High-risk Genomic Features Research Articles

MDB-05. PERSONALIZED, RISK ADAPTED THERAPY FOR PEDIATRIC PATIENTS WITH MEDULLOBLASTOMA – A SINGLE CENTER 8-YEAR RETROSPECTIVE REVIEW

Abstract BACKGROUND Clinically relevant risk stratification and optimal therapies for pediatric medulloblastoma molecular subgroups are still being investigated. METHODS We reviewed host/disease characteristics, patient/tumor specific risk adapted therapy and outcomes of patients treated for medulloblastoma at UC Davis since 2016. RESULTS Fifteen patients (age 1-19 years, 12 male, 3 with Li Fraumeni Syndrome (LFS), 2 with spinal cord disease) were included in our review. Tumor histologies included: Classic (n=8), Desmoplastic-Nodular (n=6), Anaplastic (n=1). Tumor genomic profiles were SHHP53WT(n=5), SHHP53 mutated (n=4), Group4 (n=3), NWNSHH (n=2), WNT (n=1). Gross total resection was achieved in 9 patients. Patients with post resection residual tumor, high risk genomic features or disseminated disease were stratified as high risk. We treated all radiation eligible patients (n=13) per COG ACNS0332 maintenance chemotherapy regardless of risk group with 12/13 receiving radiosensitization (Vincristine/Carboplatin) and either 23.4 Gy/36 Gy CSI (two patients treated per Headstart3D2 and ACNS0334 respectively). 2 patients with spinal cord disease were treated with intrathecal topotecan and liposomal cytarabine respectively. During ACNS0332 maintenance bacteremia, weight loss and hypomagnesemia were frequent complications. 5 patients required chemotherapy dose reductions (4 Vincristine/1 Cisplatin). Two patients with LFS developed glioblastoma/undifferentiated pleomorphic sarcoma following ACNS0332 therapy. Two patients (with WNT and NWNSHH subgroup tumors) experienced medulloblastoma relapse. These patients were treated using LITT/Intrathecal chemotherapy and ACNS0821 chemotherapy. Both are alive and one patient is NED off therapy. All patients who have not developed secondary malignancies (n=13) are alive. (follow up 7-72 months). All attend school with support, 10 have hearing impairment and 5 receive endocrine supplements. CONCLUSIONS Utilizing patient specific risk adapted therapy we have achieved favorable clinical outcomes in our patient cohort. Therapy deintensification for patients with WNT medulloblastomas should be approached with caution. Patients with LFS might require radiation sparing therapeutic protocols for longer term benefit.

Outcomes in high-risk subgroups after fixed-duration ibrutinib + venetoclax for chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL): Up to 5.5 years of follow-up in the phase 2 CAPTIVATE study.

7009 Background: The phase 2 CAPTIVATE study evaluated first-line ibrutinib (Ibr) + venetoclax (Ven) for CLL/SLL in 2 cohorts: minimal residual disease (MRD)-guided randomized discontinuation (MRD cohort) and Fixed Duration (FD cohort). Ibr±Ven retreatment was allowed in patients (pts) who had progressive disease (PD). Here, we report outcomes for pts with high-risk genomic features from the FD cohort and retreatment outcomes in pts from the FD cohort and MRD cohort placebo arm. Methods: Pts aged ≤70 y with previously untreated CLL/SLL without restriction on genomic risk factors received 3 cycles of Ibr, then 12 cycles of Ibr+Ven (Ibr, 420 mg/d orally; Ven, 5-wk ramp up to 400 mg/d orally). On-study retreatment included single-agent Ibr (FD cohort or MRD cohort placebo arm); pts with PD >2 y after end of treatment (EOT) could be retreated with FD Ibr+Ven (FD cohort). Results: In the FD cohort (n=159) with a median follow-up of 61.2 mo (range, 0.8–66.3), 5-y PFS and OS rates (95% CI) were 67% (59–74) and 96% (91–98), respectively. 5-y PFS rates were higher in pts with undetectable MRD at 3 mo after EOT in peripheral blood (83%) or bone marrow (84%) vs those without (48% and 50%, respectively). 5-y PFS rates (95% CI) in pts with genomic risk factors were: del(17p)/mutated TP53 41% (21–59), complex karyotype 57% (37–72), del(11q) 64% (30–85), and unmutated IGHV 68% (50–80) (Table). In total, 18 second malignancies occurred in 13 pts (10 events in 8 pts during FD Ibr+Ven, 6 events in 4 pts after EOT and before retreatment, and 2 events in 2 pts during retreatment). Of 202 pts who completed Ibr+Ven (FD cohort, n=159; MRD cohort placebo arm, n=43), 63 have had PD to date; PD occurred >2 y after EOT in 43/63 pts (68%). 32/63 (51%) pts initiated retreatment with Ibr (n=25) or Ibr+Ven (n=7). With a median time on Ibr retreatment of 21.9 mo (range, 0.03–50.4), ORR was 86% in 22 evaluable pts (best response: 1 CR; 1 nodular PR; 17 PR; 2 SD; 1 PD [Richter transformation]). With a median time on Ibr+Ven retreatment of 13.8 mo (range, 3.7–15.1), ORR was 71% in 7 evaluable pts (best response: 1 CR; 4 PR; 1 PR with lymphocytosis; 1 SD). Conclusions: With up to 5.5 y of follow-up, FD Ibr+Ven continues to provide clinically meaningful PFS in pts with high-risk genomic features, as well as in the overall population. Ibr-based retreatment provides promising responses in pts needing subsequent therapy after the all-oral FD regimen of Ibr+Ven. Clinical trial information: NCT02910583 . [Table: see text]

Higher Mutational Burden Is an Independent Predictor of Shorter Time to First Treatment in Untreated Chronic Lymphocytic Leukemia Patients

