Molecular Abnormalities Research Articles

The oncogenic role of LGR6 overexpression induced by aberrant Wnt/β-catenin signaling in lung cancer.

Molecular abnormalities in the Wnt/β-catenin pathway confer malignant phenotypes in lung cancer. Previously, we identified the association of leucine-rich repeat-containing G protein-coupled receptor 6 (LGR6) with oncogenic Wnt signaling, and its downregulation upon β-catenin knockdown in non-small cell lung cancer (NSCLC) cells carrying CTNNB1 mutations. The aim of this study was to explore the mechanisms underlying this association and the accompanying phenotypes. LGR6 expression in lung cancer cell lines and surgical specimens was analyzed using quantitative RT-PCR and immunohistochemistry. Cell growth was assessed using colony formation assay. Additionally, mRNA sequencing was performed to compare the expression profiles of cells subjected to different treatments. LGR6 was overexpressed in small cell lung cancer (SCLC) and NSCLC cell lines, including the CTNNB1-mutated NSCLC cell lines HCC15 and A427. In both cell lines, LGR6 knockdown inhibited cell growth. LGR6 expression was upregulated in spheroids compared to adherent cultures of A427 cells, suggesting that LGR6 participates in the acquisition of cancer stem cell properties. Immunohistochemical analysis of lung cancer specimens revealed that the LGR6 protein was predominantly overexpressed in SCLCs, large cell neuroendocrine carcinomas, and lung adenocarcinomas, wherein LGR6 overexpression was associated with vascular invasion, the wild-type EGFR genotype, and an unfavorable prognosis. Integrated mRNA sequencing analysis of HCC15 and A427 cells with or without LGR6 knockdown revealed LGR6-related pathways and genes associated with cancer development and stemness properties. Our findings highlight the oncogenic roles of LGR6 overexpression induced by aberrant Wnt/β-catenin signaling in lung cancer.

LAMP5 Is an AML-Restricted Immunotherapeutic Target Enriched in High-Risk Acute Myeloid Leukemia

LAMP5, Lysosomal Associated Membrane Protein Family Member 5, a neuronal protein that plays a role in synaptic plasticity is normally found primarily in the brain, however limited studies have identified it to be expressed in leukemia, particularly KMT2A-rearranged leukemias. Importantly, there is low expression of LAMP5 in normal hematopoiesis making it an ideal potential immunotherapeutic target for both acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). As a newly identified aberrant protein in leukemias, there is little data available on the prevalence or clinical implications of LAMP5 expression. We interrogated the transcriptome and associated clinical and laboratory data from a large cohort of pediatric AML patients to define the prevalence, co-occurring cytomolecular aberrations and clinical outcomes associated with LAMP5 expression. Ribo-depleted RNA seq data from 2,241 patients with AML (Pediatric ages 0-29 years N=1,412, from recent Phase 3 COG clinical trials; Adult ages 18-88 years from BEAT AML N=451, SWOG N=199, TCGA-LAML N=179) with available cytogenetic, molecular, and clinical data were utilized. Gene fusions, internal tandem duplications (ITD) and partial tandem duplications (PTD) were detected by Cicero. Conventional karyotyping and mutational analysis including NGS were used to determine additional cytogenetic and molecular abnormalities. Response was measured by 5-year overall survival (OS), event-free survival (EFS) and relapse risk (RR). Of the 1,412 pediatric patients, LAMP5 was expressed (positive defined as mRNA transcripts per million (TPM) >2) in 396 patients (28%) with mRNA TPM ranging from 0-884 with similar prevalence found in adult AML (28%; BEAT AML N=126/452, SWOG N= 59/199 TCGA N=50/179), but with significantly higher TPM ranging from 0-3,200. Of the 396 pediatric patients with LAMP5 expression, there was a notable enrichment in KMT2A-r AML (N=203, 51%), which accounts for 59% of the total KMT2A-r cohort. Within the KMT2A-r cohort, there is enrichment in the MLLT1 (N=17/18, 94%), MLLT3 (N=61/93, 66%) and MLLT10 (N=58/69, 84%) fusion groups. Additionally, LAMP5 expression was seen in other high risk fusion subtypes including 100% of patients with KAT6A-CREBBP (N=12/12) and 29% of NUP98 fusions (N=45/154). There is absent LAMP5 expression in normal lymphoid and myeloid cells, but there is moderate expression seen in plasmacytoid dendritic cells, which could provide a therapeutic target for Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN). Given the association with high-risk AML fusion subtypes, the impact of LAMP5 on clinical outcome in AML pediatric patients was evaluated. High rates of relapse were seen in patients with LAMP5 expression, with a relapse rate of 45% compared to 36% in LAMP5-negative patients. 5 year event-free survival (EFS) was 36% for LAMP5-positive patients compared 45% for LAMP5-negative patients (p=0.0005). Similar poor outcomes were seen with overall survival 54% for LAMP5-positive patients vs. 62% for LAMP5-negative patients (p=0.001). In an analysis of a large cohort of AML patients, we found that LAMP5 expression is highly enriched in many high-risk fusion subtypes including KMT2A-rearranged AML, KAT6A-CREBBP and NUP98 fusions. Patients with LAMP5 expression have high rates of relapse with significantly worse outcomes compared to patients without LAMP5. Given low levels of LAMP5 in normal hematopoiesis, LAMP5 is an ideal AML-restricted immunotherapy target with broad applicability for many high-risk fusion subtypes of AML. Current efforts to generate a LAMP5 chimeric antigen receptor (CAR) T cell are underway which will be used to evaluate preclinical efficacy in AML via cell- and patient-derived xenograft models with the goal to translate this novel therapy into clinical use to improve the current dismal outcomes for these high-risk patients.

A Retrospective Review Assessing the Development of Myelodysplastic Syndromes in Patients with Plasma Cell Dyscrasias

Introduction Myelodysplastic syndrome (MDS) are hematopoietic disorders defined by dysplasia of the myeloid lineage accompanied by persistent cytopenias, and recurrent cytogenetic abnormalities (MDS). Whilst therapy related myeloid disorders in patients with Multiple Myeloma have been well described, there is lack of information regarding co-occurrence of these disease states in early plasma cell disorders as well as multiple myeloma at diagnosis which may also then allude to whether there is a founder effect to the clones. Recent advances in commercial sequencing assays of genomic data have allowed for identification of relevant gene mutations in patients with hematologic malignancies, such that the presence of these gene mutations have been incorporated into classification systems. In our study, we aimed to assess the occurrence of reported MDS in patients with plasma cell disorders i.e. Monoclonal Gammopathy of unknown significance (MGUS), Smoldering myeloma (SM) and Multiple myeloma (MM) as well as relevant gene mutations that would be implicated in the pathogenesis of MDS even in those patients who do not meet the full criteria for MDS (clonal hematopoiesis of indeterminate potential; CHIP mutations). Methods In this retrospective review, clinical and bone marrow based genomic data (Tempus xT ® 684 gene DNA-based NGS platform) was gathered on 57 patients with a diagnosis of MGUS, SM, and/or MM. Pathogenic gene mutations that are frequently associated with MDS were reported in our patient population. Bone marrow morphologic assessments for MDS related changes were also collected at the time of genomic data abstraction. Those patients who had defined MDS were further subclassified using the World Health Organization 2022 fifth edition classification system. Those observed as having subtle MDS findings on bone marrow biopsy, but with identified CHIP mutations, not meeting criteria for MDS, were also identified. Results Among 57 patients with MGUS (28), SM(9), and MM(20), 2 had met criteria for defined MDS at the time of their assessment. An additional 5 had bone marrow morphologic findings concerning for MDS, but did not meet criteria to be fully defined. A total of 14 myeloid disorder related pathogenic mutations were identified in our patient population (6 in MM at disease diagnosis, 7 in MGUS, and 1 in SM). Overall, the most frequently observed recurring mutations in the cohort were that of DNMT3A (57.1%, mean VAF 4.45%), TET2 (14.3%, mean VAF 4.0%), and SF3B1 (14.3%, mean VAF 39.2%). Patients with defined MDS had recurring pathogenic mutations in genes SF3B1, ASXL1 and DNMT3A. Discussion In our cohort, we identified several patients with features both diagnostic and suggestive of myeloid disorders (MDS) during work up for a plasma cell disorder, in particular MGUS, SM, and/or MM prior to therapeutic intervention. Molecular work up also identified gene mutation subsets in plasma cell disorder patients that have otherwise been implicated in the pathogenesis of myeloid disorders. The identification of both morphologic and molecular abnormalities in our cohort may inform therapeutic considerations as well as vigilance for the discovery or evolution of myeloid disorders during follow-up , in particular when unexpected cytopenias or new clinical concerns emerge. We expect to design future prospective studies, based on our observations, to further inform of the risk of myeloid disorders in our plasma cell disorder patient cohorts, as well as understand its impact on therapies such as immunomodulatory agents, alkylators and/or autologous stem cell transplant.

