmt3a-/- cells express a hypomethylation phenotype. 2 An invariant detection of heterozygous mutations without homozygous, hemizygous, or biallelic configurations suggests absence of acquisition of more malignant phenotypes by progressive inactivation of DNMT3A. Moreover, residual DNMT3A function is essential for cell survival and potentially suggests that synthetic lethality might be a viable therapeutic strategy whereby cases with two intact alleles would be more resistant allowing a therapeutic window. Consequently, identification of biallelic DNMT3A mutant cases may be extremely instructive for the development of therapeutics targeting DNMT3A. We analyzed targeted NGS sequencing results of 4,895 cases with MN enrolled at our institution from 2002 to 2021 and retrospectively reviewed the clinical characteristics of all patients with deleterious DNMT3A mutations. DNMT3A mutations were identified in 461 patients, of whom 39 had double and 1 triple hits. Most of the mutants had AML (n=236) including biphenotypic AML (n=5), followed by MDS (n=142), MDS/MPN overlap (n=46) and MPN (n=37). In addition, mutations were identified in 9% of CHIP/CCUS (n=117) and 4% of aplastic anemia (n=68). Multiple DNMT3A hits were more often encountered in AML than MDS and MDS/MPN overlap (62.5% vs. 32.5% vs. 2.5%; P = .045). Single hits were represented by missense (73%) within the hotspot R882 (35%), frameshifts (10%), nonsense (9%), splice sites (6%) and in-frame ins/del (2%). Double hits configuration had a constellation of missense/missense (40%), missense/frameshifts (25%), missense/nonsense (13%), and missense/splice sites (10%) ( Fig1). R882 accounted for 10% of the multi hit carriers. Of note is that biallelic involvement was not confined to non-R882. Patients harboring multi hits carriedmore likely IDH2 (27.5% vs. 10.5%; OR 2.73; P = .011) and ETV6 (7.5% vs. 1.7%; OR 4.32 P = .043) mutations compared to patients with single hits DNMT3A by multivariate logistic regression analysis. Since deletion or UPD of DNMT3A locus has not been found, one can assume that all cases with one hit harbor monoallelic rather than biallelic subclones. For carriers of multiple mutations, one can stipulate that when the sum of VAFs exceeds the theoretical 60%, the presence of a biallelic subclone might be suspected. Indeed, 24 cases fulfilled this criterion. However, in 40% of patients with double hits, arithmetic VAF did not allow for unequivocal resolution of the mutational configuration, with either smaller biallelic subclones vs. subclonal mosaicism being possible. Next, we compared clinical features and outcomes of patients with mono vs. biallelic cases. In MDS, compared with single hits DNMT3A, biallelic cases showed significantly higher WBC (median 7.49 vs. 3.15 k/µL; P = .0052), ANC (4.88 vs. 1.52 k/µL; P = .0056), and platelet count (264 vs. 83 k/µL; P = .0036). In high-risk MDS and AML, with a median follow-up of 12.5 months (0.2-201), patients with biallelic DNMT3Ashowed significantly poorer 1-year OS rate than patients with single hits (42.8% vs. 65.8%; P = .0095). Longitudinal molecular analysis of 8 cases (2 MDS at onset and upon progression to sAML; 4 AML at diagnosis and following relapse after conventional intensive chemotherapy-induced remission; 1 AML at diagnosis and CR post SCT; 1 AML and donor-derived AML post SCT) demonstrated an early origin of biallelic hits with leukemogenic potential. Indeed, biallelic clones persisted or expanded in 6 transformed cases. Our study describes the likelihood that biallelic configuration of DNMT3A mutations, while rare, is indeed compatible with clonal expansion and thus questions the applicability of a synthetic lethality strategy. We are currently confirming that, indeed, truly biallelic cases vs. mosaicism are permissive using DNASeq of single sorted progenitor cells. The results of this analysis will be available at the time of ASH meeting.