Background. Recent advancements in next-generation sequencing (NGS) technologies have revolutionized the ability to comprehensively profile chronic lymphocytic leukemia (CLL), unveiling various molecular lesions. Complex mutational landscapes and diverse combinatorial patterns of genetic alterations lead to heterogeneity of clinical course and outcomes. The primary objective of this study was to identify patterns of co-occurrence (CO) and mutual exclusivity (ME) among mutations in CLL and their impact on time to first treatment (TTFT). Methods. The cohort included 795 treatment-naïve (TN) patients (pts) with CLL diagnosed according to iwCLL guidelines. The median follow-up time for the cohort was 3.91 years (range 0 - 42.8). The median time from diagnosis to mutational analysis was 6.6 months (26.50 - 33.27, 95% CI). Mutational screening was performed by a clinical targeted NGS panel, covering all or hotspot exons of 95 genes - the Rapid Heme Panel implemented by BWH (Kluk MJ, et al. J Mol Diagn. 2016;18(4):507-515). Standard protocols were applied to analyze IGHV gene mutational status, chromosomal aberrations by FISH with probes for 11q, 13q, 17p, and trisomy 12, and stimulated karyotype, where complex karyotype (CK) was defined as ≥3 abnormalities. CO and ME patterns were analyzed in pts with a higher mutational burden, determined as ≥2 distinct mutated genes, using Fisher's exact test ( p<.05). Control for false discovery rate was performed using the Benjamini, Krieger and Yekutieli method ( q=20%). TTFT was the time from diagnosis to initial treatment. Results. We detected 1798 mutations in 719 (90.4%) pts. No mutations were detected in 9.6% (n=76) patients, while a single mutated gene was found in 216 (27.2%) pts, 2 mutated genes in 206 (25.9%) pts, and mutations in 3 and ≥4 genes were found in 153 (19.2%) and 144 (18.1%) pts, respectively. The most mutated (≥10%) genes in the cohort were ATM (18.1%), NOTCH1 (17.7%), TP53 (13.2%), SF3B1 (12.3%), TET2 (10.2%), and DNMT3A (10.1%). A higher mutational burden was associated with clinical Rai stages 1-4 [ p=.003]; elevated (>3.5 mg/L) levels of baseline ß-2 microglobulin (B2M) [ p=.036] and established high-risk genomic features: del(17p) [ p<.001], del(11q) [ p=.021], CK [ p=.009], unfavorable ZAP70 [ p=.027] and unmutated IGHV (UM- IGHV) [ p<.001] (incidence of UM- IGHV cases is 48.4% (n=359) in cohort). At the same time, cases with 0-1 mutation were more likely to have del(13q) [ p=.006]. Sex and age >65 years at diagnosis were not associated with mutational burden. Otherwise, lack of any mutations was associated with absence of del(17p) (0% vs 11.1% [ p=.002]), lower rates of B2M >3.5 mg/L (3.9% vs 21.7% [ p<.001]), less frequent UM- IGHV (25.4% vs 50.9% [p<.001]), lower ratio of CK (7.0% vs 17.5% [p=.024] and age >65 years at diagnosis (21.1% vs 35.1% [ p=.014]). After controlling for multiple comparisons, no genes showed significant mutational co-occurrence. UM- IGHV cases were enriched in mutated ATM [ p=.003], NOTCH1 [ p<.00001], SF3B1 [ p=.0012] and XPO1 [ p<.00001]. Mutated NOTCH1 [ p<.00001], as well as KRAS [ p=.0012], occurred along with tri12. In contrast, UM- IGHV did not co-occur with mutations in MYD88 [ p<.00001], as previously reported. Del(13q) did not co-occur with mutated BRAF [ p=.0006] or BCOR [ p=.006]. Mutated TP53 [ p=.008] and SF3B1 [ p=.0013] were absent in tri12 positive cases. Increased mutational burden in ≥2 distinct mutated genes predicted a shorter TTFT than 0 or 1 mutated gene (HR 2.16; 95%CI 1.57 - 2.97; p<.001). Factors including Rai stages 1-4 (HR 2.63; 95%CI 1.88 - 3.7; p<0.001), UM- IGHV (HR 2.4; 95%CI 1.74 - 3.3; p<.001), CK (HR 1.47; 95%CI 1.07 - 2.0; p=.018), mutational burden in ≥2 genes (HR 1.57; 95%CI 1.14 - 2.2; p=.006) and del(17p) /TP53mut (HR 1.79; 95%CI 1.15 - 2.8; p=.01) were independently associated with worsened TTFT ( Figure 1). Neither mutated TP53 without del(17p) (HR 1.47; 95%CI 0.92 - 2.3; p=.104), or wild-type TP53 with del(17p) (HR 1.03; 95%CI 0.51 - 2.1; p=.932) were significant predictors of TTFT. Conclusions: Higher mutational burden is associated with worsened TTFT in CLL pts independently of other genomic events. In this cohort we did not see co-occurrence of specific mutations.

Genomic Profiling to Interpret the Outcomes of Early Intervention for High-Risk Smoldering Myeloma

