TP53 Alterations Research Articles

Abstract C171: Immune desert microenvironment is associated with poor outcome in Wilms tumors

Abstract Background: Presence of anaplasia is a potent marker for adverse outcome in patients with Wilms tumors with diffuse anaplasia (DAWT). Patients with WT with focal anaplasia (FAWT) are considered as intermediate risk. Besides TP53 mutations thought to arise in anaplastic components, the crosstalk between genomic alterations and immune landscape remains unknown. Methods: We performed whole-exome and/or RNA sequencing on genomic DNA derived from 12 matched tumor-normal WTs and extended analysis in an independent dataset of 9 cases. TP53 mutations and tumor infiltrating lymphocytes (TILs: CD3, CD4 and CD8) were also assessed. Validation was performed using TARGET-WT (n=96) and GEO-WT (n=12) cohorts. Prognostic role of TILs was investigated in another 55 pre-treated WTs. Results: TP53 (50%) and DROSHA (33.3%) were the sole recurrent mutations identified. TP53 mutations occurred in mutually exclusive manner with chromatin-modifying genes which were altered in both FAWT (100%) and DAWT (33.3%). Microenvironment analysis revealed a reproducible immune desert WTs with poor outcome that enriched in DAWT cases and TP53 mutation, which mirrored the inversion of CD4:CD8 ratio in TP53-mutated comparing to TP53-wild tumors (P=0.003). Immune desert WTs were also characterized by overexpression of DNA repair pathways, PRC2, HDCA, and polycomb targets of EZH2, leading to higher sensitivity to HDCA inhibitor of vorinostat. Additionally, the immunophenotypes were tightly associated with replication stress subtypes; WTs with high replication stress were susceptible to ATR and WEE1 inhibitors. High ratio of CD4/CD8 was considered as independent recurrence-free and overall survival factors for WTs (both P<0.05). Conclusions: Our results reveal that WT with anaplastic features are characterized by either TP53 alterations or chromatin-modifying genes. These data implicate TP53 as a tumor cell-intrinsic driver of an immune desert phenotype, in contrast with adult TP53 tumors. TP53 inactivation might therefore causes epigenetic deregulation across cancer sites, and has implications for immunotherapy. Citation Format: Xiaoping Su, Gabriel Malouf. Immune desert microenvironment is associated with poor outcome in Wilms tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C171.

Delineating the interplay between oncogenic pathways and immunity in anaplastic Wilms tumors

Wilms tumors are highly curable in up to 90% of cases with a combination of surgery and radio-chemotherapy, but treatment-resistant types such as diffuse anaplastic Wilms tumors pose significant therapeutic challenges. Our multi-omics profiling unveils a distinct desert-like diffuse anaplastic Wilms tumor subtype marked by immune/stromal cell depletion, TP53 alterations, and cGAS-STING pathway downregulation, accounting for one-third of all diffuse anaplastic cases. This subtype, also characterized by reduced CD8 and CD3 infiltration and active oncogenic pathways involving histone deacetylase and DNA repair, correlates with poor clinical outcomes. These oncogenic pathways are found to be conserved in anaplastic Wilms tumor cell models. We identify histone deacetylase and/or WEE1 inhibitors as potential therapeutic vulnerabilities in these tumors, which might also restore tumor immunogenicity and potentially enhance the effects of immunotherapy. These insights offer a foundation for predicting outcomes and personalizing treatment strategies for aggressive pediatric Wilms tumors, tailored to individual immunological landscapes.

CAR T-Cell Therapy Combined with PD-1 Inhibitors Significantly Improve the Efficacy and Prognosis of r/r DLBCL with TP53 Alterations

More than 40% of patients diagnosed with diffuse large B-cell lymphoma (DLBCL) eventually develop relapsed or refractory (r/r) disease and typically have poor outcomes. Autologous chimeric antigen receptor T-cell therapy (CART) has emerged as a crucial second line treatment option for r/r DLBCL, but 60-70% of patients still relapse or are refractory. Recent research has shed light on the role of TP53 alterations (mutation or deletion) in r/r DLBCL patients who do not respond well to CART cell therapy. The findings in this study will show that the combination of CART with PD-1 inhibitors (ICIs) had a significant impact on the efficacy and prognosis of r/r DLBCL patients with TP53 alterations. This retrospective analysis included adult DLBCL patients who were treated at Shanghai Tongji Hospital of Tongji University with autologous CD19 (N=20) or CD20 (N=2, patient 6 and 7, Fig.1 A) CART-cell therapy between January 1, 2019, and September 30, 2022. All enrolled patients provided their informed consent to participate in the study. The protocol of the study was reviewed and approved by the Institutional Review Board of the National Cancer Institute, ensuring ethical practices were followed. A total of 22 patients with TP53 alterations undergoing CD19-CART therapy were included, of which 2 patients received CD20 CART cell after recurrence of CD19 CART cell therapy. The total dose of CD19 or CD20-CAR T-cell is between 1- 3x10^6/kg. Sintilimab/Tislelizumab was used as PD-1 inhibitors (3 mg/kg in patients weighing <60 kg or 200 mg in patients weighing ≥60 kg) every three weeks within 6 weeks after CAR-T infusion. 1 case had grade 3-4 Cytokine Release Syndrome (CRS) and no case had CART-cell-related encephalopathy syndrome (CRES). In Table 1, the patients are divided into two groups. One group received CART cells combined with PD-1 inhibitors (ICI+), while the other group received CART cells only (ICI-). The median ICIs treatment time after CART infusion was 17 days (IQR 11-38 days). Baseline factors such as age, gender, disease severity, previous treatment history and etc. had no substantial differences between the groups. Treatment regimen and the subsequent response were shown in Fig.1 A and B. Patient 1-9 received ICIs treatment after CART cell therapy, of which 8 cases (88.9%) showed the best objective response rate (ORR) at day 90 after CART infusion (Fig.1B) and 6 cases (66.7%) achieved complete remission (CR). In comparison, among the 13 individuals who were treated with CART alone, only 3 cases (23.1%) showed the best ORR at day 90 after CART infusion and only 1 case (7.7%) achieved complete remission. We found a significant difference between the two treatment groups by performing a Chi-square test (P=0.009). Our results suggest that the addition of PD-1 inhibitors to the CART regimen significantly improves the treatment outcome in patients with TP53 alterations. In Fig.1 C and D, we show that the median progression-free survival (PFS) was NR (not reached) vs. 1.7 months (95% CI:1.0 month-2.3 months) and the median overall survival (OS) was NR vs.10.9 months (95% CI: 3.8 months-18.1 months) in the ICI+ and the ICI- groups. The p-values for PFS and OS was 0.001 (HR=0.18, 95% CI: 0.07-0.47) and 0.003 (HR=0.15, 95% CI: 0.05-0.42) between the two groups. These results suggest that patients in the combination treatment group experienced less disease progression and were more likely to survive longer. Overall, our study demonstrates the potential benefits of combining immunotherapies, specifically CART with PD-1 inhibitors, in the treatment of relapsed or refractory DLBCL patients with TP53 alterations.

Selinexor in Combination with Salvage Regimen for Refractory Diffuse Large B-Cell Lymphoma (DLBCL) Patients with TP53 Alterations