Influence of Co-Mutational Patterns in Disease Phenotype and Clinical Outcomes of Chronic Myelomonocytic Leukemia

Introduction: Chronic myelomonocytic leukemia (CMML) is characterized by recurrent somatic mutations in a conserved number of genes and functional pathways. Although specific genomic events are associated with disease phenotype and prognosis, identification of genomically-defined disease subgroups based on common recurrent cooperative genomic patterns is needed to refine disease classification and identify disease subsets with unique clinical behavior. Methods: To evaluate if CMML is defined by recurrent co-mutational profiles defining unique clinicopathologic subgroups we evaluated a cohort of 296 patients (pts) with newly diagnosed CMML. Whole bone marrow DNA was subject to 81 gene targeted next-generation sequencing analysis. Akaike information criterion (AIC) method was applied to evaluate mixture model components defining clusters based on mutational profile. Expectation-maximization (EM) algorithm was used for mixture model fitting to multivariate binary data. Unsupervised cluster membership was chosen as a function of the component with the highest weight for any individual, and we examined means of cluster centers. Cox proportional hazards models, regressing overall survival (OS) and leukemia-free survival (LFS), were fit on cluster in some cases and normalized cluster weights in other cases, with and without adjustment for age and sex. Two degree of freedom likelihood ratio tests was performed on cluster and cluster weight in all models regardless of covariate adjustment. Results: Median age of the population was 70 years [range 30-71]; 160 (54%) pts had myeloproliferative CMML (MP-CMML) and 152 (51%) had CMML-2 by WHO classification. Most frequent mutations included TET2 (51%), ASXL1 (48%), SRSF2 (40%), RUNX1 (22%), NRAS (18%), CBL (14%) and KRAS (14%) all present in &amp;gt;10% of pts. Based on frequency and co-occurrence of mutations, AIC optimization identified 3 unique clusters. Clusters based on mutation landscape are shown in Figure 1A. Unsupervised clustering allowed attribution of individual patients to specific clusters. Cluster 1 (C1, n=107), was characterized by near universal presence of ASXL1 mutations (86%), with lower frequency of TET2 mutations, and enrichment of RUNX1 (35%), NRAS (28%) and U2AF1 (18%) mutations. SETBP1 and EZH2 mutations were nearly exclusively observed in C1 (16% and 20% of C1 pts, respectively). All pts with ETV6 mutations belonged to this cluster. Cluster 2 (C2, n=135) was defined by universal presence of TET2 mutations (93%) with frequent SRSF2 co-mutation (56%) and lower frequency of ASXL1 (34%), RUNX1 (15%) or NRAS (12%) mutations. Despite their overall low frequency, BRAF mutations were restricted to C2, while CBL mutations were observed at similar frequencies in C1 and C2. This suggests that co-mutation profiles and genomic context differs among genes involved in RAS pathway signaling. Cluster 3 (C3, n=54) included a minor and more genomically heterogenous group enriched for SF3B1 (25%), KRAS (24%), DNMT3A (22%) and TP53 (15%) mutations, with absence of ASXL1 mutations, and low frequency of TET2 (12%) mutations. All BCORL1 and WT1 mutations and most ASXL2 and CEBPA mutations were in C3. RUNX1 mutations not only were more frequent among C1 but appeared at higher median VAF compared to other clusters (C1: 40%, C2: 11%, C3: 25%, p=0.003). Mutations in U2AF1 had higher median VAF in C3 compared to cluster 1 (49% vs 43%, p=0.017). C1 was enriched for MP-CMML (C1: 64%; C2: 48%; C3: 52%, p&amp;lt;0.001) and had higher frequency of del(7q)/-7 (C1: 11%; C2 0%, C3: 6%, p&amp;lt;0.001) and trisomy 8 (C1: 15%, C2: 7%, C3: 6%, p=0.05). Complex karyotype (C1: 1%, C2: 1%, C3: 22%, p&amp;lt;0.001) was nearly exclusive of C3, while C2 was more likely to be associated with a normal karyotype (C1: 59%; C1: 73%; C3: 41%, p&amp;lt;0.001) and higher median hemoglobin (C1: 9.8g/dL; C2: 12.1g/dL, C3: 9.7g/dL, p&amp;lt;0.001). In total 66% of pts received therapy with hypomethylating agents with no differences in response, median time to or duration of response between clusters. Use of Cox proportional hazards model identified that, when corrected by age and sex, patients on C1 and C3, based on attributed cluster weights, had significantly worse LFS (p=0.02, Figurer 1B) and OS (p=0.05) than those in C2. Conclusions: These data suggest that somatic mutations in CMML have unique patterns of clustering that define disease phenotype and influence disease outcomes.