Introduction Early intervention for High-Risk Smoldering Multiple Myeloma (HR-SMM) achieves deeper and more prolonged responses compared to Newly Diagnosed (ND) MM. Various clinical risk models estimate the risk of SMM progression to MM but there is significant discordance between them (Hill et al., JAMA Onc. 2021). It is unclear if beneficial outcomes of interventional studies in HR-SMM are due to treatment of less complex, susceptible disease or inaccuracy in clinical definition of cases entered. Methods To gain greater biologic insight into treatment outcomes, we performed the first whole genome sequencing (WGS) analysis of treated HR-SMM for 27 patients treated with carfilzomib, lenalidomide, and dexamethasone (KRd) and R maintenance (NCT01572480, presented in parallel). We pooled genomic features from 27 patients with HR-SMM treated with Elotuzumab (Elo)R+/-d; (E-PRISM). Genomic features were compared to those of 701 patients with NDMM from CoMMpass (NCT01454297). Results After a median follow-up of 52.8 months, median PFS was not reached with KRd/R. After 8 cycles of KRd, 19 (70.3%) achieved minimal residual disease (MRD) negativity (LOD 10 -5). At data cutoff, June 13, 2023, 14 patients (51.9%) achieved sustained MRD-negativity, 6 patients (22.2%) lost an initial MRD-negative response and 5 patients clinically progressed (18.5%). Overall, there was discordance between risk models: 3 patients (11.1%) were HR by Mayo2008 criteria, 14 (51.9%) by Mayo 20/2/20, 18 (66.7%) by PETHEMA, and 21 (77.8%) by Rajkumar/Landgren/Mateos criteria (Rajkumar et al., Blood. 2015). Eighteen (66.7%) met criteria for 2 or more scores. The estimated 5-year risk of progression ranged 4.8 to 82.1% (Pangea, median 18.6%). We compared the pooled HR-SMM to NDMM from CoMMpass. The frequency of HR translocations was similar (t(4;14), t(14;16), t(14;20); p>0.05). Consistent with the early disease stage of SMM, mutations of NRAS were lower in SMM (p = <0.001) as were events at the MYC locus (8q24; p <0.001) and gains of 1q (p = 0.039). Next, tumor suppressor genes (TSG) were interrogated together with copy number loss at their loci. Consistent with their late onset in tumor evolution, aberrations at key TSG were less common in HR-SMM (p < 0.05): CDKN2C, CYLD, TENT5C, FUBP1, MAX, NCOR1, NF1, NFKBIA, PRDM1, RB1, RPL5,and TRAF3 (p < 0.05). In a genome-corrected comparison, APOBEC (SBS2+SBS13) mutational signatures were diminished in KRd WGS compared to 60 Dara-KRd-treated NDMM (Maura et al., ASH. 2021; 48% vs 87%, p < 0.001) and in E-PRISM vs CoMMpass (15% vs 45%, p = 0.001). We next related genomic features associated with HR-SMM to treatment outcomes. Patients treated with KRd/R had yearly MRD testing and gain1q, MYC dysregulation via loss of MAX, and t(4:14) were all associated with failure to sustain MRD-negativity. Across pooled HR-SMM, inactivation of CYLD, CREBBP, MAX, and HIST1H2BK; t(4;14), APOBEC expression, loss at select GISTIC peaks ( Fig 1A) and chromothripsis all were associated with HR-SMM progression in the face of triplet therapy (p<0.05). Presence of any one or more of these features was associated with progression (p = 0.005; Fig1B). Conversely, no clinical risk score was able to discern those with this molecular high risk. Conclusion In patients treated on 2 parallel clinical trials for HR-SMM, we found a uniform and relative genomic simplicity. Moreover, non-progressors appear genomically similar to patients with non-progressive/stable MGUS and SMM under observation (Oben et al., Nat Comm 2021). However, within clinical HR-SMM, a set of high-risk genomic features portends progression despite intervention. These results suggest that clinical risk scores do not effectively discriminate between genomically indolent and aggressive disease. Though possible that results reflect treatment before the acquisition of key drivers, prior data suggest that many of these high-risk features are not acquired within the 5 years preceding clinical diagnosis of MM (Bolli et al., Nat Comm. 2018; Bustoros et al., J Clin Onc. 2020). Altogether, these results support the use of genomics to contextualize the advantage of early intervention in SMM (i.e., to avoid overtreatment of non-progressors and to better identify cases likely to progress without therapy). Fig1A: Heatmap of High-Risk Features in Patients treated with KRD/R and EPRISM. Fig1B: Kaplan-Meier curve for time to progression by presence of HR features for KRD/R.

Understanding Resistance Mechanisms and Growth Kinetics of CLL Treated with Covalent and Non-Covalent BTK Inhibitors

Resistance mechanisms to covalent BTK inhibitors (cBTKi) are well studied, with mutations in BTK at the 481 target binding site most commonly identified, and, less commonly, activating mutations in PLCϒ 2. Second site non-481 BTK mutations have been identified among patients on non-covalent BTK inhibitors (ncBTKi). The present study was designed to further evaluate these resistance mechanisms using dense serial sampling during therapy with both classes of BTKi and using mathematical modeling to analyze the rates of growth and decline of specific mutated clones. We performed whole exome sequencing on matched tumor and normal samples from 19 CLL patients treated with BTK inhibitors (Ibrutinib, Ibr, 42% (8/19); Acalabrutinib, Acala, 21% (4/19) and Pirtobrutinib, Pirto, 37% (7/19)). The median number of longitudinal samples per patient per cohort was 6 for ibr (N=51 total samples), 11 for acala (N=46) and 15 for pirto (N=105). The median number of prior therapies in both the ibr and acala cohorts was 2 and high-risk genomic features del(17p) and del (11q) were both at 50% in acala cohort and 50% and 38% in the ibr group respectively. The ibr cohort had no prior BTKi therapy whereas 1 patient in the acala cohort had received spebrutinib, another cBTKi. The average time to progression (TTP) in the ibr and acala groups was comparable at 44.1 and 44.4 months respectively. The pirto cohort was more heavily pretreated with a median of 3 prior therapies and del(17p) in 28.6% and del(11q) in 42.8%. All patients in this cohort had prior cBTKi (4 patients had 1 and 3 patients had ≥2 cBTKi) and average TTP was shorter at 15.1 months. At progression (PD), mutations in BTK C481S were found in 5 /8 patients (55%) in the ibr cohort with cancer cell fraction (CCF) > 80% in 3 patients. Two of these patients also have mutations in PLCϒ 2 (CCF > 30%). One patient in the cohort has an acquired PLCϒ 2 mutation (D1140N) with CCF>70%, without BTK C481S. Investigation of this patient's resistant clone growth kinetics (using WBC counts) demonstrates that the PLCϒ2 clone which was not detected at baseline takes over the population at ibr progression. Two patients in this cohort did not have either BTK or PLCϒ 2 mutations; however, one patient had 2 expanding subclones with known driver mutations ( TP53, BIRC3, del 8p). All 4 patients in the acala cohort have resistant clones harboring BTK C481S (CCF 16-75%) mutations, with T474I mutations present in 2 patients (CCF 4% and 26%) at progression. Growth kinetics analysis of the C481S clones for 3 patients shows steady increase during acala therapy, suggesting CLL progression in these two patients is driven by the C481S mutations. All but one patient in the pirto cohort had developed PD on cBTKi and 71% (5/7) had BTK C481S mutations prior to starting pirto (CCF 26 - 99%). In all 5 cases, the C481S clone declines on pirto and at PD is replaced by the BTK gatekeeper mutation T474I (CCF 76 - 99%) in 3 patients, the kinase-inactive mutation BTK L528W (CCF 30%) in 1 patient, and mutations in other driver genes ( XPO1, MED12) in 1 patient. Growth kinetics analysis for 1 patient shows exponential decay of the C481S clone under pirto treatment, followed by slow steady growth of the T474I clone, with a sharp increase right before PD. In another patient, exponential growth of the T474I clone occurs during pirto treatment while the C481S clone steadily declines. Interestingly this patient also had an existing PLCϒ 2 mutation (L845F, CCF 42%) at baseline, acquired during ibr treatment, which also steadily decreased on pirto. In another patient previously treated with ibr, with baseline BTK mutations in C481R (CCF 29%), C481S (CCF 18%), and L528W (CCF 2%), the L528W clone steadily increases, while both C481S and C481R clones decrease during PD. This patient exhibits extreme multiclonal diversity of BTK mutations, with 8 different BTK mutations at the DNA level at the C481 site present both at baseline and at PD, with 56% reduction in total wild type reads at PD. Of the remaining two patients without baseline C481S mutations, one patient acquired T474I (CCF 99%) and the other patient acquired 1q gain (MCL1) and t(8;14) at progression. Growth kinetics of different BTKi can vary based on their specific mechanism of action. The approach of combining WES data with growth pattern modeling can help unravel the complexities of tumor evolution and drug resistance for the different classes of BTKi. Data on comparative clone growth rates will be presented at the meeting.