CLEC2A Is a Novel AML-Restricted Immunotherapeutic Target Enriched in KMT2A-Rearranged Acute Myeloid Leukemia

KMT2A rearrangements (KMT2A-r) are a frequent event in childhood acute myeloid leukemia (AML) and in treatment related AML in adults leading to a highly refractory and deadly subtype of AML regardless of age. Targeted therapies for KMT2A-r AML have had limited success with novel therapies urgently needed. Despite successes in other leukemias, immunotherapy in AML is in its infancy in part due to significant overlap of antigens expressed in AML and normal hematopoietic cells, which would limit efficacy and increase hematopoietic toxicity. We interrogated the AML transcriptome compared to normal hematopoiesis to identify optimal targets that are silent in normal hematopoieisis and are highly expressed in AML. Here we describe a novel immunotherapeutic target, CLEC2A, a member of the C-type lectin family, that is highly enriched in high-risk AML, particularly KMT2A-r AML and absent in normal hematopoeisis. We evaluated the association between KMT2A fusions and CLEC2A expression identifying CLEC2A as a putative oncoprotein and the potential for CLEC2A to serve as an immunotherapeutic target in high-risk AML via antibody-mediated cytotoxicity. Diagnostic specimens from 1,864 patients with AML (Pediatric 0-29 years from COG Phase III trials N=1486; Adult 18-88 years SWOG N=199 and TCGA-LAML N=179) were interrogated using contemporary NGS to identify genetic aberrations. Conventional karyotyping and mutational analysis were used to determine additional cytogenetic and molecular abnormalities. As CLEC2A was entirely absent in normal bone marrow (TPM 0-0.15), positive CLEC2A expression was defined as mRNA transcripts per million (TPM) >1. Although, CLEC2A was detected in only 18% of AML patients (252/1486; 17% pediatric and 90/378; 24% adult patients), it was highly enriched in those with KMT2A-r AML with 77% (N=193) of CLEC2A positive patients having KMT2A-r, accounting for 48% of the total KMT2A-r cohort, Fig 1A. CLEC2A expression was enriched in specific fusion subgroups: MLLT10 (80%), MLLT4 (71%), and MLLT3 (48%), Fig 1B. CLEC2A expression was low to absent in a majority of other patients, though was seen in other high-risk groups including non-KMT2A MLLT10 fusions, NUP98 fusions, CBFA2T3-GLIS2 fusions, and monosomy 7. CLEC2A is also expressed in a subtype of T-ALL (HOXA activated), which is a fusion driven T-ALL. We further evaluated a potential causal link between KMT2A fusions and CLEC2A expression and inquired whether KMT2A fusion proteins might directly bind to the CLEC2A promoter and induce CLEC2A expression. We used AutoCUT&RUN profiling of genome-wide occupancy of KMT2A oncoproteins to evaluate direct binding of the KMT2A fusion protein to the CLEC2A promoter in primary AML patient samples with three different KMT2A fusions (MLLT10, MLLT4 and MLLT3). We found direct binding of KMT2A fusion proteins to the CLEC2A promoter region, indicating a causal relationship between KMT2A fusions and CLEC2A expression. We then evaluated the potential of therapeutic targeting of CLEC2A by an antibody-drug conjugate using a HumZap cytotoxicy assay. CLEC2A antibody conjugated to saporin (a toxin with cytolytic activity when internalized) was incubated with CLEC2A+ and CLEC2A- cells with target-specific cytotoxicity evaluated by colorimetric assay. CLEC2A+ OCI-AML2 cells had significantly higher rate of cytotoxicity compared to CLEC2A- control cells at 10nM Ab-toxin conjugate. Clinical outcomes for patients with and without CLEC2A expression was evaluated. Patients with CLEC2A had significantly worse outcomes (EFS 23% vs. 45.5%, p<0.0001 and OS 38% vs. 63%, p<0.0001 for patients with and without CLEC2A expression, respectively). Given high rates of co-occurring KMT2A-r AML, particularly high-risk fusions (MLLT10 and MLLT4), we evaluated clinical outcomes within the KMT2A-r cohort as these patients have poor EFS and OS. KMT2A-r patients with CLEC2A had significantly worse EFS (24% vs. 39%, p=0.0063) and OS (38% vs. 60%, p=0.0002). Within the KMT2A-r cohort, high rates of relapse were seen for patients with CLEC2A expression compared to those without CLEC2A (72% vs. 55%, p=0.0039). Here we describe CLEC2A, a novel AML-restricted cell surface target that is an ideal immunotherapeutic target. CLEC2A is highly expressed in KMT2A-r AML, entirely absent in normal hematopoietic cells, directly and causally linked to the KMT2A fusion, and can be used for target-directed cytotoxicity.

Molecular Characterisation and Outcomes of 363 Adolescent and Young Adults with AML in Saudi Arabia Risk Stratified By PCR and NGS-Based Testing

Introduction Acute Myeloid Leukaemia (AML) is characterised by cytogenetic (CGN) abnormalities and or mutations in one or more of a number of genes that allow risk stratification and guide treatment. The mutational landscape of patients from Saudi Arabia, which has a young population, has not been well characterised. One study indicates a higher rate of core binding factor and monosomies. Mutational analysis by Next generation sequencing (NGS) has not had widespread utilisation hampering the risk stratification of AML in the country. The more recent introduction of NGS panels has allowed more risk stratification. Here we analysed patients and characterised the CGN and molecular abnormalities. Methods Data were collected from 363 patients, and their cytogenetic and molecular results were reviewed. Patients were divided into 2 cohorts: Cohort A only had PCR-based testing diagnosed or treated at King Faisal Specialist Hospital and research centre - Riyadh. PCR testing included mutation analysis for FLT3, NPM1, CEBPA, c-KIT, IDH1, IDH2, WT1, DNMT3A, and JAK2; quantitative PCR for RUNX1-ETO in a subset of patients. Cohort B had PCR-based mutation testing in addition to the Next-Generation Sequencing (NGS) myeloid panel, which was Illumina-based or Ion Torrent. The panel comprises 23 hotspot genes, 17 entire genes, 29 fusion drivers, and five expression genes associated with haematological malignancies. We risk-stratified patients according to the most recent testing method available. Cohort A and Cohort B were risk-stratified, according to ELN risk classification 2017. Survival analysis for these patients was conducted. Results The median age for all patients was 39 years (13-89). PCR testing included mutation analysis for FLT3 (93.4%), NPM1 (90.4%), CEBPA (69.7%), c -KIT (54.3%), IDH1 (57%), IDH2 (57.9%), WT1 (61.2%), DNMT3A (54.5.5%), JAK2 (4.7%) and quantitative PCR for RUNX1- ETO fusion (13.2%). Cohort A comprised 262 (72.7%) patients who underwent PCR-based mutation testing only. Cohort B consisted of 101 (27.8%) patients who underwent PCR-based mutation testing in addition to NGS myeloid panel analysis. In the entire cohort of 363 patients, we found FLT3-ITD mutations in 85 patients (23.4%) and NPM1 mutations in 68 (18.7%). 36 patients (9.9%) harboured both FLT3-ITD and NPM1 mutations together. In Cohort A, FLT3-ITD detected 26.7% of patients, and 20.2% had NPM1 mutation, while 40% had no detectable mutations by conventional PCR. On the other hand, FLT3-ITD was detected in 14.9% of patients by both NGS and conventional PCR and in 14.9% of patients with NPM1. When comparing Cohort A and Cohort B, Cohort B had more mutations in genes that play an important role in myeloid malignancies, which might have better risk stratification and precision, including TP53 in 13.9% of patients and RUNX1 in 18.8% of patients and ASXL1 in 9.9% of patients. Moreover, NGS pick up more mutations in CEBPA, c-KIT, WT1, IDH1 and JAK2 genes compared to conventional PCR. Within cohort A, 9.2% of patients had normal cytogenetic testing results with no detectable mutations, whereas in cohort B, only 1% of patients had normal karyotype and molecular testing. Furthermore, six mutations were detected only by NGS but not PCR in FLT3-ITD, CEBPA, c-KIT, IDH2, WT1 and DNMT3A in 5.9% of patients. Cohorts A and B were also categorised into ELN risk groups using PCR, sequencing, and cytogenetics testing. It was found that patients at adverse risk had shorter overall survival compared to those at intermediate or favourable risk in both cohorts, with p-values of 0.030 and 0.0007, respectively (Figure 1). The use of NGS was found to be more effective than conventional testing in identifying patients with adverse risk, with a hazard ratio for death of 0.22 (95% CI, 0.08989-0.5732) compared to a hazard ratio of 0.66 (95% CI, 0.4352 -1.031) for conventional PCR testing. Conclusion In this study, we present the mutational profile of AML in young Saudi patients and identify certain frequent mutations in this population. The study presents the largest molecular profiling to our knowledge of this population. The study emphasises the need for integration of NGS to enhance risk stratification and precision, enable better characterisation of high-risk patients, and improve the potential for targeted treatments.