Single-Cell Genomics and Proteomics Reveals Venetoclax-Resistant Monocytic Differentiation of TP53 LOH Clones in TP53 Mutant AML

Introduction: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by accumulation of abnormal hematopoietic stem and progenitor cells. TP53 mutations, present in 8 - 30 % of AML, are associated with high risk of relapse and poor prognosis. The mechanisms underlying their persistence are not well understood. Here, we attempt to describe the clonal architecture and immunophenotypes of TP53 mutant ( TP53-mut) clones during therapy. Leveraging advancements in single-cell sequencing and machine learning models, this study integrated single-cell mass cytometry (CyTOF) and single-cell DNA + protein sequencing (seq) profiling of ten paired pre- and post-treatment samples from five TP53-mut AML patients. Methods: Patients 1 and 3 received treatment with CD47AB (Magrolimab), 5'-Azacitidine (Aza), and Venetoclax (Ven); Patient 2 received IMGN632 (CD123-targeting ADC), Aza and Ven. Patient 4 received p97 Inhibitor CB-5339; Patient 5 received CD47 inhibitor (ALX148), Aza, Ven. Consequently, Ven/Aza served as the therapeutic backbone for most patients. For single cell DNA+protein analysis, we sequenced a total of 44,550 cells from these 10 samples. Samples with at least 70% viability were stained with the Total-Seq™-D Human Heme Oncology Cocktail, containing 45 oligo-conjugated antibodies for surface markers relevant to AML. For mutation analysis, we utilized a validated AML custom panel (Morita et al. 2020) covering recurrent mutations in 37 genes. For CyTOF, we multiplexed samples and stained with 50 antibodies characterizing lineage, apoptosis, and signaling pathways. We successfully constructed a machine learning model for integrating both data types using our gradient boosting algorithm established pipelines and were able to predict DNA mutation status in CyTOF data with over 95% accuracy. Results: Analysis of the clonal architecture revealed the presence of TP53 mutations not only in AML blasts but also in lymphocyte subpopulations in all TP53-mut clones from the patients in this study. For example, in patient 1, as a representative case, TP53 mutations were observed in 16.5% of CD4+ T cells, 35.9% of CD8+ T cells, and 19.2% of NK cells. Clonal evolution analysis showed sensitivity of TP53-mut clones with TP53 Loss of heterozygosity ( TP53 mut + LOH) to Ven/Aza and monocytic differentiation in resistant cells, potentially a manifestation of their stem-like nature. Patient 1 displayed three distinct subclones: clone 1 harbored an ETV6 mutation (p.V322S), clone 2, derived from clone 1, acquired additional IDH1 (p.R132L) and TP53 (p.R241G) mutations, clone 3, originating from clone 2 and comprising the highest proportion, exhibited loss of the other TP53 allele (LOH), and decreased from 96.2% to 55.2% post-treatment (Figure 1A). Meanwhile, clone 1 and clone 2 increased from 1.9% to 27.3% and 1.9% to 17.4% respectively. Dissecting the phenotypic changes, clone 3 showed significant pre- and post-treatment shifts in cellular composition. Pre-treatment, it consisted predominantly of 89.7% CD34+ blasts and only 0.2% CD16+ monocytic cells. Post-treatment, CD34+ blasts decreased to 9.3%, while CD16+ monocytic cells increased to 67.8%. CyTOF analysis corroborated our findings (Figure 1B) with trajectory analysis revealing that AML cells had a stemness profile (CD34+CD38- and C-kit+) located at the beginning of the trajectory. Conversely, post-treatment AML cells displayed a loss of stemness and expressed myeloid differentiation markers, including CD33, CD11b, CD14, and CD68. We concluded that Ven-based treatments induce monocytic differentiation in resistant AML cells. CyTOF analysis of the proteomic profiles of resistant cells revealed an increase in Ki67, BCL-XL, and 4EBP1 and a decrease in CD34 and C-KIT, suggesting a potential resistance mechanism involving the upregulation of anti-apoptotic molecules and mTOR pathway. Notably, CD36, a fatty acid transporter, exhibited increased expression in monocytic cells, suggesting an altered metabolism in the survival monocytic cells. Conclusion: This study establishes a genotype-phenotype connection through single-cell proteogenomic profiling of TP53-mutated AML, describing the clonal evolution and immunophenotypic dynamics during treatment while proposing a potential mechanism of resistance.