Background TP53 has been identified as one of the most frequently altered gene in diffuse large B-cell lymphoma (DLBCL). The prognosis of DLBCL patients with TP53 mutations ( TP53mut) was poor prognosis in R-CHOP era, even with treatments like autologous stem-cell transplantation (ASCT) or anti-CD19 chimeric antigen receptor T-cell (CAR-T) therapy. Moreover, TP53 mutations are more prevalent at relapse and are associated with therapeutic resistance. Selinexor is a selective inhibitor of nuclear export with promising anti-cancer properties and preclinical studies have shown its potential to suppress tumor cells with TP53 mutations. Several clinical studies proved selinexor in combination with R-GDP/R-ICE/R-Gemox was effective in relapsed/refractory DLBCL. Method The study enrolled relapsed/refractory DLBCL patients with TP53 alterations (including TP53 mutation and/or deletion) for treatment with selinexor in combination with salvage regimens (R-GDP/R-ICE/R-Gemox) since November 2021 in our center. The treatment was administered orally as 40 mg of selinexor on days 1, 8, and 15, combined with one of the following regimens: R-GDP (R 375mg/m2 d0, gemcitabine 1g/m2*d1, cisplatin 25mg/m2 d1-d3, dexamethasone 40mg d1-d4). R-ICE (R 375mg/m2 d0, ifosfamide 1.5g/m2*3d, carboplatin (AUC 5) and etoposide 100mg/m2*3d). R-Gemox ((R 375mg/m2 d0, gemcitabine 1g/m2*d1, oxaliplatin 100mg/m2*d1) every 3 weeks as per physician's choice. Objective response rate (ORR) was evaluated every 3 cycles based on Lugano 2014 criteria and Adverse events (AE) were rated according to the NCI CTCAE 5.0. Results 20 patients were treated with selinexor plus salvage regimen in this study and received at least two cycles of treatment, making them eligible for analysis. The median age of the 20 patients was 54 years (range 15 to 77), of this patients, 12 (60%) were male, 12 (60%) patients had disease stage III-IV at screening, and 45% with IPI>2. The median number of prior regimen was 1 (range, 1-4) with 2 patients (2 L) and 1 patient (3L). ALL patients were refractory to the last line of treatment. The patients received a median of three cycles (range, 2-6) of selinexor 40mg once a week combined with salvage regimen (13 patients received selinexor plus R-GDP, 6 with selinexor plus R-ICE and 1 with selinexor plus R-Gemox). The mutational profile of patients was presented in Figure A (14 patients with TP53 mutation, 5 patients with TP53 mutation and deletion, 1 with TP53 deletion). The best overall and complete response rates were 75% and 25%, respectively. Among them, 6 patients in PR and 1 patient in SD received CART treatment, and 5 achieved PR and 2 with CR after CART treatment (Figure B). One patient experienced PD after selinexor+R-GDP and died of disease progression within one month after CART transfusion. 1 SD patient transferred to CD3/CD20 bispecific antibody clinical trial and still progressed during the bispecific treatment. Taken together, selinexor-based salvage regimen had promising response rate in refractory DLBCL with TP53 alterations, and could be a potential bridging approach before CART therapy. Patients responded to selinexor-based regimen tended to have better outcome after CART or bispecific antibody treatment. Conclusions TP53 alterations are associated with poor outcomes in DLBCL. We identified an effective dosing schedule of selinexor (40mg QW) in combination with R-GDP/R-ICE/R-Gemox for TP53-altered refractory DLBCL patients. Further research is warranted to investigate the mechanism of action behind this treatment approach

Mutually-Exclusive Pathways between IKZF1plus and RAS Mutations and TP53 double-Hit Alterations Lead Relapse in B-Other, Ph-like and Hyperdiploidy Genetic Groups in Adult B-Cell Acute Lymphoblastic Leukemia

Introduction: Adult B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a hematologic malignancy characterized by a high genetic heterogeneity and high relapse rate. Despite treatment advances have led to high cure rates in pediatric BCP-ALL (90%), improving survival in adults remains a challenge. Identification of genetic alterations driving relapse and both new prognostic and therapeutic biomarkers are important to improve survival in adults with BCP-ALL. Aim: To identify genetic alterations that lead to relapse in adult BCP-ALL patients (18-72 years) based on the tumor genetic landscape. Methods: Forty-five adult BCP-ALL patients (median age: 43 years; range 18-72 years) were studied at diagnosis and relapse by massive sequencing using a custom panel that allows detection of single nucleotide variants (SNVs) and insertions/deletions (INDELs) in 150 genes involved in BCP-ALL, in addition to copy number variations (CNVs), gene fusions and aneuploidy. Thirty-eight percent of patients belonged to the BCP-other ALL group, 16% were Philadelphia-positive (Ph+), 16% were classified as Philadelphia-like (Ph-like), 11% belonged to the high hyperdiploidy group, 8% had KMT2A rearrangements ( KMT2Ar), 4% TCF3::PBX1 fusion, 3% showed hypodiploidy, 2% low hyperdiploidy and 2% de novo MYC and BCL2 double-hit. Patients were treated according to the Spanish Adult-PETHEMA high-risk ALL protocols. Results: The most frequently deleted gene at diagnosis was IKZF1 (25/45, 56%). Among these cases, 72% (20/25) had IKZF1plus genetic profile, characterized by co-occurrence of IKZF1 deletions with at least one deletion in CDKN2A/B, PAX5 or PAR1, without ERG deletion. The IKZF1plus genetic profile was associated with specific genetic subgroups: Ph+ (5/7, 71%), Ph-like (5/7, 71%) and B-other (10/17, 59%). Moreover, it was significantly related with the presence of minimal/measurable residual disease (MRD) after induction (16/18, 89%) p < 0.001 and persistence at relapse in most patients (18/20, 90%; p < 0.001). Interestingly, among those 5 patients initially diagnosed with IKZF1 deletion but who did not meet the criteria for the IKZF1plus profile, 2 of them acquired the IKZF1plus profile at relapse. This suggests a possible cooperation of these genetic deletions contributing to therapy resistance and disease progression in these genetic subgroups. Eighty-six percent (6/7) of Ph+ patients who received imatinib treatment presented ABL1 mutations that were detected exclusively at relapse. Of these cases, 67% (4/6) were also associated with IKZF1plus at relapse (Figure 1A). Two mutually exclusive genetic patterns were identified at relapse in adult B-other and Ph-like patients. Thus, patients with IKZF1plus profile did not show RAS pathway mutations (59% and 57%, respectively), while patients with RAS pathway mutations lack in IKZF1plus profile (18% and 29%, respectively) (Figure 1B). Moreover age-related differences in the adult B-other ALL patient group were observed. The presence of mutations in RAS pathway was associated with younger age (<40 years) (3/10, 30% vs. 0/7, 0%), whereas older patients (≥40 years) predominated in the IKZF1plus profile (6/7, 86% vs. 3/10, 30%). TP53 alterations were detected at diagnosis and/or relapse in 11 patients (24%), most of which (9/11, 82%) had a heterozygous mutation plus a deletion or a homozygous mutation (double-hit). The high hyperdiploidy subgroup was enriched in TP53 mutations (4/5, 80%), most of which were already present at diagnosis (3/4, 75%). These findings indicate that genetic biomarkers usually linked to a favorable prognosis, such as high hyperdiploidy, can be associated with unfavorable genetic markers, leading to poorer outcomes in this group of patients (Figure 1C). Both the IKZF1plus profile and TP53 alterations were associated with poorer overall survival (OS) rates (P=0.034 and P=0.040, respectively) in adult BCP-ALL (Figure 2). Conclusion: Our results highlight the clinical importance of the TP53 alterations and the IKZF1plus profile as prognostic factors in adult BCP-ALL, suggesting they might help guiding more personalized therapeutic strategies to improve outcomes in this group of BCP-ALL patients. Grants: SACYL(GRS2386/A/21,GRS2385/A/21,GRS2527/A/22,GRS2506/A/22), JCyL SA118P20, FMM21/002 AP176752021, Pfizer 69383919.

TP53 and CDKN2A alterations Define a Poor Prognostic Subgroup in Patients with Nodal T-Follicular Helper Cell Lymphoma