Identification of a Relapse Signature in t(8;21) Pediatric AML

Pediatric acute myeloid leukemia (AML) is a malignancy of the blood in which myeloid progenitor cells are interrupted in their normal course of development and proliferate out of control. Recent studies such as the TARGET initiative, have revealed pediatric AML to be driven by relatively few molecular abnormalities when compared to adult AML. Most frequently occurring in genes directly involved in or regulating transcription. These molecular aberrations are drivers of disease, inform patient risk stratification and are transcriptomically unique from one another. Of these events, RUNX1-RUNX1T1 is the most common, evident in approximately 15% of pediatric AML cases. While RUNX1-RUNX1T1 is a positive outcome prognosticator, 20% of these patients go on to relapse with significantly poorer outcomes. Our objective was to identify a relapse signature that could be identified at the time of diagnosis so that alternative therapeutic strategies can be employed. Here we report the investigation of RNAseq data from 3,022 pediatric AML patient samples and identification of a transcriptomic relapse-signature (TRS) via differential expression analysis, supervised clustering and machine learning modelling. We performed differential gene expression analysis comparing diagnostic t(8;21) patient samples for those who relapsed (R) (n=38)vs. those who did not relapse (NR) (n=111). Analysis was performed using DESeq2 in R 4.3.0. P-values were adjusted with Benjamini-Hochberg correction to control for false discovery rate a significance threshold for padj of < 0.05 was applied. A list of 462 differentially genes was returned. Hierarchical clustering of the 462 differentially expressed genes revealed 4 patient clusters, each with a distinct transcriptomic signature ( Fig 1A). K-means (n=4) also returned similar results to the hierarchical clustering. Kaplan-Meier analysis of the 4 clusters showed a significant difference in patient outcomes both in terms of overall survival (P < 0.001) and event-free survival (P < 0.05) ( Fig 1B). In marked contrast to clusters 1-3, cluster 4 was highly enriched in patients who relapsed at a rate of 86%. Clusters 1, 2 and 3 had relapse rates of 36, 29 and 38 percent respectively. To identify the most relevant genes that could serve as a TRS, we trained a random forest (RF) model using transcript per million (TPM) transformed and length normalized counts for each of the 462 differentially expressed genes at the time of diagnosis between the R and NR cohort; the response variable was patient relapse outcome. Data was split into 70% training and 30% testing cohorts. As the small size of our cohort was a potentially limiting factor, we utilized 5-fold cross validation in the training of our model. Recursive feature selection was applied to the model and was iteratively trained using subsets of features (predictor genes) ranging from 1 to 100. Features were then recursively sorted by importance and an optimal number of 30 predictors were chosen. Application of our model to the testing dataset of 45 patients (R = 12, NR = 33) allowed us to accurately predict the outcome in 40 of 45 patients. This model accurately predicted 33 of 33 NR and 7 of 12 R patients. This model was both specific and sensitive for NR and specific to R but lacked sensitivity as we were only able to identify 58% of relapse patients. Finally, this 30-gene list was then compared to survival analysis on a by-gene basis which yielded a final panel of 16 genes which we call our TRS. These genes were; PRDM8, RARG, CSF1, PDE4B, CCL3, NAB1, WHRN, SGSM2, LPIN3, CHARLIE1B, SATB1, ZNF441, ZNF521, AL451123.1, TSPYL4 and B3GNT5. The RF model was re-trained on this smaller panel and re-tested with similar results. By applying differential expression analysis, K-means clustering and machine learning to RNAseq data from a cohort of 149 pediatric AML patients we successfully identified a relapse-signature using a panel of 16 genes evident at the time of diagnosis and prognostic of patient outcomes. Future efforts will focus on increasing the sensitivity of our model to relapse prediction and further validation on other pediatric t(8;21) cohorts.

Mutational and Cytogenetic Dynamics at Diagnosis and Relapse in Acute Myeloid Leukemia: Influence of Intensity and Type of Treatment

Introduction: Cytogenetic and molecular aberrations are common at diagnosis in patients with acute myeloid leukemia (AML) and may have significant prognostic impact. Relapse after prior response is associated with a poor outcome. The dynamics of cytogenetic and molecular abnormalities at relapse and their impact on outcome is less well studied. Methods: This is a retrospective single center study including patients with AML diagnosed from April 2017 to October 2022 who relapsed after achieving a prior response. Mutations were detected using a targeted 81-gene NGS panel and cytogenetics were assessed using conventional karyotyping and FISH testing. To assess disappearance, maintenance or appearance of cytogenetic and molecular aberrations, they were evaluated at diagnosis and relapse and differences in incidence were evaluated with the Chi-square and Fisher test. Results: The cohort includes164 patients who had relapsed after achieving remission. The median age at diagnosis and relapse was 67 years (range, 20-94) and 68 years (range, 21-95). 53% were male. Patients received intensive treatment (IT; 40% of patients, 41% of whom with the addition of venetoclax) or low intensity therapy (LIT; 60% of patients, 72% with venetoclax). The median time from diagnosis to relapse was 8.9 months (range, 2.2-52). According to the ELN 2022 risk classification, 15%, 15% and 70% had favorable, intermediate and adverse risk, respectively. At diagnosis, the most frequent mutations were DNMT3A (32%), TP53 (31%), RUNX1 (19%), TET2 (18%), SRSF2 (17%) and NPM1 (17%). At relapse, the most frequent mutations were DNMT3A (35%), TP53 (35%), TET2 (24%), RUNX1 (20%) and SRSF2 (17%). The median number of mutations per patient at diagnosis and relapse was 3 (0-12) and 3 (0-14), respectively (p=0.07). Most frequent karyotypes at diagnosis were diploid (34%), complex (32%), chromosome 5 abnormalities (29%) and chromosome 7 abnormalities (26%). At relapse, the most frequent karyotypes included complex (36%), chromosome 7 abnormalities (31%), chromosome 5 abnormalities (30%) and diploid karyotype (27%). When analyzing each mutation individually, the rate of mutation clearance from diagnosis to relapse was higher for FLT3-ITD (58%, p=0.01), FLT3-TKD (83%, p<0.001), KIT (88%, p=0.003), NF1 (71%, p=0.004) and WT1 mutations (71%, p=0.004), compared to other remaining mutations (32%). Conversely, ASXL1 (95%, p=0.01), DNMT3A (84%, p=0.006), SRSF2 (89%, p=0.01), TET2 (84%, p=0.02) and TP53 mutations (86%, p=0.002) persisted more frequently at relapse compared to other mutations (66%). At relapse, WT1 mutations were more frequently acquired (77%, p=0.001), compared to other mutations (36%). Diploid karyotype changed more frequently than other cytogenetic abnormalities (33% vs 5%, p <0.001), whereas complex karyotype persisted at relapse (98% vs 87%, p=0.04) more frequently. Chromosome 7 abnormalities were more frequently acquired at relapse (23%), compared to other cytogenetic abnormalities acquired at relapse (11%, p=0.04). We then compared mutational dynamics from diagnosis to relapse between patients receiving IT and LIT. NRAS mutations disappeared more frequently from diagnosis to relapse in patients treated with IT (73%), compared with patients treated with LIT (27%, p=0.01) whereas TP53 mutations were acquired more frequently in IT treated patients (67% vs 10%). Patients treated with IT acquired chromosome 7 abnormalities more frequently than patient treated with LIT (60% vs 14%, p=0.007). No significant differences were found regarding disappearance, maintenance or appearance of mutations when comparing patients treated with or without Venetoclax. Conclusion: The number of mutations does not vary significantly from diagnosis to relapse, and most mutations persist, suggesting maintenance of leukemic clones as the cause of relapse. Overall, genes involved in signaling pathways tend to disappear more frequently at relapse whereas chromatin and histone modifiers as well as TP53 mutations tend to persist. NRAS mutations disappear more frequently at relapse with IT, whereas TP53 mutations are acquired more frequently.