The genetics of transformation from myelodysplastic syndrome to secondary acute myeloid leukemia.

e19073 Background: Gene mutations play key role in the transformation from myelodysplastic syndrome (MDS) to secondary acute myeloid leukemia (s-AML). The aim of this study was to explore the clonal progression pattern from MDS to s-AML. Methods: A total of 663 patients diagnosed with MDS (n = 291), s-AML (n = 86), and primary AML (p-AML) (n = 286, M3 excluded) were enrolled in this study from May 2018 to December 2021, and the median age was 57 year-old (range 1~88). The diagnosis was established according to the WHO criteria. The MDS patients were divided into low-risk MDS ( n = 158) and high-risk MDS (n = 133) according to 2012 IPSS-R. Next generation sequencing was performed to detect the mutations of entire coding regions of 112 genes related with hematologic tumors in all patients. Results: It was found that mutations from 31 genes occurred in both MDS and AML, including DNA methylation ( DNMT3A, TET2, IDH1, IDH2, WT1), chromatin modification ( SETBP1, ASXL1, EZH2, PHF6), RNA splicing ( U2AF1, SF3B1, SRSF2, ZRSR2), transcription regulation ( TP53, CEBPA, RUNX1, ETV6, GATA2, BCOR, BCORL1), signal transduction pathways ( NRAS, KRAS, PTPN11, NOTCH1, FLT3, JAK2, KIT), and others ( NPM1, FAT, STAG2, DDX41). By enrichment analysis, those mutations were classified into two categories: type A mutations ( FLT3, IDH1, NPM1, NRAS, PTPN11, WT1, CEBPA) and type B mutations ( IDH2, KRAS, U2AF1, ZRSR2, SRSF2, STAG2, DNMT3A, EZH2, RUNX1, ETV6, TP53). The type A genes were significantly enriched in p-AML than in MDS, while some type B mutations, particularly RNA splicing, were significantly enriched in MDS than in p-AML. The VAFs of type A mutations were significantly lower than those of type B mutations. The longitudinal analysis of 10 patients with s-AML revealed two main models of clonal evolution, linear evolution and clone sweeping. Although the two models differed in the disease development, new sub-clones appeared in 9/10 patients. Interestingly, many of the new mutations were type A mutations (n = 7, 7/10), and 7 out of 10 patients carried type B mutations when they were at MDS state. The VAF data also showed that the preexisting mutations were generally higher than the newly emerging genetic alterations. Finally, an individual case was used to delineate the clone evolution. The patient was initially diagnosed with 5q syndrome and U2AF1 mutation (type B) was identified. After treatment, the patient experienced remission, and developed a new ETV6 mutation while the clonal size of U2AF1 decreased. When the patient relapsed, the clone size of ETV6 decreased while U2AF1 mutated clone size were amplified, a typical “clone sweeping” pattern. When the patient eventually transformed to s-AML, three type A mutations ( NRAS, KRAS and PTPN11) appeared simultaneously. Conclusions: This study revealed that the type A mutations are mainly responsible for the progression of MDS to AML, and the type B mutations are related to the clonal origin of MDS.