Nodal T-follicular helper cell lymphoma (nTFHL) is a subset of peripheral T-cell lymphoma (PTCL) characterized by a distinct immunophenotype (such as CD10, BCL6, CXCL13, PD1, and ICOS) and mutations (including TET2, RHOA G17V, and IDH2 R172). However, the impact of molecular classification based on genetic profiling on prognosis in nTFHL remains largely unknown. Here we performed targeted-capture sequencing (targeted-seq) covering 235 T/NK-cell lymphoma-related genes with a mean depth of 526×. Then, we analyzed 49 genes which were reported as drivers in the previous PTCL studies to reveal the associations between clinical phenotypes and somatic alterations in a cohort of 153 patients whose clinical information was available and who were pathologically diagnosed with nTFHL according to the WHO-HAEM5. When mutation and copy number alteration (CNA) data were combined, we identified recurrent alterations in 40 among 49 driver genes. TET2 was most frequent (68%), followed by RHOA (51%), IDH2 (27%), DNMT3A (20%), PLCG1 (9%), TP53 (7%), KMT2C (6%), VAV1 (6%), CD28 (6%), KMT2D (6%), NOTCH1 (5%), and CDKN2A (5%). To create a molecular classification based on genetic alterations in nTFHL, we conducted hierarchical clustering using driver alterations and arm-level CNAs. This analysis identified four molecular subgroups named after their characteristic genetic alterations ( Fig. 1A). TR-ID (+) ( n = 52) and TR-ID (-) ( n = 60) were defined by TFH-related mutations ( TET2 and RHOA). Among them, TR-ID (+) harbored IDH2 and/or DNMT3A mutations. A53 ( n = 8) was notable for biallelic inactivation of TP53 and/or CDKN2A and associated with marked aneuploidy. NSD ( n = 33) had no subgroup-defining alterations with the fewest number of mutations. Clinically, TR-ID (+) tumors were mostly nTFHL-angioimmunoblastic-type (AI), which is consistent with the enrichment of IDH2 and/or DNMT3A mutations. On the other hand, TR-ID (-) tumors exhibited a higher proportion of nTFHL-NOS. NSD exhibited lower LDH levels and was significantly associated with younger age and localized stage than other subgroups. A53 showed the worst prognosis with a median overall survival (OS) of 15.1 months (mos) ( Fig. 1B). By contrast, the OS of NSD was significantly superior to the others (median OS not reached). The OS of TR-ID (+) and TR-ID (-) was comparable with a median OS of 40.6 and 46.4 mos, respectively. Notably, A53 remained significant in multivariate analyses adjusted for IPI or PIT score. Thus, genetic profiling enables to classify nTFHL patients into genetically and clinically distinct subgroups, including the unfavorable prognostic subgroup (A53). Next, to identify potential genes linked to the poor prognosis of the A53 subtype, we examined the prognostic impact of individual alterations. Among the genes examined, TP53 and CDKN2A, hallmarks of A53, were significantly associated with shorter OS in univariate analysis. Consequently, cases with TP53 and/or CDKN2A alterations showed a poor prognosis (median OS 11.4 vs 181.2 mos, P = 8.2×10 -7), thereby reinforcing the negative prognostic impact of A53. Then, we investigated other prognostic factors within each molecular subgroup. First, in TR-ID (+) and (-) cases, we examined the EBV status, which was known to be associated with worse prognosis in nTFHL-AI. Among them, 22 (16%) cases were EBV-positive. Despite no observed differences in genetic and clinical factors, EBV-positive cases exhibited a worse prognosis (median OS 66.5 vs 14.9 mos, P = 0.0018). Next, we assessed the influence of TCR clonality on prognosis in NSD cases. The clonal T-cell fraction assessed by targeted-seq was highest in A53 (median, 75%) but lowest in NSD (median, 16%). OS of NSD cases was further stratified by T-cell clonality (median OS not reached vs 67.7 mos for low and high clonal T-cell fraction; P = 0.042), while the presence of driver alterations failed to predict the prognosis. These findings suggest that assessment of T-cell clonality helps to identify the favorable prognostic subgroup characterized by low tumor content. In summary, we defined four molecular subgroups with different clinical features and also clarified subgroup-specific prognostic factors in nTFHL. Particularly, we identified the molecular subgroup with unfavorable prognosis (A53) for which different clinical approach should be warranted. This classification will refine the patient prognostication and stratification in nTFHL.

Varnimcabtagene Autoleucel (ARI-0001) for Relapsed or Refractory Chronic Lymphocytic Leukemia (CLL) and Richter Transformation (RT)

Background: The prognosis of CLL patients that do not respond to targeted therapy is unfavourable, especially in the case of adverse genomic aberrations (e.g. TP53 alterations or complex karyotype) or after transformation to aggressive B lymphoma (Richter transformation, RT). In patients with refractory CLL, anti-CD19 CAR-T (CART19) therapy has achieved complete response (CR) rates of 19-45%, with RT usually excluded from pivotal trials. However, long-term remission in CLL patients still remains a challenge with CART19 therapy. Methods: We present the outcomes of all patients with relapsed or refractory (R/R) CLL with or without RT treated with the academic CART19 varnimcabtagene autoleucel (var-cel) from November/2017 to May/2023, including patients from the CART19-BE-01 trial and subsequent compassionate use programme. Patients received lymphodepletion with fludarabine (90 mg/m2) and cyclophosphamide (900 mg/m2) followed by 0.1-1 (CLL) and 0.5-5 (RT) x10e6 CART19 cells/kg in single or fractionated administration (10%, 30% and 60%) in a single institution. Results: A total of 20 patients underwent leukapheresis and var-cel production. At screening patients had a median age of 58 years (44-74), 47% were females, with a median of 4 prior lines of therapy (2-9) including ibrutinib (89%), venetoclax (53%), R-CHOP (58%) and allo-HCT (21%). All patients had high-risk features, including unmutated IGHV (90%), TP53 lesions (89%), complex karyotype (43%) and RT (63%), as well as elevated LDH (74%), extramedullary disease (84%), and CSF infiltration (16%). Median bone marrow infiltration at screening was 18% (3-85), and median tumour metabolic volume (TMV) was 55 ml (0-1217). Var-cel manufacturing was performed in a median of 8 days (7-9). One patient required 2 apheresis and 1 RT patient died due to progressive disease without receiving var-cel. All patients received bridging therapy (BT), based on BTKi (53%), venetoclax (26%), chemotherapy (10%), steroids (10%) and radiotherapy (5%). Despite BT, all patients received var-cel either with stable disease (44%) or progressive disease (56%), in a median of 29 days (18-81) from apheresis to infusion. Fifty-eight percent of patients received 100% of the planned dose. The remainder received 10-30% due to early cytokine release syndrome (CRS), with a final median infused dose of 1 (0.4-5) x10e6 CART19 cells/kg. CRS was observed in 89% of patients, being severe in 11%. Only mild ICANS was developed in 11%. Tocilizumab and corticosteroids were administered in 44% and 17% of patients, respectively. Median duration of CRS and ICANS was 4.5 days (1-17) and 3 days (2-4), respectively. Absolute B-cell aplasia (0 B-cells/mL) was achieved in 94% of patients in a median of 14 days (7-34), with median duration not reached for CLL and RT. Tmax peak CART19 concentration was observed at day +24 (median, 7-148). With a median follow-up of 8,4 months (0.3-66.7), the overall response rate was 83%, with 83% achieving an MRD-negative CR (flow) in bone marrow (BM) and peripheral blood, and 67% achieving CR on extramedullary lesions (PET/CT). Median PFS and DOR was not achieved for either CLL or RT (figure 1). Disease progression was observed in 7 (39%) patients in a median of 63 days (7-237), 43% of which occurred due to CD19-negative antigen escape despite active CART19 persistence. No relapses have been observed after CR was achieved. By univariate analysis there was no significant differences for PFS regarding presence of RT, SD vs PD at infusion, high vs low LDH, BM infiltration (> or < 20%), or TMV (> or < 25 ml). However, PFS was shorter among patients with both, high BM infiltration plus high TMV, in comparison to patients with either low burden at BM and/or TMV (median PFS 2 months vs not reached, p = 0.0293) (figure 2). Conclusions: Administration of the CART19 var-cel (ARI-0001) was feasible in 95% of CLL/RT patients, with robust and durable var-cel engraftment in 89% of treated patients, and durable complete responses observed in 61% of patients. These initial outcomes or var-cel in this population contrasts with the overall findings of CART19 therapy in CLL/RT and encourages to further develop var-cel on this high-risk population.

Remodeling of the Immune Microenvironment By Oncogenic MYD88 Dictates Immunotherapy Responses across Indolent and Aggressive B-Cell Lymphomas