Relapse after First-Line Fixed Duration Ibrutinib + Venetoclax: High Response Rates to Ibrutinib Retreatment and Absence of BTK Mutations in Patients with Chronic Lymphocytic Leukemia (CLL)/Small Lymphocytic Lymphoma (SLL) with up to 5 Years of Follow-up in the Phase 2 Captivate Study

Background: CAPTIVATE (PCYC-1142) is a multicenter phase 2 study of ibrutinib + venetoclax as first-line treatment for CLL/SLL in 2 cohorts: minimal residual disease (MRD)-guided randomized-discontinuation (MRD cohort) and Fixed Duration (FD cohort). Results from the FD cohort with 4 years of follow-up (Barr, ASCO 2023) showed 4-year progression-free survival (PFS) and overall survival (OS) rates of 79% and 98%, respectively. After completing fixed-duration treatment, ibrutinib-based retreatment was allowed per protocol in patients with an indication for treatment after experiencing progressive disease (PD). Here, we report retreatment outcomes in patients from the FD cohort or the MRD cohort placebo arm, as well as updated results with an additional year of follow-up (up to 5 years) from the FD cohort. Methods: Patients aged ≤70 years with previously untreated CLL/SLL received 3 cycles of ibrutinib, then 12 cycles of combined ibrutinib + venetoclax (ibrutinib, 420 mg/day orally; venetoclax, standard 5-week ramp up to 400 mg/day orally). Response was assessed by investigators per International Workshop on CLL (iwCLL) 2008 criteria. Duration of response (DOR), PFS, and OS were estimated using Kaplan-Meier methodology. Per protocol, on-study retreatment included single-agent ibrutinib; patients with PD >2 years after treatment completion could be retreated with the FD regimen (3 cycles of ibrutinib + 12 cycles of ibrutinib + venetoclax). Results: Of 202 patients treated with fixed-duration ibrutinib + venetoclax in the FD cohort (n=159) or the MRD cohort placebo arm (n=43), 53 have had PD to date (Table 1), with PD occurring >2 years after completion of treatment in the majority of patients (33/53 [62%]). Of the 40 patients with available samples at PD, one had an acquired resistance-associated mutation in BCL2 (A113G); no other patient had clinically relevant mutations in BTK, BCL2, or PLCG2. A total of 22 patients have initiated retreatment on study with single-agent ibrutinib. With a median time on retreatment of 17 months (range, 0-45), overall response rate (ORR) in 21 evaluable patients was 86% (with best responses of complete response [CR], n=1 [5%]; partial response [PR], n=17 [81%]; PR with lymphocytosis, n=1 [5%]; stable disease, n=1 [5%]; PD [Richter transformation], n=1 [5%]). The most frequent adverse events (AEs; occurrence ≥10%) during single-agent ibrutinib retreatment were COVID-19 (n=6, all grade 1/2), diarrhea (n=5), hypertension (n=4), and pyrexia (n=3). No dose reductions or discontinuations due to AEs occurred among retreated patients. Eighteen patients have not received subsequent treatment, 7 patients have initiated other subsequent therapies, and 6 patients have started retreatment with ibrutinib + venetoclax (time on retreatment, 5-15 months). Best responses in patients retreated with ibrutinib + venetoclax are CR, n=2; PR, n=3; and SD, n=1. Response data for the patient with BCL2 (A113G) is pending. To date, with a median time on study of 56 months (range, 1-61) for patients in the FD cohort, the 54-month PFS and OS rates were 70% (95% CI, 62-77) and 97% (95% CI, 93-99), respectively. Best response rates remained unchanged from the 4-year follow-up analysis (CR, including CR with incomplete bone marrow recovery [CRi], 58%; ORR, 96%). In patients who achieved CR/CRi (n=92), median duration of CR/CRi was not reached; 90/92 patients (98%) achieved durable CR/CRi (lasting ≥12 cycles). PFS in patients with high-risk features was promising (Table 2), but it was numerically lower in the subset with del(17p)/mutated TP53 (54-month rate, 45% [95% CI, 25-64]). Serious AEs considered related to study treatment and second malignancies continued to be collected after completion of fixed-duration treatment. One AE of basal cell carcinoma occurred during this additional year of follow-up. In total, second malignancies have occurred in 8% of patients since completion of ibrutinib + venetoclax treatment. Conclusion: Ibrutinib-based retreatment results in the CAPTIVATE study show promising responses in patients needing subsequent therapy after receiving this all-oral, once-daily fixed-duration regimen for first-line treatment of CLL/SLL. With up to 5 years of follow-up, fixed-duration ibrutinib + venetoclax continues to provide deep remissions with clinically meaningful PFS, including in patients with high-risk genomic features.