IDENTIFICATION OF GENOMIC BIOMARKERS OF DISEASE PROGRESSION AND SURVIVAL IN NEWLY‐DIAGNOSED PRIMARY CNS LYMPHOMA

Introduction: There is a significant unmet need for robust genomic biomarkers that identify patients with newly-diagnosed primary CNS lymphoma (PCNSL) at high risk of progression, both during standard methotrexate-based induction as well as after dose-intensive consolidation. Methods: We performed targeted next-generation sequencing of 529 cancer genes of formalin-fixed, paraffin-embedded tumors from 74 patients with newly diagnosed primary CNS diffuse large B-cell lymphoma using the UCSF500 Cancer Panel and the Institute for Human Genetics CLIA Laboratory. The assay detects structural variants including single nucleotide variants, small insertions and deletions, and copy-number alterations (CNAs). Sixty-four EBV-negative PCNSL patients treated with a standard methotrexate, temozolomide, rituximab (MTR) induction were available for complete analysis. Results: We identified frequent mutations involving MYD88 (77%), CD79B (41.9%), ETV6 (27%) and BTG1 (25.7%) as well as frequent CNA involving 6q loss (62.5%), 9p loss (34.4%) and 12 gain (31.3%). Three genomic alterations were most significantly associated with early disease progression in PCNSL: (1) Alterations at 6p21.3, predominantly copy neutral loss of heterozygosity (CN-LOH) at the HLA Class I (HLA-A, B, C) and Class II loci (HLA-DR, DP, DQ, TAP1) as well as homozygous deletion of HLA Class II; (2) Mutations of tumor suppressor genes BTG1 and ETV6. Overall, these genomic alterations were detected in 28 out of 31 progression events in the cohort. The subgroup with either CN-LOH or homozygous deletion at 6p had the earliest progression, followed by the subgroup with mutations at either BTG1/ETV6 and no 6p CN-LOH or homozygous deletion, compared to no alterations at these 3 loci. 10 of 18 tumors with these alterations at 6p also contained BTG1 and/or ETV6 mutations. Survival analysis demonstrates that the subgroup with 6p CN-LOH or homozygous deletion had the earliest progression, followed by the subgroup with BTG1/ETV6 mutations compared to no alterations at these 3 loci (PFS p = 3.7e-5, OS p = 0.0017, logrank test, Figure 1). Multivariate Cox proportional hazard analysis demonstrated a significant 3.24-fold increased risk of progression with 6p CN-LOH/homozygous deletion or BTG1/ETV6 mutations (p = 3.5e-5, adjusted by Age, KPS, IELSG, MSKCC, IOL, Maintenance, and Consolidation). The research was funded by: National Cancer Institute NIH R01CA139-83-01A1 Keywords: aggressive B-cell non-Hodgkin lymphoma, diagnostic and prognostic biomarkers, genomics, epigenomics, and other-omics No conflicts of interests pertinent to the abstract.

The clinical and molecular spectrum of ETV6 mutated myeloid neoplasms.

ETV6 mutations are rare but recurrent somatic events in myeloid neoplasms and are negatively prognostic in myelodysplastic syndrome. We set out to examine the clinical and molecular characteristics of patients undergoing investigation for myeloid neoplasms, found to have deleterious ETV6 mutations. ETV6 mutations occurred in 33 of 5793 (0.6%) cases investigated and predominantly in high-risk disease entities including MDS with increased blasts, primary myelofibrosis and AML, myelodysplasia-related. In three cases, isolated iso (17q) karyotype was concurrently detected, an otherwise rare karyotype in myeloid neoplasms. ETV6 mutations were frequently subclonal and never occurred as an isolated abnormality with ASXL1 (n = 22, 75%), SRSF2 (n = 14, 42%) and SETBP1 (n = 11, 33%) the predominant co-mutations. Restricting to patients with MDS, higher rates of ASXL1, SETBP1, RUNX1 and U2AF1 mutations occurred in ETV6 mutated cases, relative to a consecutive control cohort with wild-type ETV6. The median OS of the cohort was 17.5 months. This report highlights the clinical and molecular associations of somatic ETV6 mutations in myeloid neoplasms, suggests their occurrence as a later event, and proposes further translational research questions for their role in myeloid neoplasia.

Single-cell analysis of megakaryopoiesis in peripheral CD34+ cells: insights into ETV6-related thrombocytopenia

BackgroundGermline mutations in the ETV6 transcription factor gene are responsible for familial thrombocytopenia and leukemia predisposition syndrome. Although previous studies have shown that ETV6 plays an important role in megakaryocyte (MK) maturation and platelet formation, the mechanisms by which ETV6 dysfunction promotes thrombocytopenia remain unclear. ObjectivesTo decipher the transcriptional mechanisms and gene regulatory network linking ETV6 germline mutations and thrombocytopenia. MethodsPresuming that ETV6 mutations result in selective effects at a particular cell stage, we applied single-cell RNA sequencing to understand gene expression changes during megakaryopoiesis in peripheral CD34+ cells from healthy controls and patients with ETV6-related thrombocytopenia. ResultsAnalysis of gene expression and regulon activity revealed distinct clusters partitioned into 7 major cell stages: hematopoietic stem/progenitor cells, common-myeloid progenitors (CMPs), MK-primed CMPs, granulocyte-monocyte progenitors, MK-erythroid progenitors (MEPs), progenitor MKs/mature MKs, and platelet-like particles. We observed a differentiation trajectory in which MEPs developed directly from hematopoietic stem/progenitor cells and bypassed the CMP stage. ETV6 deficiency led to the development of aberrant cells as early as the MEP stage, which intensified at the progenitor MK/mature MK stage, with a highly deregulated core “ribosome biogenesis” pathway. Indeed, increased translation levels have been documented in patient CD34+-derived MKs with overexpression of ribosomal protein S6 and phosphorylated ribosomal protein S6 in both CD34+-derived MKs and platelets. Treatment of patient MKs with the ribosomal biogenesis inhibitor CX-5461 resulted in an increase in platelet-like particles. ConclusionThese findings provide novel insight into both megakaryopoiesis and the link among ETV6, translation, and platelet production.