TAS0612, a Triple Inhibitor for RSK, AKT, and S6K, Is a Promising Anti-Myeloma Agent Regardless of Types of Cytogenetic/Genetic Abnormality

Introduction: Despite advancements in therapeutic approaches, treatment outcome for multiple myeloma (MM) remains unsatisfactory. One critical factor of the poor outcomes is the complex inter-patient and intra-clonal heterogeneity of cytogenetic, genetic, and molecular abnormalities. To overcome this, the exploration of therapeutic target molecules that play a universal and essential role in MM regardless of the types of molecular profile is crucial even in the post-genomic era. We have previously demonstrated that RSK2 Ser227 at the N-terminal kinase domain (NTKD), as the downstream signaling hub of the RAS/ERK pathway, plays essential roles in the proliferation and survival of myeloma cells (Shimura Y, Mol Cancer Ther 2012). We also identified that RSK2-NTKD is constitutively activated by constitutive active PDPK1, the master serine-threonine kinase of >20 AGC kinases, in myeloma cells of approximately 90% of MM patients regardless of cytogenetic abnormalities (Chinen Y, Cancer Res 2014, Tatekawa S, Br J Haematol 2017). Moreover, the combinatory blockade of RSK2 and AKT, one of the other important molecules regulated by PDPK1, exhibited synergistic anti-myeloma efficacy through the modulation of various critical gene sets involved in myeloma pathophysiology, such as MYC (Isa R, Int J Mol Sci 2022). Based upon these, this study investigates the anti-myeloma potency of TAS0612 (Taiho Oncology Inc., Princeton, NJ) that targets RSK, including RSK2, AKT, and S6K, and inhibits the bindings to their respective substrate molecules (Shibata T, Mol Cancer Ther 2020). Methods and Results: Firstly, we examined the activation status of RSK, AKT, and S6K in eight human myeloma-derived cell lines (HMCLs) with diverse genetic and molecular profiles at the protein level. RSK2 Ser227 was found to be commonly activated through phosphorylation in all HMCLs examined. In contrast, the activation patterns of p-AKT Ser473 and p-S6K Thr389 were inconsistent among eight HMCLs, and depending on cell types. Despite these cell type-dependent effects, the exposure to TAS0612 resulted in the accumulation of p-total RSK Ser380, p-AKT Ser473, and p-S6K Thr389 in the majority of HMCLs examined, and this led to the subsequent inactivation of their respective target substrates, such as p-YB1 Ser102, p-PRAS Thr246, and p-S6 Ser235/236, through dephosphorylation. In accompany with these molecular effects, the modified MTT assay showed the dose-dependent growth inhibitory effects of TAS0612 in all cell lines with various types of cytogenetic/genetic abnormalities with IC50 values mostly below 0.5 μM (48 hours). In addition, flow cytometry analyses for the cell cycle analysis and the apoptosis assay by the counterstaining of propidium iodide and Annexin-V showed that TAS0612 induced G1/S cell cycle arrest and apoptotic cell death. Furthermore, patient-derived primary myeloma cells were labeled with anti-CD138 MicroBeads, and were positively isolated from bone marrow mononuclear cells from patients with newly diagnosed MM (n=7) and relapsed/refractory MM (n=11), and, then, were treated by TAS0612. As the results, the ex vivo treatment of 2.5-5.0 μM TAS0612 for 72 hours showed robust cell reductive effects on primary-myeloma cells from all 18 patients examined irrespective of cytogenetic profile. To clarify the precise molecular effects of TAS0612 treatment in myeloma cells, we conducted a comprehensive molecular analysis with TAS0612 treatment by gene expression profiling. The results showed that TAS0612 treatment significantly modulated the gene sets involved in Myc signaling, mTOR signaling, and the core serum response (CSR). Additionally, TAS0612 caused the concomitant upregulation of several bona-fide tumor suppressor genes, including TP53INP, HBP1, FBOX32, and YPEL3, while the downregulation of oncogenes LYAR and HSPA1. Intriguingly, according to MMRF CoMMpass Study, 8 of 18 upregulated genes by TAS0612 in HMCLs were reported to be associated with favorable survival outcomes when highly expressed in myeloma cells. Conclusion: Our findings strongly support the potential of TAS0612 as an effective anti-myeloma agent. Further preclinical investigations are necessary to substantiate these results and facilitate its future clinical development.

Real World Outcomes in Patients with Ph-like ALL at the University of New Mexico

Introduction: Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a heterogenous subtype of ALL characterized by different translocations and molecular mutations, resulting in a gene expression profile similar to Philadelphia chromosome positive (Ph+) ALL without an identified BCR::ABL1 translocation. Unfortunately, Ph-like ALL is characterized by worse response rates to conventional therapies and poor overall survival compared to other ALL subtypes. It is reported that 20-30% of patients with newly diagnosed ALL in the United States have Ph-like ALL and the incidence appears to vary according to ethnicity. While many therapies are under investigation including the addition of a tyrosine kinase inhibitor or ruxolitinib to conventional chemotherapy, a standardized and molecularly-based approach to treating patients with Ph-like ALL is not yet defined. There also remain questions about the efficacy of integrating inotuzumab ozogamicin or blinatumomab into first-line therapy for these patients. In addition, recent retrospective data has demonstrated promising effects of using traditional salvage therapies for ALL such as Car T cells, inotuzumab, or blinatumomab in patients with Ph-like ALL. However, the optimal sequence of treatment as well the efficacy of combining salvage therapies with agents such as ruxolitinib remains unknown. Herein, we present our institutional experience with diagnosing and treating adult patients with Ph-like ALL at the University of New Mexico. Our goal was to characterize the demographics, molecular and cytogenetic landscape, and treatment outcomes at a medical center that serves a patient population enriched for this disease. Methods: After IRB approval, we performed a retrospective chart review of patients diagnosed and treated at the University of New Mexico between January 1, 2018 and April 1, 2023. We included patients who were 18 years or older at the time of diagnosis, received first-line therapy at the University of New Mexico, and had gene expression profiling or FISH testing that was consistent with Ph-like ALL. Statistical analysis was performed using SPSS Statistics v.27 (IBM, 2020). Results: We identified 9 patients who met inclusion criteria. All 9 patients self-identified as either ‘American Indian or Alaska Native’ or ‘Hispanic or Latino.‘ The median age at diagnosis was 34 and the mean BMI at diagnosis was 34.6. 5 patients were CD20 positive and 1 patient had a concurrent IKZF1 mutation. All patients received induction chemotherapy with either a BFM regimen or HyperCVAD. 5 (55%) patients were refractory to induction and 6 (66%) patients eventually underwent allogeneic stem cell transplant as part of their treatment. 1 patient received Car T cell therapy with Brexucabtagene autoleucel following relapse after allogeneic stem cell transplant. 1 patient died 124 days after diagnosis and 8 patients are alive currently. 4 patients had IGH:: CRLF2, 2 patients had P2RY8::CRLF2,1 patient had GTF2I::PDGFRB,1 patient had IGH::BCL2,and one patient had both a positive low-dose array and a positive gene expression profile without an identified molecular or cytogenetic abnormality consistent with Ph-like ALL. Discussion: We present our preliminary experience of patients with Ph-like ALL diagnosed and treated at the University of New Mexico. Our patients were young with a median age of 34. Consistent with published data describing patients with Ph-like ALL, our patients had poor responses to traditional ALL treatments and most commonly had an identified fusion with CLRF2. Our data supports the urgent need for the development of further treatment options for patients with Ph-like ALL as well as clinical trials aimed at standardizing management.