Targeted NGS Panel Guides Risk-Adapted Treatment Intention in Newly Diagnosed Myeloma Patients

Introduction While overall survival has improved, patients with high-risk multiple myeloma (MM) have poor outcomes. Fluorescent in situ hybridisation (FISH) is widely used to identify high-risk genomic features at diagnosis, but a significant minority of patients classified with standard-risk disease progress rapidly and in retrospect may have warranted more intense frontline therapy. Recently, we implemented the Myeloma Genome Project Panel (MGPP) into clinical workflows - a myeloma-specific targeted sequencing panel capturing 228 genes, 6 translocation regions and 56 copy number abnormalities (CNAs) in a single assay [PMID: 35522533]. Given that MGPP captures many prognostic regions beyond the limited number assessed by FISH, there is potential to better identify high-risk patients. However, the utility of MGPP in supporting clinical risk designation and therapy choice when compared with FISH in newly diagnosed MM is unknown. Methods A prospective cohort study was conducted to compare the impact of MGPP vs. FISH on baseline risk stratification and treatment intention, in 55 unselected newly diagnosed MM patients. For MGPP, libraries were generated from 100ng DNA from bone marrow (BM) derived CD138 + MM cells and matched germline peripheral blood (Roche KAPA HyperCap Target Enrichment/Hyperplus kit). Reads were aligned to hg38, and somatic mutations, CNAs and translocations called with a custom pipeline. ISO-accredited FISH analysis was performed in NHS laboratories. In a multicentre multidisciplinary team (MDT) meeting, four blinded haematologists independently reviewed each clinical case presented twice with either FISH or MGPP, in a random order. Clinicians designated risk status and treatment intentions using a structured proforma. Therapeutically actionable variants could be selected as per the MyDRUG trial [ClinicalTrials.gov: NCT03732703]. A consensus MDT outcome for high-risk or more intensive therapy required at least 3 out of 4 concordant decisions. Results Data is presented here for 23 of 55 patients. The mean age was 68.9 years, 57% were transplant eligible, with R-ISS-1 (35%), R-ISS-2 (26%) and R-ISS-3 (39%). Firstly, MGPP had greater technical success than FISH, reporting successfully in 100% vs. 83% cases from the same diagnostic BM samples respectively (n=4 assay failures with FISH). Secondly, MGPP reported more genomic features than FISH, detecting 231 vs. 18 somatic variants at 127 vs. 7 regions, respectively. Thirdly, MGPP captured equivalent loci at greater resolution, detecting subclonal CNAs missed by FISH (Figure 1). In a head-to-head comparison with FISH, these additional genomic insights from MGPP influenced clinical treatment decisions. A clinician-led MDT reclassified 9 (39%) patients designated as standard-risk by FISH to high-risk status when presented with MGPP (Table 1). Reclassified patients were enriched for prognostically significant MYC translocations (17%) and subclonal 17p loss (22%), 1p loss (17%) and 1q gain (13%) CNAs that were missed by FISH. Altered risk designation influenced frontline treatment intention; clinicians opted for intensification of induction therapy in 13% (FISH) vs. 48% (MGPP) high-risk patients, and considered tandem autologous transplant as an option in 0% (FISH) vs. 23% (MGPP) transplant-eligible patients. FISH identified a therapeutically actionable variant in 3 (13%) patients [venetoclax, n=3]. MGPP identified 13 (57%) additional patients with opportunity for targeted therapy [MEK inhibitor, n=11; BRAF V600E inhibitor, n=2], which the MDT considered as a treatment option in all cases if available in trial. The full dataset and analysis will be presented at time of the conference. Conclusions We demonstrate that MGPP impacts clinical risk designation and treatment intention in newly diagnosed MM. MGPP had greater technical assay success than FISH and captured a greater range and depth of somatic variants. Importantly, these additional insights led a clinical MDT to reclassify 39% patients as high-risk, consider intensification regimen in 39% cases and potential for actionable targeted therapy in 57% patients. Our results support MGPP as a robust alternative to FISH in supporting risk-adapted treatment decisions. We will implement MGPP in additional large prospective cohorts over the next year, to better understand its prognostic utility and feasibility in routine clinical workflows.

FISH-ing for answers: Can genomic arrays add to our understanding of disease biology in low-risk chronic lymphocytic leukaemia?

Patients with chronic lymphocytic leukaemia can have an indolent or aggressive clinical course. Current guidelines recommend performing immunoglobin heavy chain testing, four-colour probe fluorescence in situ hybridization testing and mutational analysis for TP53 mutations as part of routine prognostic testing to determine if high-risk genomic features are present. Rigolin et al. demonstrate that genomic microarray testing can identify high-risk genomic features in patients deemed low risk by current testing standards and is independently associated with shorter time to first treatment in their cohort. Commentary on: Rigolin et al. Additional lesions identified by genomic microarrays are associated with an inferior outcome in low-risk chronic lymphocytic leukaemia patients. Br J Haematol 2023;202:953-959.