Spectrum and clinical features of gene mutations in Chinese pediatric acute lymphoblastic leukemia

PurposeThe 5-year survival rate of children with acute lymphoblastic leukemia (ALL) is 85–90%, with a 10–15% rate of treatment failure. Next-generation sequencing (NGS) identified recurrent mutated genes in ALL that might alter the diagnosis, classification, prognostic stratification, treatment, and response to ALL. Few studies on gene mutations in Chinese pediatric ALL have been identified. Thus, an in-depth understanding of the biological characteristics of these patients is essential. The present study aimed to characterize the spectrum and clinical features of recurrent driver gene mutations in a single-center cohort of Chinese pediatric ALL.MethodsWe enrolled 219 patients with pediatric ALL in our single center. Targeted sequencing based on NGS was used to detect gene mutations in patients. The correlation was analyzed between gene mutation and clinical features, including patient characteristics, cytogenetics, genetic subtypes, risk stratification and treatment outcomes using χ2-square test or Fisher’s exact test for categorical variables.ResultsA total of 381 gene mutations were identified in 66 different genes in 152/219 patients. PIK3R1 mutation was more common in infants (P = 0.021). KRAS and FLT3 mutations were both more enriched in patients with hyperdiploidy (both P < 0.001). NRAS, PTPN11, FLT3, and KMT2D mutations were more common in patients who did not carry the fusion genes (all P < 0.050). PTEN mutation was significantly associated with high-risk ALL patients (P = 0.011), while NOTCH1 mutation was common in middle-risk ALL patients (P = 0.039). Patients with ETV6 or PHF6 mutations were less sensitive to steroid treatment (P = 0.033, P = 0.048, respectively).ConclusionThis study depicted the specific genomic landscape of Chinese pediatric ALL and revealed the relevance between mutational spectrum and clinical features of Chinese pediatric ALL, which highlights the need for molecular classification, risk stratification, and prognosis evaluation.

Molecular Profiles and Clinical Features of Myeloproliferative Neoplasms Unclassifiable (MPN-U) with and without JAK2/CALR/MPL Mutations