Development of First in Class DNA-Zip Code Drug Conjugate (ZDC) in Multiple Myeloma

Multiple myeloma is a heterogeneous malignant plasma cell disorder with complex molecular and genetic abnormalities. Significant advances have been made in the treatment of multiple myeloma; however, a large proportion of patients fail to attain a favorable response and relapse. Due to efficacy and toxicity, the development of drug conjugates for multiple myeloma has been limited. Our lab discovered that circulating tumor DNA (ctDNA) serves as a cell-specific mechanism for genetic transmission. Certain retrotransposon sequences within the ctDNA were identified as being crucial for the tropism of ctDNA to target tumor cells (Cinar et al bioRxiv.2022). We therefore query whether these transposons can be exploited for the targeted drug delivery. To do so, chemically synthetize and CY5-labeled multiple retrotransposons DNA sequences (a.k.a Zip Codes, ZC) to perform high through put screening assessing for cell targeting. Our findings showed that the AluSp and MER11c DNA sequences (MM-ZC1 and 2) with unique MM mutations were the most efficient and specific DNA sequences for targeting myeloma cells. Furthermore, Flow cytometry and CYTOF validated the specific MM cell targeting on full bone marrow samples from MM patients. Based on this analysis we used MMZC1 for further drug development. We design a drug conjugation approach for the MMZC and screen various drugs for their killing potential. Two potent MM ZC drug conjugates (ZDC) were identified by high throughput viability screening assay: ZC-DM4, a microtubule inhibitor, and ZC-Carfilzomib, an irreversible proteasome inhibitor. We move forward exploration with ZC-DM4 due to limited carfilzomib-linker drug availability. Experiments cancer cell lines in vitro demonstrated that MMZC-DM4 had a potent killing effect on MM cells (IC50: 3.25 nM) but not on other cancer cell lines. These results were the validated in vivo. Maximum tolerated dosing studies (MTD) demonstrated excellent tolerability in all doses (ranges from 1 to 20 mg of MMZC-DM4/Kg (equivalent to 0.007-0.149 mg of DM4/kg). To look for an efficacy signal of MMZC-DM4, MM xenograft mice were given MMZC-DM4 twice a week for three weeks. Due to limitations in production, we treated the animals biweekly with three distinct low doses of MMZC-DM4: 1.9, 3.75, and 7.5 mg/kg (equivalent to 0.014, 0.028, and 0.056 mg of DM4/kg) and compared their response to mice not treated with MMZC-DM4 and mice treated weekly with bortezomib. MMZC-DM4 at such small doses reduced the tumor by 30% without affecting body weight, WBC, HB, AST, or platelets. In contrast, Bortezomib was associated with 90% growth inhibition at the expense of significant weight loss that required treatment interruptions and thrombocytopenia. Currently, investigations are being conducted to examine the therapeutic efficacy of greater doses of MMZC-DM4. This study described the first-in-class MM targeted medicine delivery employing an MM zic code drug conjugate. Our findings suggest new method for targeted delivery therapeutic cargo material directly to cancer cells that could revolutionize cancer treatment.

Survival Outcomes Associated with Molecular and Cytogenetic Alterations in AML Patients Treated with Hypomethylating Agent and Venetoclax

Molecular profiling has improved prognostication and helped identify novel therapeutic targets in AML. Nonetheless, it has also created a complex web of molecular profiles and cytogenetic abnormalities and in many cases it remains unclear which specific alterations primarily drive leukemogenesis. We sought to review our patients (pts) treated with a hypomethylating agent (HMA) + Venetoclax (Ven), to evaluate molecular and cytogenetic profiles with their associated outcomes. We identified 142 pts with AML treated with HMA + Ven at Northwell Health between January 2019 and December 2023. Through retrospective chart review, we obtained patient and disease characteristics, treatment regimens, clinical outcomes as well as molecular and cytogenetic profiling (using commercial AML panels) prior to the initiation of HMA + Ven. Bone marrow biopsy pathology reports were reviewed to identify the subtype of AML and grouped into De novo AML, AML with MDS related changes (AML-MRC) and therapy-related AML (t-AML). Median relapse free survival (mRFS) and median overall survival (mOS) in months (m) as defined by ELN 2022 (Dohner et al, Blood 2022), were estimated with Kaplan-Meier curves and compared utilizing log-rank testing. T-test was used to evaluate significant differences between categorical data. Of the 142 pts identified, the median age was 77. The majority of patients had adverse (n = 99) or intermediate risk (n = 31) genetics as defined by the 2022 ELN genetic risk classification. The overall response rate (ORR) was 42% with mOS of 9.6m. AML-MRC patients (n=80) had mOS of 9.1m and mRFS of 11.6m with 61 pts receiving HMA + Ven as frontline treatment. 47 pts with De novo AML had mOS of 13.4m and mRFS of 16.1m with 36 pts receiving HMA + Ven as frontline therapy. Only 15 pts had t-AML with mRFS of 12.3m and mOS of 8.8m with 10 pts receiving HMA + Ven as frontline therapy. There was no significant difference in mRFS or mOS between these groups, although there was a trend favoring De novo AML. 47 different molecular alterations were identified among the 142 patients. Figure 1 illustrates outcomes associated with the 16 most prevalent molecular alterations found in our AML population. Mutational burden was similar between AML types (2.7 vs 3.0 vs 2.4 mutations per pt). De novo AML was associated with an increased mutation burden in signaling molecules (60%) and transcription factors (47%) compared to AML-MRC (29%, 31%). AML-MRC had a higher occurrence of mutations in epigenetic regulatory genes (79%) and splicing factors (31%) compared to De novo AML (55%, 19%). Mutations in splicing factors were associated with a significant increase in both mRFS and mOS(p = 0.01) compared to pts without mutations. Pts with DNMT3A, NPM1 or SRSF2 mutations had the highest ORR to HMA + Ven (63%, 64% and 63% respectively). RUNX1, TP53, complex cytogenetics and del 7q were associated with worse ORR (46%, 36%, 46% and 42% respectively) as well as decreased mOS. SRSF2, mutated in both AML-MRC and De novo AML, not only had an elevated ORR, but improved mRFS and mOS. Contrarily, mRFS and mOS were not significantly improved despite the high ORR in DMT3A mutated pts. DNMT3A was mutated most often in AML-MRC and was associated with a higher rate of other epigenetic regulatory gene co-mutations. The same is true for patients with KMT2A mutations (ORR 50%, mOS 2.8m, mRFS 6.1m) which suggests ineffectiveness of HMA+ Ven in maintaining remissions with this alteration with possible early selection for resistant clones. RUNX1 mutations were associated with an improved mRFS (16.1m) despite lower mOS (8.8m). NPM1 mutations had the highest mRFS of 34.4m. The survival advantage may be secondary to the absence of adverse cytogenetics in 88% of these pts. IDH2 mutations was associated with a significantly improved mOS compared to unmutated IDH2; however this may be confounded by the use of an IDH2 inhibitor at relapse. Our review of molecular alterations in AML pts identified several molecular alterations such as SRSF2, DNMT3A, RUNX1 which we found to be associated with favorable responses when treated with HMA + Ven. In addition, we demonstrated that NPM1 mutation remains favorable in patients treated with HMA + Ven. Our findings help contribute to the ever-growing, complex molecular and genomic profiling of AML patients.