Residual Disease Kinetics Among Patients with High-Risk Factors Treated with First-Line Fixed-Duration Ibrutinib Plus Venetoclax (Ibr+Ven) Versus Chlorambucil Plus Obinutuzumab (Clb+O): The Glow Study

Background: In the GLOW study (NCT03462719), fixed-duration Ibr+Ven demonstrated superior progression-free survival (PFS), deeper, better sustained undetectable minimal residual disease (uMRD) responses, and fewer patients (pts) requiring subsequent anti-cancer treatment versus Clb+O in older and/or comorbid pts with previously untreated chronic lymphocytic leukemia (CLL; Kater AP, et al. NEJM Evidence. 2022). Unmutated IGHV (uIGHV) and TP53 mutations are risk factors associated with worse outcomes for both chemoimmunotherapy and venetoclax plus anti-CD20 therapies for CLL. Here we investigate MRD kinetics and outcomes of Ibr+Ven in GLOW according to these risk factors. Methods: Pts aged ≥ 65 years or 18 to 64 years with cumulative illness rating scale score > 6 or creatinine clearance < 70 mL/min were enrolled and randomized 1:1 to Ibr+Ven (3 cycles of Ibr lead-in, followed by 12 cycles of Ibr+Ven) or 6 cycles of Clb+O, with a cycle defined as 28 days. Pts with del(17p) or known TP53 mutations at screening were excluded, and central evaluation of TP53 mutational status was performed during the study. The primary end point was PFS by independent review committee. Among pts with partial response or better, MRD in peripheral blood was evaluated using next-generation sequencing via clonoSEQ on-treatment and at 3-6 month intervals post-treatment. uMRD results are reported in peripheral blood (PB) at < 10-4 unless otherwise noted. Since the primary analysis, a post hoc retrospective reclassification of the IGHV status of baseline samples was conducted to reduce the number of unknowns. We used clonoSEQ data as part of CLL clonal testing (Adaptive Biotechnologies, Seattle, WA). Results: There were 106 pts randomized to Ibr+Ven and 105 to Clb+O. In the Ibr+Ven arm, uMRD rates increased from 46.2% after 6 cycles of the combination to 54.7% at 3 months after end of treatment (EOT+3), demonstrating that the majority of disease clearance in the PB occurred early, during the first 6 months of combination treatment. Post-treatment, 77.6% (45/58) of pts in the Ibr+Ven arm sustained their uMRD status from EOT+3 to EOT+18, compared with 12.2% (5/41) in the Clb+O arm. In the Ibr+Ven arm, 17/24 patients with intermediate MRD ≥ 10-4 to < 10-2 at EOT+3 did not worsen through EOT+18. Among pts with detectable MRD (≥ 10-4) at EOT+3, 6.5% (2/31) clinically progressed by EOT+18 in the Ibr+Ven arm versus 68.1% (32/47) in the Clb+O arm. After reclassification of baseline samples, uIGHV / mutated IGHV (mIGHV) / unknown status was 63.2%/30.2%/6.6% in the Ibr+Ven arm and 54.3%/33.3%/12.4% in the Clb+O arm. In the Ibr+Ven arm, rates of uMRD after 6 cycles of combination treatment and at EOT+3, respectively, were 52.2% and 59.7% in pts with uIGHV and 31.3% and 40.6% in pts with mIGHV (Fig A). On-treatment MRD kinetics differed by IGHV status in the Ibr+Ven arm, with uMRD achieved at a higher rate and earlier in pts with uIGHV. In the Ibr+Ven arm, uMRD was sustained post-treatment (from EOT+3 and EOT+18) in 80.0% (32/40) of pts with uIGHV and 76.9% (10/13) of pts with mIGHV. Among pts with detectable MRD (≥ 10-4) at EOT+3, 2/16 with uIGHV and 0/14 with mIGHV had clinically progressed by EOT+18 in the Ibr+Ven arm; corresponding rates were 83.3% (25/30) and 42.9% (6/14) in the Clb+O arm. Five of 7 pts with TP53-mutated CLL achieved uMRD at EOT+3 in the Ibr+Ven arm; TP53 variant allele frequencies ranged between 5.9% and 29.6% for these 5 pts and all maintained uMRD through EOT+18. With a median study follow-up of 34.1 months, PFS rates after IGHV reclassification were well sustained post-treatment regardless of IGHV status in the Ibr+Ven arm, while uIGHV pts in the Clb+O arm relapsed more quickly (Fig B). PFS, overall survival, and subgroup analyses with longer study follow-up will be presented. Conclusion: All-oral, once-daily, fixed-duration Ibr+Ven achieved uMRD responses that were better sustained than Clb+O during the first 18 months post-treatment. Notably, with Ibr+Ven, uMRD rates were higher and achieved earlier in pts with uIGHV CLL versus mIGHV CLL, while uMRD was similarly sustained post-treatment irrespective of IGHV status. Clinical progressions in the first 18 months post-treatment with Ibr+Ven were uncommon even among pts with detectable MRD ≥ 10-4. MRD kinetics and sustained responses demonstrate strong efficacy of the fixed-duration Ibr+Ven combination in older pts with high-risk genomic features. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Real-World Outcomes with First-Line Ibrutinib (Ibr) Versus Chemoimmunotherapy (CIT) in Patients with Chronic Lymphocytic Leukemia (CLL)/Small Lymphocytic Lymphoma (SLL): Final Analysis Results from the InformCLL Registry