The MYD88 L265P mutation is detected in a variety of lymphoma subtypes, ranging from indolent MALT or lymphoplasmacytic lymphoma (LPL) to aggressive DLBCL with activated B-cell (ABC) phenotype. Whether oncogenic MYD88 L265P constitutes a common founder mutation and how it drives lymphomas with different clinical, histopathological, and immunological characteristics, remains unknown. To address this fundamental question, we screened mice genetically engineered to express an orthologous MYD88 L252P mutation crossed with animals carrying secondary genetic lesions common in MYD88 L265P lymphomas, triggered at two B-cell differentiation stages. Several mouse strains developed indolent or aggressive lymphomas depending on the cell of origin and the secondary genetic lesion. In two of the models, human-like MALT or LPL were progressively driven by mutant MYD88 activated from immature pre-B lymphocytes with either constitutive BCR signaling or BCL2 expression. High-throughput cellular and molecular characterization of the tumor immune microenvironment (TME) by single-cell RNA sequencing coupled with BCR/TCRseq revealed bi-directional B-cell interactions with CD4 + Tfh and Th1 cells from early disease state, promoting survival of B-cell clones through CD40L:CD40 signaling. During progression, IL10-secreting regulatory T (Treg) cells were recruited into the tumor niche through a Ccl5-Cxcr3 axis to suppress CD8 + T-cell cytotoxicity. In patients with MYD88 L265P LPL characterized at progressive disease states, CD40:CD40L interaction between tumor and immune cells took place early while Tregs accumulated at late stage. In the LPL model and in human MYD88 L265P-LPL cells, CD40 signaling decreased effects of standard-of-care drugs including BTK inhibitors. Accordingly, anti-CD40 therapy disrupted B/T-cell interactions and increased ibrutinib activity. In conclusion, oncogenic MYD88 triggered at early B-cell stages promotes indolent lymphomas that are sustained by CD40 signaling, which restricts therapy responses that can be restored upon CD40 blockade. When MYD88 L265P was activated in mature germinal-center B cells together with either Prdm1 or Trp53 deletion, mice developed extranodal ABC-DLBCL (MCD/C5 genomic class). IHC, flow cytometry and single-cell RNAseq revealed that DLBCL with Prdm1 loss showed morphologically heterogeneous B cells with abundant immune and T cells with activated/exhausted phenotypes, which recapitulated the inflammatory/immunosuppressive TME category in DLBCL patients (IN-LME, Kotlov- Cancer-Discovery-2021). In contrast, DLBCL with Tp53 deletion exhibited monotonous B-cell infiltrates with high proliferation index and a TME with depletion of T cells with effector/memory phenotypes and CD4 +CD25 +Foxp3 + Tregs, consistent with the immune depleted TME category (DP-LME). Analysis of 1,039 DLBCL patients demonstrated that majority of MCD cases with MYD88 L265P showed either an IN-LME (43%) or DP-LME (44%). Consistent with the models, ABC-DLBCL patients with MYD88 L265P and TP53 loss/mutation exhibited highly proliferative disease with a DP-LME, while ABC-DLBCLs with MYD88 L265P but without TP53 abnormalities showed an IN-LME. Notably, the number of infiltrating CD4 + T cells correlated with TP53 activity score (PROGeNY) across MCD-DLBCLs. Overall, the presence or absence of TP53 alterations in MYD88 L265P ABC-DLBCL induces TME characterized as DP-LME or IN-LME, respectively. Since DP-LME carries poor response to immune-chemotherapy (Kotlov-Cancer-Discovery-2021), we tested anti-CD19 CAR T-cells in the models. While CAR T-cells were initially effective in the two DLBCL models, progression occurred earlier in DLBCL with DP-LME than in IN-LME, which remained in remission 100 days after cell infusion. Responses correlated with persistence of circulating CD4 + CAR T cells. These data highlight that a TP53-driven DP-LME may limit immunotherapy activity in DLBCL, providing a scientific explanation to the poor outcome of DLBCL patients with TP53 alterations to CD19-directed CAR T cells (Shouval-JCO-2021). Collectively, our study defines the cellular origins and the stepwise genetic alterations of indolent and aggressive lymphomas with MYD88 L265P, dissects distinct immunological paths underlying progression driven by oncogenic MYD88, and builds proof-of-concept for advancing precision immunotherapy in B-cell lymphomas.

Selinexor in Combination with Salvage Regimen for Refractory Peripheral T-Cell Lymphoma (PTCL) Patients

Background Peripheral T-cell lymphomas, not otherwise specified (PTCL-NOS) are a diverse and aggressive type of non-Hodgkin lymphomas with a poor prognosis when treated with conventional chemotherapy. The standard CHOP chemotherapy regimen typically yields an overall response rate (ORR) of 60-80%, a complete response (CR) rate of 30-40%, and long-term survival, measured by 5-yr OS，in the range of 20-30% in non-ALCL (anaplastic large cell lymphoma) subtypes. Azacitidine plus CHOP has achievied a 75% CR in newly diagnosed PTCL, but patients with DNMT3A mutation showed adverse progression-free survival (PFS), indicating that genetic mutations may influence resistance to chemotherapy. Selinexor has shown promising results in refractory lymphoma patients by inhibiting oncogenes, therefore, the efficacy of selinexor combined salvage regimen in refractory PTCL remains great interest. Method Refractory PTCL patients were enrolled to be treated with selinexor plus GDP/ICE/Gemox since December 2021 at our center. Selinexor was administered orally (40 mg day 1, 8, 15) plus GDP (gemcitabine 1g/m2*d1, cisplatin 25mg/m2 d1-d3, dexamethasone 40mg d1-d4), ICE (ifosfamide 1.5g/m2*3d, carboplatin (AUC 5) and etoposide 100mg/m2*3d), Gemox (gemcitabine 1g/m2*d1, oxaliplatin 100mg/m2*d1) every 3 weeks as per physician's choice. Objective response rate (ORR) was evaluated every 3 cycles based on Lugano 2014 criteria and Adverse events (AE) were rated according to the NCI CTCAE 5.0. Results 10 patients were treated with selinexor plus salvage regimen in this study and received more than two cycles of the treatment, making them eligible for response evaluation in this poster. The median age of the 10 patients was 65 years (range from 42 to 79), 8 (80%) were male, 9 (90%) had disease stage III-IV at screening, and 60% of all patients had an IPI intermediate to high risk. All of the patients were refractory to the last line of treatment. Among 10 patients, 2 were angioimmunoblastic T-cell lymphoma (AITL), 3 with PTCL-NOS, 3 with ALK-ALCL, 2 with monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL). As shown in Figure 1, 3 patients had TP53 alterations, 2 patients with DNMT3A mutation. Patients received a median of three cycles (range, 2-6) of selinexor 40mg once a week combined with salvage regimen（4 patients received Selinexor-GDP, 3 with selinexor-ICE, 3 with selinexor-Gemox）. The best overall and complete response rates were 70% and 50%, respectively. In terms of MEITL refractory to conventional CHOP treatment, 1 achieved PR but progressed and died after stop treatment for three months due to Covid19 and 1 in CR with selinexor maintenance. Conclusions There are limited options for the treatment of refractory PTCL. We identified a dosing schedule of selinexor (40mg qw) with GDP/ICE/Gemox that is efficiency inrefractory PTCL and is worthy of further study on its mechanism of action.

Higher TP53 somatic mutation prevalence from liquid biopsy analysis in ever smoker non-small-cell lung cancer patients

ObjectiveCigarette smoking is a primary risk factor, linked to 80% of LC deaths. TP53, a key gene, is implicated in various cancers, with TP53 alterations in 36.7% of cancers. This research aims to investigate TP53 mutations detected in NSCLC patients by liquid biopsy and explore the relationship between these mutations and smoking history. Material and methodThe study enrolled a total of 340 patients diagnosed with non-small cell lung cancer (NSCLC). For sequencing, the Illumina NextSeq 500 system was utilized. The oncogenicity of the variants was assessed according to the ClinGen/CGC/VICC SOP and the variants were categorized into four tiers according to AMP/ASCO/CAP. ResultsThe most common mutations were in TP53 (48.7%), followed by EGFR, PIK3CA, and PTEN. Missense mutations were frequent, with TP53 and EGFR having higher rates in ever-smokers. No indels or complex mutations were found in ever-smokers. Patient age ranged from 20 to 86 years. Tier I-II variants were more common in ever-smokers, while Tier III variants were prevalent in never-smokers. TP53 mutations were more frequent in ever-smokers, showing a strong association with smoking. Domain distribution showed differences in PIK3CA. Transversion/transition ratios varied by gene and smoking status. DiscussionThe presence of TP53 mutations is strongly associated with both cigarette smoking and elevated Tv/Ti ratios. The tier status of TP53, EGFR, and PTEN variants does not show a specific domain distribution, but interesting associations are observed between the tier status and domain distribution in PIK3CA variants. Therefore, further comprehensive investigations are needed to explore this entity, as well as the underlying factors contributing to the increased Tv/Ti rates in the TP53 gene. Such research will provide deeper insights into the genetic alterations associated with smoking and tumor heterogeneity, ultimately aiding in the development of targeted therapies.