B-Lymphoblastic Leukemia Presenting with Eosinophilia: A Case Report and Review

B-lymphoblastic leukemia (B-ALL) presenting with eosinophilia represents a rare entity. In particular, the unique clinical manifestations as well as the genetic and molecular pathogenesis of the associated eosinophilia have been topics of debate and investigation. Herein, we present a case of B-ALL presenting with concomitant eosinophilia and a review of the published cases, including 120 additional cases. The patient, at presentation, was a 20-year-old female who presented with cardiac, neurologic, and cutaneous signs of eosinophilia and with leukocytosis (WBC 51, 40% eosinophils, 0% blasts), anemia, and thrombocytopenia. Imaging revealed multi-focal brain infarcts, pulmonary infiltrates, and myocarditis. Empiric steroids, colchicine, and intravenous immunoglobulin were initiated. One week after presentation, bone marrow biopsy revealed a hypercellular (>95%) marrow with 50% blasts and marked eosinophilia, which on later review revealed an immunophenotype most consistent with B-ALL (positive for Pax5, CD10, CD19, CD20, cCD22, CD34, CD45, CD79a, HLA-DR, and TdT and negative for MPO and CD117). Conventional cytogenetic analysis of the bone marrow was unable to be performed. Fluorescence in situ hybridization (FISH) revealed an IGH rearrangement in 10.5% of nuclei analyzed. After three weeks of treatment with steroids and resolution of symptomatic organ involvement, a repeat bone marrow biopsy did not show any evidence of malignancy or genetic abnormalities. The patient was continued on a steroid taper, did not initiate further antileukemic therapy, and was lost to follow up. Ten weeks after initial presentation and after completing a steroid taper, the patient presented with diffuse bone pain. Repeat bone marrow biopsy showed B-ALL with 64% blasts and increased eosinophils, normal conventional cytogenetics and hematologic malignancy sequencing panel, and FISH with gain of Xp in 20.5% of nuclei analyzed; a lumbar puncture did not detect blasts in the cerebrospinal fluid. The patient began induction therapy with aBFM, rituximab, PEG-asparaginase, and intrathecal cytarabine. A bone marrow biopsy performed four months after her initial presentation revealed a mildly hypocellular marrow with 3% B-lymphoblasts and no eosinophilia, suggesting residual disease, with no evidence of cytogenetic or molecular genetic abnormalities. As a result, therapy with blinatumomab was initiated. A follow up bone marrow biopsy performed six months after her initial presentation revealed a hypocellular marrow with multilineage maturation and no excess blasts with normal cytogenetic and molecular genetic studies. A literature review identified 120 additional cases of ALL with eosinophilia. In summary, it tends to present in adolescent males, often with mild anemia and thrombocytopenia and no peripheral blasts, which can lead to a delay in diagnosis of ALL. The eosinophilia is often symptomatic, with cardiopulmonary involvement being the most common, and can lead to rapid mortality in a substantial number of cases. A significant proportion of cases of ALL with eosinophilia involve t(5;14)(q31;q32), leading to overexpression of IL-3, which was not definitively found in this patient; however, there are numerous other recurrent abnormalities that may be contributing to the pathogenesis, both concurrently with and in the absence of this translocation, including other rearrangements of IGH as well as IKZF1 and CDKN2A abnormalities. Prompt diagnosis, now commonly using sensitive molecular diagnostic assays, and initiation of glucocorticoids for symptom control and subsequent antileukemic therapy, are essential to avoiding complications of eosinophilia in such patients.

Oral Decitabine/Cedazuridine Vs Intravenous Decitabine for Acute Myeloid Leukemia: Final Results of a Randomized, Crossover, Registration-Enabling, Pharmacokinetics Study

Background: Parenterally administered hypomethylating agents (HMAs), decitabine (DEC) and azacitidine (AZA), are approved in Europe for adult patients with acute myeloid leukemia (AML) who are not candidates for standard induction chemotherapy as single agent or in combination with venetoclax. Cedazuridine(C) is a novel, potent, and safe inhibitor of cytidine deaminase (CDA) and when given in combination with decitabine, cedazuridine enables efficient oral availability of decitabine.ASTX727 (DEC-C) is a fixed-dose combination (FDC) tablet of 35 mg DEC and 100 mg cedazuridine, DEC-C has been approved for MDS in the US, Canada, and Australia. Here we present final results using DEC-C in an AML population appropriate for single-agent decitabine treatment. Aims: Describe the final clinical outcomes of patients with AML with additional analysis of genetic profiles. Methods: The ASCERTAIN study used a randomized two-period, two-sequence, two-treatment, crossover study design. Patients were randomized 1:1 to either Sequence A: DEC-C (35 mg DEC/100 mg cedazuridine) in Cycle 1 followed by IV-DEC at 20 mg/m 2 in Cycle 2, or Sequence B: receiving IV-DEC in Cycle 1 followed by DEC-C on Cycle 2 to compare pharmacokinetics (PK) [primary endpoint Area Under the Curve (AUC) equivalence over 5 days of dosing]. All patients received DEC-C from Cycle 3 until treatment discontinuation to assess safety and clinical efficacy. Patients were eligible as per the EMA-approved decitabine label (newly diagnosed AML who are not candidates for standard induction chemotherapy). Clinical responses were assessed according to modified International Working Group (IWG) 2003 response criteria. Pre-treatment peripheral blood was used for DNA isolation from leukocytes, and molecular abnormalities identified using a NGS hematologic malignancy panel. Cox-regression analysis on the various factors (eg binary mutational status, CR, etc.) was used for analyses of risk-factors for overall survival (OS). Results: 89 patients were randomized, of whom 87 were treated. The median age of patients was 78.0 years (range, 61 to 92) with 31 (35.6%) males and 56 (64.4%) females. Cytogenetic risk classification was poor-risk in 33 (37.9%), intermediate-risk in 45 (51.7%), and 9 (10.4%) not evaluated patients. For the primary endpoint, preliminary PK data was available from 69 patients who successfully completed PK assessments for both IV-DEC and DEC-C cycles, and the DEC AUC 0-24 (h*ng/mL) 5-Day geometric mean estimate was 904 for DEC-C and 907 for IV-DEC resulting in an oral/IV geometric LSM AUC ratio of 99.64% (90% CI of 91.23-108.8%). Safety findings were consistent with those anticipated for IV-DEC (related Grade ≥ 3 AEs in more than 10% were thrombocytopenia, neutropenia, anaemia, and febrile neutropenia). As of the database lock (25May2023), median follow up was 24.5 (20.2, 25.0) months (25% of 19.7 and 75% of 25.2 months). The best response was complete response (CR) in 19/87 (21.8%, 95% CI: 13.7, 32.0%); CR with incomplete blood cell count recovery (CRi) in 5 patients (5.7%); and CR with incomplete platelet recovery (CRp) in 2 (2.3%); resulting in composite response rate [CR + CRi] of 27.6%. The median overall survival was approximately 8.9 months (95% CI: 6.0, 13.1).These results obtained with DEC-C are consistent with those observed for IV-DEC. Multiple genes, including ASXL1, TP53, RUNX1, and SRSF2 genes were present in more than 20% of the AML patients. TP53 mutation was associated with worse survival. Summary/Conclusion: This randomized phase 3 study in AML patients not candidates for standard induction chemotherapy demonstrates that Daily X 5 dosing of the oral FDC of DEC-C resulted in an equivalent DEC AUC exposure to IV-DEC at 20 mg/m 2 over 5 days. Pharmacodynamic data showed similar demethylation rates (≤1.1% difference). In addition, safety findings and observed clinical activity (response rates and OS) are consistent with published data from IV-DEC, suggesting that DEC-C has the potential to be an oral alternative to the standard IV-DEC Daily×5 regimen. These findings support the use of DEC-C in patients with AML who are not candidates for standard induction chemotherapy.

Reclassification of Ascertain (ASTX727-02) Myelodysplastic Syndrome (MDS) Patients: Outcomes Including Clinical Response, Overall Survival (OS), and Leukemia Free Survival (LFS) Based on IPSS-R and IPSS-M Scoring Systems