Background: The therapeutic landscape for CLL/SLL has rapidly evolved with the introduction of novel agents such as Ibr. The informCLL registry (PCYC-1134; NCT02582879) is the largest US-based prospective, observational registry of patients (pts) initiating FDA-approved treatment for CLL/SLL in the era after approval of Ibr. Here, we report real-world (RW) outcomes in pts with CLL/SLL receiving first-line (1L) therapy, including comparison of 1L Ibr versus CIT, from the final analysis of informCLL. Methods: Pts with CLL/SLL who initiated FDA-approved treatment (within ±45 days of enrollment) were enrolled between 10/2015 and 6/2019. Pts were primarily enrolled from community-based practices (comprising 93% of sites). Data were collected for baseline characteristics, treatment patterns, and safety. Time to next treatment (TTNT) was estimated by Kaplan-Meier method and for comparison of outcomes with 1L Ibr versus CIT, by Cox proportional hazards regression analysis in weighted cohorts. Inverse probability of treatment weighting (IPTW) was performed to balance the baseline characteristics between cohorts. Adverse events (AEs) were evaluated using overall incidence and exposure-adjusted incidence rates (EAIRs). Results: Of the 1459 eligible pts enrolled, 854 were treated in the 1L setting (59%). In the overall 1L cohort, median age was 70 years (≥75 years in 33%); 90% had ECOG performance status of 0 or 1; 47% had Rai stage III/IV (among n=547 with Rai staging); median Charlson Comorbidity Index (CCI) score was 1 (range 0-12) with CCI ≥3 in 16%; median time from initial diagnosis to 1L treatment was 19 mo. FISH testing data were available in 57% of pts in the 1L cohort; among these pts, 12% had del(17p). The most common 1L therapies were Ibr (45%; single-agent Ibr in 43% of all 1L therapies) and CIT (43%: most commonly BR, 24%); immunotherapy was given in 11% while chemotherapy (0.9%) and other novel agents (0.7%) were rare. With a median follow-up of 31.8 mo in the 1L cohort, median TTNT was not reached (NR); estimated proportions of pts without next-line therapy (NLT) were 79% at 24 mo, 71% at 36 mo, and 64% at 48 mo. The 1L cohort included 383 pts treated with Ibr and 363 pts treated with CIT; median follow-up was 31.4 mo for the Ibr cohort and 34.3 mo for CIT. Compared with the CIT cohort, pts in the Ibr cohort were older, had longer time from diagnosis to treatment, were more likely to have a history of other malignancy, and were more likely to have del(17p) or TP53 mutation (Table). Baseline characteristics in the weighted cohorts were balanced. In the IPTW-adjusted cohorts, median TTNT was NR for Ibr and 56.5 mo for CIT; TTNT was improved with Ibr relative to CIT (hazard ratio 0.744; 95% CI, 0.563-0.981) (Figure). Estimated proportions free of NLT in the weighted Ibr cohort were 75% at 36 mo and 69% at 48 mo; rates in the weighted CIT cohort were 66% and 57%, respectively. Median duration of index treatment was 24.0 mo for 1L Ibr and 4.7 mo for CIT. In the Ibr cohort (n=383), serious AEs occurred in 144 pts (38%), most commonly (≥3% of pts) pneumonia (n=23; 6%) and atrial fibrillation (Afib; n=21; 5%); AEs led to discontinuation of Ibr in 135 pts (35%), most commonly Afib (n=19; 5%) and fatigue (n=12; 3%). In the CIT cohort (n=363), serious AEs occurred in 85 pts (23%), most commonly febrile neutropenia (n=13; 4%) and pneumonia (n=11; 3%). AEs led to discontinuation of CIT in 61 pts (17%), and no single AE term led to discontinuation in ≥3% of pts (most common was anemia, 2%). EAIRs per 100 pt-mo for serious AEs were 1.93 with Ibr and 4.55 with CIT. EAIRs per 100 pt-mo for AEs leading to discontinuation were 1.53 with Ibr and 3.09 with CIT. Conclusion: In this large RW registry of pts with CLL/SLL, results from IPTW-adjusted analysis showed that 1L Ibr was associated with longer TTNT than CIT, with sustained benefit up to 4 years of follow-up. Pts receiving 1L Ibr therapy tended to be older, more often had a history of other malignancy, and more often had high-risk genomic features (del(17p) or TP53 mutation among those tested) than pts treated with CIT. The spectrum and frequency of AEs observed with these 1L regimens appear consistent with data from clinical studies and other RW studies. When adjusted for exposure, rates of AEs leading to discontinuation and serious AEs were lower with Ibr than CIT. Future analyses examining the impact of factors such as age/comorbidity and race are warranted to further our understanding of RW outcomes in pts with CLL/SLL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Individualized Treatment-Adjusted Risk Stratification in Newly Diagnosed Multiple Myeloma

Introduction. For newly diagnosed multiple myeloma (NDMM) patients, median overall survival (OS) and progression free survival (PFS) have dramatically improved during recent years due to the introduction of novel agents. Unfortunately, a subset of patients with NDMM does not benefit from newer therapies reflected in persisting poor outcomes. In contrast, another subset has favorable outcomes despite receiving limited therapy. Though having demonstrated that several genomic events contribute to clinical outcomes, yet the "one-size-fits-all" treatment paradigm remains dominant for NDMM. Here, we present the first artificial intelligence individualized prediction model for NDMM to facilitate individually tailored therapeutic decisions. Methods. We included 1840 patients with available clinical and genomic data from the following cohorts: MMRF CoMMpass (n=1062), MGP (n=492), Moffit AVATAR (n=177), and MSKCC (n=109). The median follow up was 42 months. To build a treatment-adjusted predictive model of individualized risk for patients with NDMM, we considered 160 variables across clinical (e.g., age, ECOG, sex, ISS), therapeutics, genomics, and time-dependent treatments such as autologous stem cell transplant (ASCT) and continuous treatment (Palumbo et al. JCO 2015). A multi-state model was designed across two phases: induction (phase 1), and post-induction (phase 2). Phase 1 included patients that: 1) completed the induction without progression (PD); 2) PD of failed to respond during induction remaining alive after; 3) PD during induction and subsequently died. Phase 2 have patients that: 4) PD after induction and were alive; 5) PD after induction and died; 6) reached remission after induction and were alive; 7) responded after induction and died due to other causes. We leveraged and compared survival methods based on deep neural networks (Neural Cox Non-proportional-hazards;NCNPH), Random Survival Forest (RSF), and Cox proportional-hazard(CPH). Results. NCNPH showed the best cross-validated prognostic performance for OS with median Uno's concordance (C=0.67), followed by RSF (C=0.65) and CPH (C=0.64; Fig. 1a-b). Overall, the model significantly outperformed R2-ISS (C=0.6), ISS (C=0.59) and R-ISS (C=0.57; Fig. 1b). Additionally, the model found 28 genomic features to increase concordance accuracy for PFS by (3% in phase 1 and 1.5% in phase 2), and with greater effect on OS (10% in phase 1 and 5% in phase 2). The 14% of patients who did not respond in phase 1 were enriched for ISS3, age >75 y, 1q amp, NSD2 translocation, TP53 mutations, and deletions on 17p13 and 1p. Varying therapies emerged as a key determinant of risk, in particular, in phase 2, supporting the idea that effective combinations can have a different impact in individual patients and have the potential to significantly change the clinical outcome despite poor prognostication. The model not only predicts patient risk but also the impact of various treatment strategies (i.e., treatment variance). We identified 9 distinct clusters (C#1-9) based on predicted risk and treatment variance. C#8 and C#9 show favorable outcome, especially with ASCT and continuous treatment. C#4 and C#5 included patients with favorable outcome but low treatment variance where ASCT had marginal impact. C#6 had a substantial presence of high-risk patients associated with low variance, age >75y, 1q gain, and NSD2 translocations. Interestingly, NSD2 translocated patients not included in C#6 had an intermediate favorable outcome (p<0.0001). Early PD was observed in C#1 and C#7, both enriched for low treatment variance, and high risk genomic and clinical features. Finally, we identified a group of high-risk patients (C#2 and C#3) with high treatment variance whose poor outcome was mostly driven by a suboptimal treatment (i.e., use of doublet, no ASCT, no continuous treatment) rather than presence of distinct clinical and genomic features, highlighting the need for treatment to be considered to build more robust and accurate prognostic models. Conclusion: This work shows the first comprehensive model integrating new and historical features to train a neural network for individualized risk prediction in NDMM. Utilizing data from 1840 patients that received a variety of therapies, the model captures the interaction of genomic, clinical and therapy factors, enabling personally-tailored therapeutic decisions in NDMM. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Final Results of the Phase 1/2 Study of Acalabrutinib Monotherapy in Treatment-Naive Chronic Lymphocytic Leukemia with >6 Years of Follow-up