Can Emergency Hematopoiesis Due to Sepsis Lead to Clonal Hematopoiesis? Implications for Understanding the Pathogenesis of Clonal Evolution

O.O & T.K are co-first authors. Clonal (myelo) hematopoiesis of indeterminate potential (CHIP) arises from somatic mutations in myeloid genes, providing a proliferative and survival advantage to the affected “CHIP-initiating” early hematopoietic precursor cells. Understanding the conditions that lead to the emergence of detectable clones (early seeding of myeloid neoplasia-MN) is of great interest due to its clinical implications. Among CH facilitating states, aging has been extensively studied, but a clear distinction between the impact of chronological versus biological aging remains challenging. Additionally, other factors contributing to CHIP development may include chemotherapy, genetic predisposition, bone marrow failure states, or immunodeficiency. However, not all CHIP-promoting factors have been identified because they are subtle, pathophysiologically complex, and thus remain cryptic. We hypothesized that episodes of emergency hematopoiesis (EH), such as those caused by acute infections, could potentially result in acquisition of CHIP with repeated episodes of EH resulting in clonal expansion. If this hypothesis is confirmed, one could envision that both instances of significant hematopoietic expansion (high leukocytosis) and repeated cycles of EH could be at play in conjunction with chronological factors. For instance, the older an individual is, the greater is the number of EH episodes possible. To examine our theory, we prospectively collected blood samples from patients admitted at the intensive care unit (ICU) of Cleveland Clinic and Yale University. Inclusion criteria required a white blood cell (WBC) count ≥ 15K/uL. Patients with known or prior malignancies and those exposed to chemotherapy were excluded. For relevant comparisons, we assessed CH incidence in our cohort against a group of patients with solid tumors screened for CH (n=107) but without acute infections, along with historical CHIP cohorts. CH screening employed a targeted NGS myeloid gene panel with a reported VAF cut-off of 2%. A total of 78 individuals admitted to the ICU with possible infections and leukocytosis were enrolled in this study. The median age was 70 years (IQR: 61-77), with a M:F ratio of 1.7 (Table 1). Time from leukocytosis onset to sampling was 3 days (IQR: 1-5), the median WBC at ICU admission was 18 K/uL (IQR: 16-21), and the median absolute neutrophil count (ANC) was 16 K/uL (IQR: 12-20). Overall, 94 variants were identified including 16 (median VAF 50.1) variants of potentially germline origin, and 4 variants of unknown significance. We observed 74 CHIP-associated mutations in 37 (47%) patients at a median VAF of 14% (4-47%). The landscape of CHIP mutations included alterations in DNMT3A (20%), TET2 (12%), ASXL1 (12%), SMC1A, TP53, and PPM1D genes (6% each). Although higher rates of CHIP were expected in the cancer cohort, no difference was found between the two groups (40% vs. 47% in the ICU, p=0.3). DNMT3A, ASXL1 and PPM1D mutations were more frequently encountered in the cancer cohort (Table 1). The prevalence of CHIP in the ICU cohort was higher in older age groups: 30-39 (29%), 50-69 (49%), and ≥70 (51%), compared to the expected frequency in comparable age ranges (and median range) in a historical healthy population, which was 1%, 4%, and 10%, respectively (<0.00001; Fig.1). Notably, CHIP was more prevalent among smokers (57%; p=0.003). No significant differences were found when comparing CHIP + and CHIP - patients of the ICU cohort with regards to WBC (median 18K/uL both). Similarly, CHIP prevalence did not change according to the degree of leukocytosis in an analysis where patients were ranked by WBC (≥18K/uL at 44% vs. <18K/uL at 46%). When looking at the impact of CHIP on critical care outcomes, a logistic regression model accounting for age, gender, and mutation type revealed that the presence of DNMT3A mutations was associated with a higher risk of diagnosis of overt septic shock (log OR= 2.4, 95% CI 0.19-5.4, p<0.05). In summary, our prospective observational study has shown that sepsis is associated with preferential mutant clone expansion, primarily due to EH rather than the extent of leukocytosis and may be contributing to the acquisition of new clones. Whether such episodes result in permanent acquisition of new CHIP mutations with potential for MN progression will be the subject of longitudinal analysis of these samples, and findings will be presented at the ASH meeting.

Del(20q) As a Somatic Gene Rescue in Adult Patients: Can Germline Mutations Other Than SBDS be Found in Affected Patients?

Deletions involving chromosome 20 (20q-) are present in up to 5-8% of myeloid neoplasms (MN) and have been associated with either myelodysplastic (MDS) or myeloproliferative (MPN) features, chiefly myelofibrosis. Theoretically, any chromosomal deletion may result in haploinsufficient expression of tumor suppressor genes (TSGs) or in loss of a protective allele in heterozygous carriers of germline (GL) variants or heterozygous somatic (SM) mutations. However, deletions have also been implicated as a maladaptive somatic gene rescue (SGR) event in carriers of GL bone marrow failure (BMF) genes such as SAMD9 and SBDS. The latter is found in Shwachman-Diamond syndrome whereby the upregulated EIF6 gene, responsible for hematopoietic dysfunction, is clonally removed by SM 20q deletion event. We identified an interesting 35-years-old patient with mild cytopenia and 20q- in which a cryptic homozygous SBDS c.A148T GL mutation was found. This prompted us to search in other adult patients with 20q deletion for: i) other cases with SBDS gene alteration (both hetero and homozygous), ii) other GL variants which could be clonally relieved by compensatory 20q- or, iii) disease-prone GL variants on 20q, whereby either disease-prone suppressive allele is included in the deleted region. Within a cohort of 5,308 cases with various MN, 215 patients with 20q- were identified. WES results were available for 350 patients. We applied a stringent bioanalytic algorithm to identify unique GL alterations (not deposited in SM databases) in genes expressed in hematopoietic tissues and involved in BMF and cancer, and a population allelic frequency of <1% which were classified as pathogenic (P), likely pathogenic (LP), and VUS with particular level of clinical suspicion (sVUS). In 76 of 215 patients with 20q-, 346 GL mutations in genes of potential interest were identified and further analyzed. No P/LP variants were detected on genes within commonly deleted region on chr.20q, and no additional carriers of SBDS variants were found. However, we identified 9 pathogenic GL variants in potentially pertinent genes including GL alterations in DDX41, STAG2 and TP53 which have been described in the context of MN. However, these gene variants were also present in patients with diploid 20q. The remaining 6 variants included heterozygous P/LP GL alterations in 3 different Fanconi anemia genes ( FANCA, FANCM, FANCD2), SUZ12, and TINF2. The latter, TINF2, a telosome gene, known to be mutated in dyskeratosis congenita (DC), carried an LOF c.605-1G>A in a patient with MDS/MPN with a family history of cancer who later developed 20q-. The patient did not show any symptoms of DC-like features, which usually present at an early age. Since FANCA LOF with SGR via overepression of EIF6 has previously been described 1, we investigated and did not identify any cases in our cohort of EIF6 SGR resultant overexpression. While occasional patients with no previously diagnosed SBDS can be found among MDS with 20q-, screening for SBDS genes demonstrates that such a genetic configuration among adult patients with 20q is very rare. In addition, only 9 out of 215 patients with 20q- carried other pathogenic GL variants in non-recurrent genes which appear to be likely coincidental. This suggests that del20q is not a SGR in response to a GL mutation, but rather a SGR due to other aforementioned mechanisms, which are currently being explored in our cohort of patients.

The Relapse Mechanisms and Genomic Landscape Differ in KMT2A-r Pediatric Leukemia in Relation to Relapse Time