Background: Oral decitabine/cedazuridine (ASTX727) is a fixed dose combination of decitabine (35 mg) and the cytidine deaminase inhibitor cedazuridine (100 mg) given once daily X 5 days on a 28-day cycle producing pharmacokinetic (PK) exposure equivalent to the standard intravenous (IV) decitabine regimen of 20 mg/m 2 daily X 5 days on a 28-day cycle. This was demonstrated in the pivotal ASCERTAIN study (Garcia-Manero, et al, ASH 2019) as it provided a PK bridge to existing decitabine data and demonstrated median OS was 31.7 mo. (Savona,et al. Intl. MDSF International Congress on MDS, 2021). Subjects were initially classified by the International Prognosis Scoring System (IPSS) for historical reasons, however IPSS-R and IPSS-M are enhancements to IPSS that provide dynamic risk assessment for predicting clinical outcomes in MDS. Here, the objective was to re-classify the MDS subjects enrolled on the ASCERTAIN study by IPSS-R and IPSS-M and measure the impact of informing patient outcomes based on re-calculated risk assessment. Methods: One hundred thirty-three subjects with MDS/CMML (chronic myelomonocytic leukemia) were enrolled in ASCERTAIN and were randomly assigned either IV decitabine for cycle 1 and oral decitabine/cedazuridine for cycle 2 or the opposite treatment sequence. All subjects continuing beyond cycle 2 received oral decitabine/cedazuridine for all subsequent cycles until treatment discontinuation for disease progression, toxicity, patient's decision, or HSCT. Whole blood collected prior to treatment was used for DNA isolation and molecular abnormalities identified using next-generation sequencing (NGS) hematologic malignancy panel of 179 genes including all genes commonly mutated in MDS. In the initial analysis of clinical outcomes, subjects were classified by IPSS with response assessment by IWG 2006 IPSS low and Int-1 risk levels were categorized as lower-risk MDS (LR-MDS), whereas IPSS Int-2 and high-risk categories were categorized as higher-risk MDS (HR-MDS). Subjects with sufficient data based on (e.g., available heme parameters, cytogenetics, NGS etc.) were reclassified by IPSS-R and IPSS-M. Subjects with IPSS-R score of ≤3.5 or IPSS-M of either very low, low, or moderate low were categorized as LR-MDS. Similarly subjects with IPSS-R score of >3.5 or an IPSS-M categorization of either moderate high, high, or very high were categorized as HR-MDS. Reclassified subjects were reassessed for CR (Complete Response), OS, and LFS and Harrell's concordance index (c-index) was used to describe the level of agreement between each scale and outcomes. Results: Based on the available data, the number of MDS subjects in the different risk classifications were the following: IPSS: 117, IPSS-R: 104, and IPSS-M: 105. Thirteen and 12 subjects on the IPSS could not be reclassified in the IPSS-R and IPSS-M, respectively, including 5 Int-1 and 2 low-risk MDS cases. CMML subjects were excluded from these analyses. Re-classification generally resulted in the upgrade of the subjects from LR-MDS to HR-MDS (Fig. 1). Thirty-one (26.5%) subjects from IPSS were reallocated in the IPSS-R to different risk categories; 3 (9.7%) were downgraded and 28 (90.3%) were upgraded. Similarly on reclassification with IPSS-M 34 (32.4%) of the patients reclassified; 5 (14.8%) were downgraded and 29 (85.3%) were upgraded. For IPSS LR-MDS, 23.2% of patients achieved CR, and 22.9% in the IPSS HR-MDS. Similarly, 21.6% patients achieved CR in the IPSS-R LR-MDS, and 23.9% in the IPSS-R HR-MDS; 26.3% patients achieved CR in the IPSS-M LR-MDS, and 20.9% in the IPSS-M HR-MDS. The c-index for the IPSS was .64 (OS) and .67 (LFS), IPSS-R was .70 (OS) and .71 (LFS), and .75 (OS) and .78 (LFS) for the IPSS-M (Table1). Conclusion: Reclassification from IPSS to IPSS-R or IPSS-M upgraded multiple subjects from a LR to a HR category, describing the ASCERTAIN patient population as a majority higher risk population with worse prognosis than previously assumed based on the IPSS. The efficacy as measured by the CR rates did not change when the LR and HR categories were defined by the different risk stratification systems. In contrast, the c-index improves with migration from IPSS to IPSS-R to IPSS-M, indicating an increased discriminatory ability of IPSS-M score in comparison to IPSS and IPSS-R, to predict patient outcomes.

A Novel Prognostic Model for Patients with Acute Myeloid Leukemia in First Relapse with Improved Prognostic Accuracy

Introduction Despite high rates of complete remission (CR) after intensive induction chemotherapy in newly diagnosed AML, relapse is frequent and associated with poor outcome with a median overall survival (OS) of 3-5 months. While cytogenetic and molecular markers are associated with outcome in newly diagnosed patients, the prognostic value in the relapsed setting is unclear, even though it may facilitate therapeutic decision making. Genetic data was only limitedly available when earlier models for relapsed patients were developed, such as reported by HOVON-SAKK (Breems, JCO 2005) and GOELAMS (Chevallier, Leukemia, 2011). Therefore, a comprehensive analysis of clinical, cytogenetic and molecular variables in a prognostic model for outcome after relapse is needed. We set out to evaluate the impact of these variables on outcome after first relapse in the current therapeutic era, and develop a new prognostic model and compare that model with earlier models. Methods A total of 946 (44%) relapsing patients out of 2127 newly diagnosed AML patients who participated in prospective HOVON-SAKK trials of intensive induction chemotherapy between 2000-2018 were included in this analysis. A random survival forest machine learning algorithm was used to identify top markers impacting 1 year survival after relapse among 45 candidate predictors, including 7 clinical parameters, and 9 cytogenetic and 29 molecular abnormalities present at diagnosis. Cox regression with backward selection was performed to obtain hazard ratios (HRs) from relevant predictors identified by the random survival forest algorithm. A clinical prognostic tool was developed with points assigned to each marker based on the rounded logarithm of HR. Four groups were defined based on quartiles of the individual predictions. Prognostic accuracy of risk models was assessed using Harrel's C-index. Results The median age of relapsed patients was 58 years (range: 18-81), with 56% being male. Adverse risk AML according to ELN2022 risk was found in 48% of patients, whereas favorable and intermediate risk were classified in 22% and 31%, respectively. Prior allogeneic stem cell transplantation (SCT) in first CR was performed in 33% of patients, while 14% received autologous SCT. The median time between CR and relapse was 14 months (range: 0-124). The median follow-up time after relapse for patients alive was 49 months (range: 0-124). The random survival forest identified 16 parameters that were associated with 1 year OS based on variable importance, including: age at relapse ≥60 years, relapse-free interval ≤1 year, white blood cell count ≥10 x 10e9/L at diagnosis, prior allogeneic SCT, absence of t(8;21)/inv16, and presence of complex or monosomal karyotype (CK/MK), -5 or del(5q), -7, t(v;11q23), chromosome 17 alterations (-17, del(17p) or abn(17p)), FLT3-ITD, and mutations found in either TP53 with VAF ≥10%, DNMT3A, EZH2, NPM1, or NRAS. From these parameters, nine remained significant with Cox regression: age (HR 1.48, p<0.01), relapse free interval ≤1 year (HR 1.74, p<0.01), white blood cell count ≥10 x 10e9/L at diagnosis (HR 1.23, p=0.02), prior allogeneic SCT (HR 1.58, p<0.01), CK/MK (HR 1.53, p<0.01), no t(8;21)/inv(16) (HR 2.34, p<0.01), t(v;11q23) (HR 1.51, p=0.02), mutated TP53 with VAF ≥10% (HR 1.70, p<0.01), FLT3-ITD (HR 1.32, p<0.01). Next, weights were assigned to these variables based on the multivariate HRs (Figure 1A). Scores were calculated for individual patients and four groups were defined. OS at 1 year estimated 54±3% in the favorable risk group (≤5 points), 35±3% in the intermediate group (6-7 points), 18±3% in the high risk group (8-9 points), and 8±2% in the very high risk group (≥10 points) (Figure 1B). The prognostic accuracy for 1 year OS as measured by the C-index was 0.70. In contrast, in this cohort C-indices for the HOVON-SAKK and GOELAMS models were 0.65 and 0.64, respectively. In addition, comparing the earlier models with the new model, 50% of patients in the adverse group of the HOVON-SAKK model were classified to the favorable (14%) and intermediate group (36%) in the new model. In the GOELAMS model, 42% of intermediate risk patients were considered high (10%) or very high risk (32%) in the new model. Conclusion Analysis of clinical, cytogenetic and molecular variables identified nine variables for a new prognostic model which was associated with distinct OS at 1 year after first AML relapse and improved prognostic accuracy.

The Occurrence of Infection and TP53 Mutation Are Risk Factors for Cardiovascular Toxicity of Acute Myeloid Leukemia Induction Therapy