Introduction: Myeloproliferative neoplasms (MPNs) are clonal hematopoietic neoplasms and include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), etc., each with specific diagnostic criteria. Patients who display features compatible with MPN but do not meet the diagnostic criteria for a specific entity are commonly assigned a diagnosis of MPN, unclassifiable (MPN-U). JAK2, CALR, and MPL are well-known driver mutations in PV, ET, and PMF. With the advancement and application of next-generation sequencing (NGS), the molecular profiles of the above 3 well-defined MPNs have been extensively studied. However, the molecular profile of MPN-U remains ill-defined. In this study, we aimed to describe the clinical and molecular features of MPN-U in our institution and then compare these features between patients with and without JAK2, CALR, or MPL mutations to better understand the clinicopathologic characteristics and prognosis of MPN-U. Method: The patients with a diagnosis of MPN-U and available NGS test results at our cancer center were identified and divided into two groups: cohort A) MPN-U with mutations in JAK2, CALR, or MPL, and cohort B) triple-negative. The patients' survival data, clinical parameters, bone marrow findings, and cytogenetics were collected for comparison. Baseline characteristics and somatic mutation distributions were compared using the chi-square test (categorical variables) and Wilcoxon rank sum test (continuous variables). Overall survival (OS) was calculated using the Kaplan-Meier method and compared using the log-rank test. A Cox proportional-hazards model was used to evaluate the association between OS and clinical factors. Results: Out of 8285 patients in our institutional clinical molecular database which houses NGS, we identified and confirmed MPN-U diagnosis in 53 patients. Among this group, 39 patients harbored JAK2 (n=36), CALR (n=1), MPL (n=1), or JAK2 and CALR co-mutations (n=1) and were assigned to cohort A. The remaining 14 patients were triple-negative and assigned to cohort B. The triple-negative patients in cohort B had higher median WBC count (18.5 x 10 9/L vs 9.98 x 10 9/L, p=0.04) and bone marrow cellularity (81% vs 64%, p=0.02) (Table 1). The mutational profile of cohort B was enriched for CUX1, ETV6, NRAS, SETBP1, and SRSF2 mutations. ASXL1 and SETBP1 were the most frequently mutated genes in the triple-negative group, and were often co-mutated with ETV6, NRAS, and/or SRSF2 (Figure 1). TET2 mutations appeared more common in cohort A, but this finding was not statistically significant. There were no significant differences in the other parameters, including gender, bone marrow blast percentage, karyotype, hemoglobin concentration, platelet count, and bone marrow fibrosis. Kaplan-Meier analysis demonstrated that the median OS time in cohorts A and B was not reached, and survival differences were not statistically significant (p-value 0.23). We used a Cox proportional-hazards model to evaluate the association between OS and clinical factors. Via backward elimination, we uncovered that high WBC count and low hemoglobin concentration were significantly associated with worse outcome (hazard ratios of 1.04 and 1.33, respectively, and p-values of 0.007 and 0.01). Conclusion: In our small cohort, the patients with MPN-U who were triple-negative for JAK2,CALR, and MPL mutations had more frequent CUX1, ETV6, NRAS, SETBP1, and SRSF2 mutations. ASXL1 and SETBP1 were the most frequently mutated genes in the triple-negative group, and were often co-mutated with ETV6, NRAS, and/or SRSF2. In addition, triple-negative patients had higher WBC counts and higher bone marrow cellularity. A Cox proportional-hazards model identified high WBC count and low hemoglobin concentration as being significantly associated with a worse outcome. Kaplan-Meier analysis did not reveal a difference in OS between triple-negative and JAK2, CALR, or MPL mutated MPN-U. A larger cohort is needed to evaluate the survival outcome of these two distinct groups. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Next-Generation Sequencing of Newly-Diagnosed Primary CNS Lymphoma Reveals Alterations in BTG1, ETV6, and 6p Are Associated with Chemoresistance and Inferior Progression-Free Survival