The genomic landscape and mechanisms driving relapse in KMT2A-rearranged ( KMT2A-r) infant and childhood acute lymphoblastic (ALL) and acute myeloid leukemia (AML) are not completely understood. We therefore studied 36 KMT2A-r ALL (n=19) and AML (n=17) patients of which 25 relapsed and 11 remained in remission. Twenty diagnose-relapse-germline trios and 5 multiple relapse samples were analyzed by whole genome (WGS) and whole exome sequencing (WES) and 30 patients longitudinally by using patient-specific mutations identified by WGS/WES, including the KMT2A-r (average coverage 3300X). The mutational burden increased from diagnosis to relapse and relapse evolved through branching evolution. Relapse was seeded by multiple diagnostic clones in 56%, by a single sweeping clone detected at diagnosis in 22%, and by a single sweeping clone not detected at diagnosis in 22%. Notably, the evolutionary patterns correlated to relapse time, where multiple diagnostic clones seeding relapse were connected to an earlier relapse with all very early relapse ALL (3/3, relapse <9 months from diagnosis) and half of the early AML relapse showing this pattern (2/4, relapse <1 year in complete remission, CR1). By contrast, later relapse was connected to a sweeping clone at relapse with 67% of early relapse ALL (>9 months from diagnosis) and 40% of late relapse AML (>1 year in CR1) showing this pattern. Pathway analysis showed that cell cycle genes, glucocorticoid signalling, purine metabolism, mismatch repair, and B-cell differentiation, were enriched in early relapse ALL (83%, 5/6) and included TP53, CREBBP, NT5C2 PMS2, PRPS2, NR3C1, IKZF1, with none of the very early relapse infant ALL harboring such alterations (n=4). Further, TP53 and IKZF1alterationsco-occurred (n=4/4). These results were validated in public data sets of 98 KMT2A-r ALL infants (n=84) and children (n=14) at diagnosis and relapse (n=24) and showed that 50% of early relapse ALL, and none of the 8 very early relapse ALL, had such alterations. Ultra-deep sequencing did not detect the CREBBP, NT5C2, PRPS2or TP53 mutations at diagnosis and manual inspection of the WGS reads failed to detect the PMS2 and NR3C1 deletions. In AML, TP53 and CCND3 alterations were maintained, and gain of WT1 was seen in late relapse AML. Signalling mutations were the most common type of mutations at diagnosis (64%) and relapse (56%) and the frequency was similar in patients that remained in remission and in those that relapsed (55% versus 60%). One infant ALL and four AML patients had multiple relapses, allowing us to study how the genetic landscape evolved across consecutive relapses. This showed a stepwise replacement of clones during treatment in agreement with a fitter clone that evolves under chemotherapeutic selective pressure. Longitudinal analysis allowed sensitive detection of residual leukemia cells and showed that the relapse clone could be detected at diagnosis in 64% of patients. Further, infants with >10% of molecularly detectable leukemia cells after induction therapy, had a high risk of a very early relapse. Ultra-deep sequencing allowed detection of the relapse clone up to 4 months before relapse. In 11 of the 30 patients (3 remission and 8 relapse), low-frequency KMT2A-fusion positive leukemic cells were found at remission outside of the MRD time points. Our longitudinal data also provided unique insights into clonal response to treatment by showing that 1) a change in therapy can favour the eradication of one clone and expansion of another, 2) a clone that initially was the most sensitive clone to therapy, was the one that eventually caused relapse, and 3), a diagnostic clone can be undetectable for a long time before expanding to cause relapse, suggesting that molecular monitoring with personal mutations is a powerful tool to follow response to therapy. These results provide new biological insights into the relapse mechanisms in KMT2A-r leukemia. The data shows different clonal evolution patters depending on when in time the patient relapsed, with very early relapse ALL being seeded by multiple diagnostic subclones and a paucity of acquired genetic alterations at relapse. By contrast, early relapse ALL was characterized by a single diagnostic clone seeding relapse by a clonal sweep along with acquired mutations in chemoresistance-associated genes. To validate and extend these findings, we are currently analyzing 11 additional infant relapse samples with WGS.

Detection of Novel Tyrosine Kinase Fusion Genes as Potential Therapeutic Targets in Bone and Soft Tissue Sarcomas Using DNA/RNA-based Clinical Sequencing.

Approximately 1% of clinically treatable tyrosine kinase fusions, including anaplastic lymphoma kinase, neurotrophic tyrosine receptor kinase, RET proto-oncogene, and ROS proto-oncogene 1, have been identified in soft tissue sarcomas via comprehensive genome profiling based on DNA sequencing. Histologic tumor-specific fusion genes have been reported in approximately 20% of soft tissue sarcomas; however, unlike tyrosine kinase fusion genes, these fusions cannot be directly targeted in therapy. Approximately 80% of tumor-specific fusion-negative sarcomas, including myxofibrosarcoma and leiomyosarcoma, that are defined in complex karyotype sarcomas remain genetically uncharacterized; this mutually exclusive pattern of mutations suggests that other mutually exclusive driver oncogenes are yet to be discovered. Tumor-specific, fusion-negative sarcomas may be associated with unique translocations, and oncogenic fusion genes, including tyrosine kinase fusions, may have been overlooked in these sarcomas. (1) Can DNA- or RNA-based analysis reveal any characteristic gene alterations in bone and soft tissue sarcomas? (2) Can useful and potential tyrosine kinase fusions in tumors from tumor-specific, fusion-negative sarcomas be detected using an RNA-based screening system? (3) Do the identified potential fusion tumors, especially in neurotrophic tyrosine receptor kinase gene fusions in bone sarcoma, transform cells and respond to targeted drug treatment in in vitro assays? (4) Can the identified tyrosine kinase fusion genes in sarcomas be useful therapeutic targets? Between 2017 and 2020, we treated 100 patients for bone and soft tissue sarcomas at five institutions. Any biopsy or surgery from which a specimen could be obtained was included as potentially eligible. Ninety percent (90 patients) of patients were eligible; a further 8% (8 patients) were excluded because they were either lost to follow-up or their diagnosis was changed, leaving 82% (82 patients) for analysis here. To answer our first and second questions regarding gene alterations and potential tyrosine kinase fusions in eight bone and 74 soft tissue sarcomas, we used the TruSight Tumor 170 assay to detect mutations, copy number variations, and gene fusions in the samples. To answer our third question, we performed functional analyses involving in vitro assays to determine whether the identified tyrosine kinase fusions were associated with oncogenic abilities and drug responses. Finally, to determine usefulness as therapeutic targets, two pediatric patients harboring an NTRK fusion and an ALK fusion were treated with tyrosine kinase inhibitors in clinical trials. DNA/RNA-based analysis demonstrated characteristic alterations in bone and soft tissue sarcomas; DNA-based analyses detected TP53 and copy number alterations of MDM2 and CDK4 . These single-nucleotide variants and copy number variations were enriched in specific fusion-negative sarcomas. RNA-based screening detected fusion genes in 24% (20 of 82) of patients. Useful potential fusions were detected in 19% (11 of 58) of tumor-specific fusion-negative sarcomas, with nine of these patients harboring tyrosine kinase fusion genes; five of these patients had in-frame tyrosine kinase fusion genes ( STRN3-NTRK3, VWC2-EGFR, ICK-KDR, FOXP2-MET , and CEP290-MET ) with unknown pathologic significance. The functional analysis revealed that STRN3-NTRK3 rearrangement that was identified in bone had a strong transforming potential in 3T3 cells, and that STRN3-NTRK3 -positive cells were sensitive to larotrectinib in vitro. To confirm the usefulness of identified tyrosine kinase fusion genes as therapeutic targets, patients with well-characterized LMNA-NTRK1 and CLTC-ALK fusions were treated with tyrosine kinase inhibitors in clinical trials, and a complete response was achieved. We identified useful potential therapeutic targets for tyrosine kinase fusions in bone and soft tissue sarcomas using RNA-based analysis. We successfully identified STRN3-NTRK3 fusion in a patient with leiomyosarcoma of bone and determined the malignant potential of this fusion gene via functional analyses and drug effects. In light of these discoveries, comprehensive genome profiling should be considered even if the sarcoma is a bone sarcoma. There seem to be some limitations regarding current DNA-based comprehensive genome profiling tests, and it is important to use RNA testing for proper diagnosis and accurate identification of fusion genes. Studies on more patients, validation of results, and further functional analysis of unknown tyrosine kinase fusion genes are required to establish future treatments. DNA- and RNA-based screening systems may be useful for detecting tyrosine kinase fusion genes in specific fusion-negative sarcomas and identifying key therapeutic targets, leading to possible breakthroughs in the treatment of bone and soft tissue sarcomas. Given that current DNA sequencing misses fusion genes, RNA-based screening systems should be widely considered as a worldwide test for sarcoma. If standard treatments such as chemotherapy are not effective, or even if the sarcoma is of bone, RNA sequencing should be considered to identify as many therapeutic targets as possible.

Minimal Residual Disease-Guided Combination of Ibrutinib and Venetoclax Compared to FCR in Untreated Patients with CLL of Intermediate Risk : Interim Results of MRD Kinetics in the Eradic Trial from the Filo Group