Introduction: For almost 50 years,induction therapy (IT) is the standard of care for acute myeloid leukemia (AML) patients. Nevertheless, little is known about cardiovascular (CV) toxicity during IT. We aimed to describe CV events (CVE)occurring during IT and to identify clinical, hematological and molecular risk factors of such events. Methods: Two hundred and twenty-four patients of 18 years or more (median age 61 (51;67) years, 58% males), treated with ITbetween 2014 and 2021 were enrolled in this study. Two hundred and one (90%) received an anthracycline-based IT, the others received gemtuzumab ozogamicin as part of a clinical protocol research. Survival from the time from initiation of IT until death or until the initiation of the second course of therapy (either salvage regimen in case of primary refractory or relapsed AML, or intensive consolidation therapy in case of response) was considered. The primary endpoint was the time to occurrence of the first CVE after IT initiation, with death as a competing event. Multivariate analysis included significant covariate, identified by univariate models among initial characteristics and occurrence of infection (coded as time dependent covariate). Results: Hematological characteristics were as follows: European LeukemiaNet (ELN) 2022 risk of myelodysplastic neoplasm (MDS)/AML was low, intermediate and adverse in 13%, 29% and 58% of patients respectively. Main mutations encounters were: DNMT3A, FLT3, NPM1, TET2, NRAS, RUNX1, ASXL1, IDH2, PTPN11, BCOR, SRSF2, WT1 and TP53. Main CV risk factors were tobacco (36%), arterial hypertension (35%), obesity (24%), hyperlipidemia (22%), diabetes mellitus (11%). Baseline left ventricular ejection fraction (assessed by transthoracic echocardiography) was >45% in all patients, >55% in 95% of patients. Seventy-five patients (33%) presented a CVE during IT. Eighty-six percent of CVE were severe (grade 3 or more). Patients presenting CVE during IT were significantly older (p=0.02) and presented more often a past history of dilated cardiomyopathy (p=0.04), arterial hypertension (p=0.005) or dyslipidemia (p=0.005). At baseline, CVE patients presented a greater left auricle volume (p=0.005), higher tricuspid regurgitation grade (p=0.01), and more often a right ventricular dilatation or a significative valvopathy (respectively p=0.01 and p=0.03). There was no difference in CVE occurrence between patients treated with and without anthracyclin (p=0.2). Competing risk models identified the following adverse characteristic for the risk of first CVE, namely the occurrence of the first infectious event (Hazard ratio [HR]= 2.43, p=0.005), TP53 mutation (HR=1.79, p=0.04). No other clinical characteristics nor mutation (including TET2 and DNMT3A) were identified. Multivariate analyses demonstrated that TP53 mutation (HR=1.78, p=0.04) and occurrence of infection (HR=2.29, p=0.008) retained independent prognostic value, see Table 1. In a response stratified model, only TP53 mutation was a risk factor of first CVE (HR=2.46, p=0.008). Conclusions: CVE occurred in 33% of patients during IT and were severe. The major adverse role of onset of infection for CVE occurrence after IT could overcome the prognostic value of mutations usually associated with CV risk in the healthy population (i.e. TET2, DNMT3A, ASXL1, ...). TP53 mutation was the only molecular abnormality associated with CVE, in agreement with the increased risk of doxorubicin-induced cardiac toxicity in a mouse model of TP53 clonal hematopoiesis developed by Sano et al. These results suggest that TP53 mutated patients could benefit from careful CV monitoring and optimization of primary prevention treatment.

Engagement of Mesenchymal Stromal Cells in the Remodeling of the Bone Marrow Microenvironment in Hematological Cancers.

Mesenchymal stromal cells (MSCs) are a subset of heterogeneous, non-hematopoietic fibroblast-like cells which play important roles in tissue repair, inflammation, and immune modulation. MSCs residing in the bone marrow microenvironment (BMME) functionally interact with hematopoietic stem progenitor cells regulating hematopoiesis. However, MSCs have also emerged in recent years as key regulators of the tumor microenvironment. Indeed, they are now considered active players in the pathophysiology of hematologic malignancies rather than passive bystanders in the hematopoietic microenvironment. Once a malignant event occurs, the BMME acquires cellular, molecular, and epigenetic abnormalities affecting tumor growth and progression. In this context, MSC behavior is affected by signals coming from cancer cells. Furthermore, it has been shown that stromal cells themselves play a major role in several hematological malignancies' pathogenesis. This bidirectional crosstalk creates a functional tumor niche unit wherein tumor cells acquire a selective advantage over their normal counterparts and are protected from drug treatment. It is therefore of critical importance to unveil the underlying mechanisms which activate a protumor phenotype of MSCs for defining the unmasked vulnerabilities of hematological cancer cells which could be pharmacologically exploited to disrupt tumor/MSC coupling. The present review focuses on the current knowledge about MSC dysfunction mechanisms in the BMME of hematological cancers, sustaining tumor growth, immune escape, and cancer progression.

Incidental detection of FGFR3 fusion via liquid biopsy leading to earlier diagnosis of urothelial carcinoma

The rising utilization of circulating tumor DNA (ctDNA) assays in Precision Oncology may incidentally detect genetic material from secondary sources. It is important that such findings are recognized and properly leveraged for both diagnosis and monitoring of response to treatment. Here, we report a patient in whom serial cell-free DNA (cfDNA) monitoring for his known prostate adenocarcinoma uncovered the emergence of an unexpected FGFR3-TACC3 gene fusion, a BRCA1 frameshift mutation, and other molecular abnormalities. Due to the rarity of FGFR3 fusions in prostate cancer, a workup for a second primary cancer was performed, leading to the diagnosis of an otherwise-asymptomatic urothelial carcinoma (UC). Once UC-directed treatment was initiated, the presence of these genetic abnormalities in cfDNA allowed for disease monitoring and early detection of resistance, well before radiographic progression. These findings also uncovered opportunities for targeted therapies against FGFR and BRCA1. Overall, this report highlights the multifaceted utility of longitudinal ctDNA monitoring in early cancer diagnosis, disease prognostication, therapeutic target identification, monitoring of treatment response, and early detection of emergence of resistance.

MODL-15. ESTABLISHMENT OF ORGANOID MODELS OF PATIENT-DERIVED GH-PRODUCING PITUITARY ADENOMA

Abstract BACKGROUND Growth hormone-producing pituitary adenomas (GHomas) reveal unfavorable clinical course due to systemic complications such as excessive sweating, impaired glucose tolerance, and hypertension, in addition to its characteristic facial appearance. For GHoma, pharmacological treatments including somatostatin analogs and dopamine agonists are widely performed, however, a subset of case reveals dismal prognosis. We need to elucidate molecular mechanisms contributing to GHoma growth, however, experimental models of GHoma such as cell line and animal model are quietly limited. OBJECTIVE In recent years, organoid models using 3D-culture technologies have gained attention as useful research models for various types of cancers. This study aims to establish a novel organoid model derived from GHoma patients. Using established GHoma organoid model, we analyzed their histological characteristics. METHODS Surgical specimens from five cases of GHoma were finely dissected to approximately 1mm and embedded in Matrigel basement membrane matrix. The specimens were then cultured under 37°C conditions in a 5% CO2 incubator using a medium supplemented with various growth factors. After 28 days of culture, formalin-fixed paraffin-embedded sections were prepared, and the histological similarity with patient tumors was examined. RESULTS Hematoxylin and eosin staining showed that organoid models consisted of acidophilic, granular cytoplasm and small round nuclei, maintaining a cell morphology similar with the original tumor. Immunohistochemical staining revealed positive expression of growth hormone, Pit-1, and CAM5.2, which are specific markers for GHoma. CONCLUSIONS We successfully established a patient-derived organoid model of GHoma that retains histological and endocrinological characteristics. We believe that this model could be a valuable research model for elucidating the molecular mechanisms of GHoma and developing novel treatment approaches targeting important molecular abnormalities. Additionally, in clinical settings, this model might be useful for predicting the responsiveness to drug treatment and selecting appropriate therapies for individual patients.

EPCO-34. IMAGE-BASED PHENOTYPIC HIGH-CONTENT CRISPR-CAS9 SCREEN FOR CHARACTERIZING CANCER DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA

Abstract The genomic landscape of pediatric high-grade glioma is characterized by a high level of aneuploidy but few focal amplifications or homozygous deletions. Cancer aneuploidies are the principal source of tumor heterogeneity driving tumor growth and therapy resistance. Here, we deployed an image-based phenotypic high-content CRISPR-Cas9 screen to identify aneuploidy-associated pediatric glioma driver genes. Through integrated computational analyses combining whole-genome sequencing datasets from 106 pediatric gliomas and 81 canine gliomas, we identified a set of 460 genes present in regions of aneuploidy in both diseases. We designed a custom guideRNA library to systemically knockout the 460 gene set using an arrayed CRISPR-Cas9 knockout screen in two pediatric high-grade glioma cell lines. By deploying 72 of 384-well plates on automated confocal Opera Phenix High-Content Screening System and dyes staining cell membrane, nucleus, and apoptotic cells, we established 5 million live-cell images across three timepoints (day 7, 8, 9 post-transduction). Each gene was randomized to 32 randomized wells across four 384-well plates to gather robust morphological profiles. Through image-based nucleus and cell segmentation workflow, we characterized 50 million single cells across 27,648 wells over three time points. Using semi-supervised machine learning methods, we derived 1,050 cell morphological features to characterize knockout phenotypes, e.g., viability, growth, and morphology (size, shape, texture of nucleus and cells) across cells. The top ranked genes were then linked to oncogenes and tumor suppressors based on pathway and ontology analysis as well as functional in vitro and in silico validation using Pediatric Cancer Dependency Map. We find convergence of the most impactful molecular abnormalities - based on their knockout phenotypes - on candidate signaling pathways for the development of new drugs and repurposing of existing drugs for pediatric high-grade glioma.