Introduction: There is a significant unmet need for the development of reliable genetic biomarkers that identify patients with newly-diagnosed primary CNS lymphoma (PCNSL) who are at high risk of progression, both during standard methotrexate-based induction as well as delayed progression after receipt of dose-intensive consolidation. Currently, little is known about the genetic subtypes of PCNSL and the basis for differences in chemo-immunotherapeutic response. We hypothesized that an integrated clinical-genomic analysis may reveal new determinants of tumor progression and may ultimately guide a precision medicine-based approach to the selection of effective treatment regimens. Methods: We performed targeted next-generation sequencing of 529 pan-cancer genes of pre-treatment, formalin-fixed, paraffin-embedded tumors from 52 patients with CNS diffuse large B-cell lymphoma. We identified structural variants including single nucleotide variants, small insertions and deletions, and copy-number alterations. Clinical records were retrospectively reviewed to determine patients' baseline characteristics, IELSG index, and progression-free survival (PFS). 44 EBV-negative PCNSL patients treated with methotrexate, temozolomide, rituximab (MTR) induction with adequate genomic samples were available for complete analysis. Statistical testing was performed using R. Results: We identified three candidate genomic alterations that were significantly associated with chemotherapy resistance in PCNSL: (1) Alterations at 6p21.3, including both copy neutral loss of heterozygosity (CN LOH) at the HLA Class I (HLA-A, B, C) and Class II loci (HLA-DR, DP, DQ, TAP1) as well as homozygous deletion of HLA Class II; (2) Mutations of tumor suppressor genes BTG-1 and ETV6 (Fisher's exact, p < 0.01). Overall, these genomic alterations were detected in 18 out of 19 progression events in the cohort (Fisher's exact, p < 0.001). 7 of 9 tumors with 6p CN LOH also contained mutations at BTG-1 and/or ETV6. Kaplan-Meier survival analysis shows three subgroups stratified by alteration type with distinct PFS outcomes (Figure 1). The subgroup with either CN LOH or homozygous deletion at 6p had the earliest progression, followed by the subgroup with mutations at either BTG-1/ETV6 and no 6p CN LOH or homozygous deletion, compared to no alterations at these 3 loci (Log-rank, p < 0.01). Patients with hemizygous loss at 6p exhibited a trend towards worse outcome compared to no 6p loss. Furthermore, multivariate Cox proportional hazard analysis demonstrated a statistically significant 2.7-fold increased risk of progression with 6p CN LOH/homozygous deletion or mutations involving BTG-1/ETV6 (Table 1). While etoposide-cytarabine consolidation and maintenance lenalidomide were each significantly associated with a decreased risk of progression, age at diagnosis, Karnofsky performance status, intraocular disease status, and IELSG index were not significantly associated with PFS. Conclusions: Through harmonizing clinical and next-generation sequencing data, in this retrospective analysis we identify pathogenic alterations involving BTG-1 and ETV6, as well as major alterations at 6p21.3, that correlated with accelerated disease progression and an early tumor resistance phenotype in PCNSL. While 6p loss has been identified as a mechanism of tumor immune escape in PCNSL, our results suggest that 6p CN LOH may be a novel mechanism associated with early progression. Of note, in a parallel investigation using patient-derived CNS lymphoma tumor cells engrafted in a murine orthotopic xenograft model, we have demonstrated that lenalidomide significantly induces transcription of 6p21.3 genes involved in antigen presentation and immunomodulation, including HLA-A, TAP-1, and lymphotoxins. Taken together, 6p21.3 copy number loss, in particular CN LOH and homozygous deletion, as well as mutations in BTG-1 and ETV6 may be a promising biomarker set, potentially useful in risk stratification in clinical trials as well as to identify high risk patients more likely to derive benefit from lenalidomide. Prospective validation studies are planned to confirm these results. Supported by NCI. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Myelodysplastic Syndrome with Monosomy 7 in a Patient with Ataxia-Pancytopenia Syndrome

Abstract Introduction/Objective Ataxia-pancytopenia syndrome is caused by mutations in SAMD9L, a tumor suppressor gene on chromosome 7 with roles in normal hematopoiesis and cerebellar development. Syndrome manifestations consist of a combination of progressive ataxia, multilineage cytopenias, and increased risk of myeloid neoplasms associated with monosomy 7. Histopathologic and radiologic descriptions of this recently described disorder are scarce and treatment strategies are not standardized. Additionally, features that predict spontaneous hematologic remission of myeloid neoplasms are incompletely understood. Therefore, detailed discussions of this disorder and its possible outcomes are warranted. Methods/Case Report A six-year-old boy was brought to his doctor when his parents noticed head tilting while reading and impaired coordination. Brain MRI revealed extensive T2/FLAIR hyperintensities of white matter, cerebellar hypoplasia, and a thinned corpus callosum. Further evaluation excluded autoimmune etiologies, infectious diseases, and inherited leukodystrophies. Whole exome sequencing demonstrated a previously uncharacterized heterozygous mutation in SAMD9L, c.2062T&amp;gt;A; p.Tyr688Asn. Subsequent testing revealed pancytopenia. A bone marrow biopsy showed small megakaryocytes with abnormal nuclear lobation and erythroid progenitors with nuclear blebbing and binucleation. Blasts were borderline increased (4%). Fluorescence in-situ hybridization and karyotype showed monosomy 7. A myeloid next-generation sequencing panel identified an ETV6 mutation (p.Gln143Ter, VAF=5.4%). A diagnosis of myelodysplastic syndrome with monosomy 7 in the setting of ataxia-pancytopenia syndrome was rendered. The patient underwent allogeneic stem cell transplant and is doing well at last follow-up. Results (if a Case Study enter NA) N/A Conclusion Ataxia pancytopenia syndrome is a recently described and incompletely understood disorder. Some myeloid neoplasms in ataxia-pancytopenia syndrome can undergo somatic revertant mosaicism via uniparental disomy, resulting in spontaneous hematologic remission. Factors that predict spontaneous remission are unclear; however, secondary mutations have been associated with poorer outcomes. This case emphasizes the value of comprehensive genetic testing modalities in challenging cases. Screening for SAMD9L mutations in cases of pediatric myelodysplastic syndrome could be considered.