With the emergence of targeted therapies, defining the best strategy for first-line treatment in chronic lymphocytic leukemia (CLL) patients has become challenging. The aim of the ERADIC phase 2 study was to compare the efficacy of a standard FCR regimen to that of an MRD-guided combination of ibrutinib and venetoclax (IV), in fit patients with CLL of intermediate risk defined by either unmutated IGHV status, 11q deletion or complex karyotype in the absence of TP53 alteration. MRD was assessed in bone marrow (BM) or peripheral blood (PB) by flow cytometry. After a lead-in phase of ibrutinib as a single agent from month (M)1 to M3, the total duration of treatment with the IV combination was based on BM M9 MRD. If it was <0.01% (uMRD) at that time, treatment was continued for 6 additional months (M15) then stopped. If M9 BM-MRD was ≥0.01%, IV treatment was continued for 18 additional months (M27). BM-MRD was reassessed at that time-point in both arms. Additionally, PB-MRD evaluation was performed every 6 months.The primary endpoint will be the percentage of patients with BM uMRD at M27. Here, intermediate safety data and MRD kinetics (M9 to M21) are presented. Between September 2019 and February 2021, 120 patients were randomized 1:1 between the two treatment arms. The median age was 59 [34-72] and 61 [34-74] year-old in the FCR and IV arms, respectively. Patient characteristics were well balanced between the 2 arms in terms of gender (male 72% FCR, 74% IV), PS ECOG 0-1 (59% FCR, 68% IV) and Binet stage (A, B and C 15%, 64%, 21% for FCR ; 8.5%, 59% and 32% for IV). An11q deletion was found in 20% and 24% of the cases in the FCR and IV arms, respectively and all patients but one had unmutated IGHV. At the time of data cut-off for this analysis, the median follow-up was 29.7 months [range: 25.3- 32.8]. Sixty-three serious adverse events (SAE) have been reported so far, 32 in the FCR arm and 31 in the IV arm. In the FCR arm, the most frequent SAE were infections (N=12 including 4 COVID-19), febrile neutropenia (N=5) biological tumour lysis syndrome (N=3), and secondary malignancies (N=2, including 1 myelodysplastic syndrome and 1 acute myeloid leukemia). In the IV arm, the most frequently reported SAE were infections (N=8 including 4 COVID-19), cardiovascular events (N=7), biological tumour lysis syndrome (N=5), acute renal failure (N=2) and secondary malignancies (N=2, including 1 colorectal cancer and 1 skin basal cell carcinoma). Four grade 5 adverse events were reported, respectively 2 in the FCR arm (1 septic shock and 1 AML) and 3 in the IV arm (2 sudden deaths and one death COVID-19-related). In the FCR arm (intention to treat [ITT] n=57), 59.6% of the patients had BM-uMRD at M9. The kinetics of PB-uMRD was 68% at M9, 65% at M15 and 52% at M21. In the IV arm (ITT n=54), the rate of BM-uMRD at M9 was much lower at 33%. PB-MRD kinetics showed levels of uMRD of 52%,70% and 67% at M9, M15 and M21 respectively. In terms of response, CR/CRi rates were 56% for the FCR arm and 66% for the IV arm. Three patients progressed in the FCR arm (1 at M9 and 2 at M15) and 2 in the IV arm, at respectively M13 and M39. Among the 13 patients who achieved BM-uMRD at M9 in the IV arm, 10 have indeed stopped according to the protocol and only 1 has progressed at M39. In conclusion, monitoring MRD kinetics in this trial showed a stable level of PB-uMRD in the FCR arm yet a clear increase in the IV arm between M9 and M15. Toxicity remains an important parameter in both treatment arms that will have to be taken into account when determining whether treatment should be continued because of detectable BM-MRD at M9 (IV arm). Upcoming data of the primary enpoint analysis at M27 will be of great interest to try to determine the best strategy.

Multi-Hit TP53 Mutations in Myeloid Neoplasms: Prognostic Impact of Morphologic Subtype Designation and Variant Allele Frequency

Background: Biallelic TP53 alterations result from either sequence variations or deletions involving TP53 and are not necessarily synonymous with “multi-hit TP53”. According to the 2022 international consensus classification (ICC) for myeloid neoplasms (MN), multi-hit TP53 signifies i) the presence of two or more distinct TP53 mutations, each with variant allele frequency (VAF) ≥10%, ii) a single TP53 mutation with VAF ≥50%, or iii) a single TP53 mutation with VAF ≥10% accompanied by a cytogenetically-apparent del(17p13.1), copy-neutral loss of heterozygosity (LOH) at the 17p TP53 locus, or, in the absence of LOH information, complex karyotype ( Arber et al. Blood 2022;140: 1200). The current study is focused on MN with multi-hit TP53 and examines the additional prognostic impact of morphologic subtype designation, bone marrow (BM) or peripheral blood (PB) blast percentage, TP53 VAF, and MN with diagnostic qualifiers (i.e., therapy-related, or secondary progressing from myelodysplastic/myeloproliferative/overlap syndromes/neoplasms). Methods : The current study was conducted under an institutional review board approved minimum risk protocol that allowed retrospective collection and analysis of data from Mayo Clinic patient records. Multi-hit TP53 was defined as per ICC criteria as outlined above ( Arber et al. Blood 2022;140: 1200). Morphologic subtype designations of MN were according to ICC criteria and assigned at the time of TP53 detection. NGS and cytogenetic information was available in all study patients. Survival analyses were calculated from time of TP53 mutation detection. Conventional statistical methods were applied using JMP Pro 16.0.0 software (SAS Institute, Cary, NC, USA). Results : Initial screening flagged 143 patients with biallelic TP53 abnormalities derived from formal laboratory reports of NGS data and cytogenetic studies; of these, 130 met ICC criteria for multi-hit TP53: pure erythroid leukemia (PEL; N=24), acute myeloid leukemia (AML)-not PEL (N=54), myelodysplastic syndromes (MDS; N=36), MDS/AML (N=11), and other MN (N=5). Of these 130 informative cases, 128 (98%) harbored complex/monosomal karyotype (CK/MK). Further analysis excluded patients with “other” MN (N=5) and those without CK/MK (N=2), the latter to mitigate the confounding effect of CK/MK on survival and the former because of small sample size and disease heterogeneity. Clinical and laboratory characteristics of the 124 study patients are outlined in table 1. Survival analysis stratified by ICC-defined MN subtypes revealed the prognostic relevance of morphological distinction between PEL vs “AML-not PEL” (p<0.01; HR 2.4) and PEL vs “ TP53-muated MDS/AML” (p=0.02; HR 2.3) while survival was similar between “AML-not PEL” and “ TP53-mutated MDS/AML” (p=0.9; Figure 1a). Survival in “ TP53-mutated MDS” was significantly longer, compared to PEL (p<0.01; HR 0.2), “ TP53-mutated AML-not PEL” (p=0.01; HR 0.5), and “ TP53-mutated MDS/AML” (p=0.07; HR 0.5), the latter with borderline significance (Figure 1a). Multivariable analysis confirmed the independent prognostic relevance of ICC subtype designation (p<0.01) and also revealed additional negative prognostic contribution from advanced age (p=0.02), male gender (p=0.02), MN, secondary (p<0.01), MN, therapy-related (p=0.03), and DNMT3A mutation (p=0.02). Significance was retained in all instances, with the exception of MN, therapy-related (p=0.15), when analysis was repeated after excluding PEL cases (Figure 1b). Conclusions : The current study confirms the prognostic validity of the ICC morphologic subtype designation and TP53 VAF classification threshold, in the context of multi-hit TP53. The study also highlights the prognostic distinction between PEL and “ TP53-mutated AML-not PEL” and the prognostic alignment between the latter and “ TP53-muated MDS/AML”, both of which displayed inferior survival, compared to “ TP53-mutated MDS”. The study also suggests additional prognostic contribution from secondary and therapy-related qualification while the observation regarding DNMT3A mutation requires validation with higher number of informative cases.

Predicted Functional Consequences of TP53 Alterations and Prognosis in TP53-Mutated Mantle Cell Lymphoma

Background: Mantle cell lymphoma (MCL) cases with TP53 mutations ( TP53mut) are associated with poor responses to chemoimmunotherapy (Eskelund Blood 2017). Across myeloid and solid tumors, predicted functional consequences and pathogenicity of specific TP53 mutations have been linked to differential patient outcomes (Pollock Breast Cancer Res Treat 2022, Yabe Cancers 2021). We aimed to characterize the impact of these features and associated molecular alterations on treatment outcome in TP53mut MCL patients treated with standard frontline regimens and on the ongoing phase 2 BOVEN trial. The BOVEN trial aims to assess the efficacy of frontline treatment with zanubrutinib, obinutuzumab, and venetoclax in TP53mut MCL (Kumar Blood 2021). Methods: The BOVEN trial enrolled 25 patients with TP53mut MCL. Retrospective chart review was performed for 22 patients with TP53mut MCL treated at frontline with standard chemoimmunotherapy regimens (Joffe Blood 2019). Tumor histology and FISH were obtained for each case. Mutational profiling (SNV/indels, CNA) was obtained prior to therapy with various CLIA-certified targeted sequencing platforms (Cheng J Mol Diagn 2015, Dias-Santagata EMBO Mol Med 2010). Mutations in TP53 were annotated using predicted phenotypes and pathogenicity from the TP53 Database (de Andrade Cell Death Differ 2022) and from phenotypic annotation of TP53 mutations (Giacomelli Nat Genet 2018). The primary outcome measures were overall and progression-free survival (OS/PFS). Results: Each patient included in the BOVEN cohort featured variants in TP53 with 26 SNV/indels across all 25 patients. There were 25 SNV/indels across all 22 patients treated with standard regimens. Within the trial cohort 14/25 cases had evidence of biallelic inactivation of TP53 with co-occurring SNV/indels in the gene and 17p loss by FISH or TP53 copy losses by SNParray; the comparator cohort featured 11/22 cases with biallelic losses. Across cohorts, most mutations were missense (>80% in both), with the majority occurring in the DNA binding domain of the p53 protein (76% and 91%, respectively), and with >30% at known hotspot codons in both cohorts. Most mutations (>70% in both cohorts) were predicted to adversely impact WT p53 function, including nonfunctional transactivation activity and dominant negative effect on the WT allele. The majority were also predicted to be highly pathogenic by bioinformatic methods (AGVGD, SIFT, PolyPhen2, PHANTM, REVEL, BayesDel). However, none of these features correlated with outcome. In the BOVEN cohort the variant allele frequency (VAF) of the TP53 SNV/indels approached significant association with poor PFS (HR 33.2, p=0.05) but not OS (HR 28.6, p=0.09). In contrast, in the comparator cohort TP53 VAF appeared to have an opposite effect direction, though this was not significant for PFS (HR 0.98, p=0.2) or OS (HR 0.97, p=0.06). We next investigated the impact of co-occurring molecular alterations on outcome. Besides TP53, the most frequently mutated genes in the trial cohort were KMT2D (24%), ATM (16%), NOTCH2 (12%), and CCND1 (12%). Alterations in these genes did not correlate with outcome. Within the comparator cohort the recurrently mutated genes were SMARCA4 (23%), ARID1A (18%), ARID1B (14%), ATM (14%), and CCND1 (14%). As described previously in this cohort (Joffe Blood 2019), alterations in SMARCA4 were associated with worse PFS (HR 4.2, p=0.02) but not OS (HR 2.2, p=0.27). Mutational burden (SNV and CNA load) was not prognostic in either 12/25 BOVEN samples sequenced with the same panel or the comparator cohort. There was no significant difference in outcome between patients with single mutations in TP53 vs. those with biallelic losses in TP53 in either cohort. Conclusion: Across patients with TP53mut MCL treated either with standard frontline chemoimmunotherapy or on the BOVEN trial, predictions of intrinsic pathogenicity and functional consequences of the TP53 alterations were not prognostic. The impact of TP53 mutation VAF remains unclear, with seemingly opposite effect directions between the two cohorts, though neither finding was significant. As previously described in the comparator cohort, alterations in SMARCA4 are associated with worse PFS in TP53mut MCL, though this was not observed in the BOVEN cohort. There were no significant differences in outcome among patients with biallelic inactivations in TP53 or with higher burdens of somatic alterations.

EPCO-20. DYNAMICS OF TUMOR GENOME SHAPING AND CLINICAL RESPONSE IN GLIOBLASTOMAS UNDER IMMUNE CHECKPOINT INHIBITORS

Abstract Immune checkpoint inhibitors (ICI) have shown remarkable success in several tumor types; however, this success has not been common in glioblastomas (GBMs). Given the immune-suppressive tumor microenvironment, the timing when to apply ICI may be a determining factor for clinical success. With this hypothesis, we compiled a longitudinal cohort of GBMs treated with different ICI schemes and a control cohort (upfront ICI (n=16), recurrent ICI (n=23), and control cohort by standard of care (n=33)). We investigated the genomic correlates to clinical response. Neither ICI itself nor different timing strategies failed to show a survival benefit for GBMs. However, the upfront-ICI cohort had more long-term survivors (overall survival >= 36 months) than the recurrent-ICI cohort (37.5% (n=6/16) vs. 26.1% (n=6/23)). Genomic analysis revealed that alterations in the PI3K-pathway or TP53 were associated with a poor response to ICI, while BRAF mutation was related to a favorable response. Interestingly, only TP53 alteration was associated with a worse prognosis in GBMs treated with upfront ICI. Tumor mutational burden (TMB) or the amount of neo-antigens failed to show any correlation with the response to ICI. However, ICI-treated GBMs experienced divergent evolution regarding the TMB, while GBMs treated by standard of care only exhibited unidirectional change. We also explored the immunogenomic shifts following different treatment modalities. ICI-treated GBMs showed more variable changes in both HLA alleles and neo-antigen burden (p-value=0.41 & 0.008, respectively). Among the upfront-ICI cohort, GBMs with a better response showed an increased neo-antigen burden upon recurrence (p-value=0.03), suggesting the selection of fitting clones during therapy. Collectively, we observed that that GBMs experienced distinct evolutions under different treatment schemes. The vulnerability of GBMs to ICI should be considered in the context of tumors’ capability to dynamically shape the tumor genome to fit into therapeutic pressure.

PATH-27. DROPLET DIGITAL PCR ENHANCES DETECTION OF HOTSPOT MUTATIONS IN CIRCULATING TUMOR DNA FROM CEREBROSPINAL FLUID OF PATIENTS WITH HIGH-GRADE GLIOMA

Abstract Molecular profiling of circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) has the potential to enhance diagnosis, prognosis, and longitudinal monitoring for glioma patients through a minimally invasive approach. We previously detected somatic mutations from gliomas in CSF samples using MSK-IMPACT™, a 505-gene FDA-authorized next-generation DNA sequencing panel, and detected tumor-derived mutations in 50% of samples of patients with high-grade gliomas (HGG). To investigate whether we could enhance sensitivity of CSF ctDNA profiling and biomarker detection, we tested MSK-IMPACT™ pre-capture NGS residual DNA libraries from 43 CSF ctDNA samples by droplet digital PCR (ddPCR) for detection of key recurrent alterations in IDH1, BRAF, TERT, H3F3A, and TP53 using previously validated probes. Residual libraries contained a median of 18.0ng of DNA library (range, 0.0153-18.0ng). Of the 7 samples positive for IDH1 R132H, TERT C228T, or TERT C250T mutations in MSK-IMPACT™, we found that ddPCR accurately detected all mutations (7/7, 100%), confirming sensitivity of ddPCR in CSF ctDNA. We also tested 36 mutation-negative samples by MSK-IMPACT™ for the corresponding undetected mutations, of which 7 were tested for two mutations. Overall, ddPCR detected 41.9% (18/43) of previously undetected mutations. Specifically, we found that ddPCR rescued hotspot mutations such as BRAF V600E (2/3, 66.7%), IDH1 R132G/H (3/8, 37.5%), TERT C228T (11/26, 42.3%), and TERT C250T (2/4, 50.0%). Collectively, our results suggest that a combined-modality approach involving MSK-IMPACT™ and ddPCR enables comprehensive assessment of limited CSF ctDNA samples with high sensitivity and provides a minimally invasive methodology to molecularly profiling glioma.

RADT-12. GENOMIC CHARACTERISTICS AND CLINICAL OUTCOMES OF STEREOTACTIC RADIOSURGERY FOR COLORECTAL CANCER BRAIN METASTASES

Abstract PURPOSE Brain metastases (BM) from colorectal cancer (CRC) portend a limited prognosis but are poorly understood, both clinically and biologically. This study defined the clinical outcomes and genomic features of CRC BM treated with stereotactic radiosurgery (SRS). METHODS Patients with newly diagnosed CRC BM treated with SRS at a single institution between 2009 and 2022 were included. Next-generation targeted sequencing using MSK-IMPACT of at least one intracranial or extracranial tumor was required. Overall survival (OS) was evaluated using Kaplan-Meier analysis. Intracranial progression (IP) and local recurrence (LR) were evaluated using competing risk analysis, accounting for death. RESULTS We identified 124 patients with 304 BM, of which, 66 BM received SRS postoperatively. The median prescription was 27 Gy in 3 fractions. Median OS after SRS was 7 months. Poorer KPS, progressive extracranial disease, and lung metastases independently predicted poorer OS. Twelve months after SRS, cumulative incidences of IP and LR were 37% per patient and 6.1% per lesion treated, respectively. Three or more BM at diagnosis independently predicted earlier IP. Biologically effective dose less than the median predicted LR, independent of tumor size. Genomic data were obtained from 68 primary tumors, 63 extracranial metastases, and 33 BM. BM demonstrated significantly greater fraction genome altered, chromosomal instability, and TP53 alterations compared to extracranial metastases and primary tumors. Among patients who had IP, compared to those who had no IP within 6 months, BM contained more frequent alterations in KRAS (56% vs. 43%), SMAD4 (44% vs. 0%), and APC (77% vs. 57%). CONCLUSIONS Among CRC BM treated with SRS, OS and IP were correlated with extracranial and intracranial disease burden, and LR was correlated with SRS dose. Genomic characteristics differed between BM and extracranial disease, and between patients who did and did not experience IP. Further investigation of these genomic differences is underway.