Background: Acalabrutinib is a next-generation, covalent Bruton tyrosine kinase inhibitor approved for the treatment of patients with treatment-naive (TN) or relapsed/refractory chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL). A previous analysis of the phase 1/2, multicenter ACE-CL-001 study (NCT02029443) demonstrated durable responses and good long-term tolerability of acalabrutinib as first-line therapy in patients with CLL at a median follow-up of 53 months (Byrd et al. Blood. 2021;137:3327-38). Here, we report the final analysis in the TN cohort of that study, the longest running study of acalabrutinib, with over 6 years of follow-up. Methods: Patients included in the study were aged ≥18 years with TN CLL/SLL who met the 2008 iwCLL criteria for treatment, were inappropriate for or declined standard chemotherapy, and had ECOG performance status 0-2. All TN patients were treated in the phase 2 portion of the study and received acalabrutinib 100 mg twice daily (BID) or 200 mg once daily (QD), later switching to 100 mg BID, until progressive disease (PD) or unacceptable toxicity. The primary endpoint was safety. Secondary endpoints included investigator-assessed overall response rate (ORR), time to response (TTR), duration of response (DOR), and progression-free survival (PFS), with a post hoc analysis of event-free survival (EFS). Results: Ninety-nine patients (n=62 100 mg BID; n=37 200 mg QD) were treated. The median age was 64 years; 47% of patients had Rai stage 3-4 disease, 10% had del(17p), 14% had TP53 mutation, 17% had del(11q), 62% had unmutated IGHV, and 18% had complex karyotype. At the final data cut-off date of July 15, 2021, the median study follow-up was 73.7 months (range 0.92-82.4), and 70 (71%) patients remain on acalabrutinib treatment. The most common reasons for treatment discontinuation were adverse events (AEs) (10%) and PD (6%). The most common AEs (Table 1) were consistent with those reported in the prior update (53-month median follow-up). The only grade ≥3 AEs with a ≥50% increase in incidence since the prior update were pneumonia (4% [prior update] vs 8%) and syncope (4% [prior update] vs 6%). AEs that led to treatment discontinuation were amyotrophic lateral sclerosis, angiosarcoma, cardiac failure, cerebral hemorrhage, gastric hemorrhage, glioblastoma multiforme, non-cardiac chest pain, prostate cancer, sepsis, small cell lung cancer, and urinary tract infection (in 1 patient each). All-grade and grade ≥3 events of clinical interest included infection (87% and 19%, respectively), bleeding events (74%, 7%), major bleeding events (8%, 7%), and hypertension (29%, 13%). Atrial fibrillation/flutter occurred in 6% of patients (3% grade ≥3). Second primary malignancies excluding non-melanoma skin (all grades) occurred in 14% of patients Two deaths were reported (cardiac failure, n=1; multiple organ dysfunction syndrome, n=1); neither was considered treatment related. ORR was 97% (9% complete response; 88% partial response). Median TTR was 3.7 months (range 1.7-22.1). Median DOR was not reached; the estimated 66-month DOR rate was 89% (95% CI 80-94). ORR of 100% was seen across high-risk groups: del(17p) (9/9), del(11q) (15/15), unmutated IGHV (57/57), and complex karyotype (12/12). Median PFS was not reached; the estimated 72-month PFS rate was 87% (95% CI 77-93; Figure 1). The estimated 72-month EFS was 78% (95% CI 68-85). Reported EFS events overall included AEs (n=10/99, 10%), disease progression (n=9/99, 9%), and new anticancer therapy (n=3/99, 3%). Conclusions: The final data from ACE-CL-001 further support the long-term efficacy and safety of acalabrutinib monotherapy, with high response rates and rapid, durable responses seen in patients with TN CLL regardless of high-risk genomic features. With over 6 years of follow-up, this study firmly establishes the tolerability and safety profile of acalabrutinib seen consistently in subsequent studies, with a low incidence of atrial fibrillation/flutter seen and no new long-term safety issues identified. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A Methodologically Updated De-Novo Extraction of Copy Number Signatures in Multiple Myeloma: Clinical Significance and Putative Aetiologies

BACKGROUND: The tumor genomes of most Multiple Myeloma (MM) patients are heavily burdened with highly heterogenous copy number (CN) alterations, as detected by multiple molecular methods including whole genome sequencing (WGS), and have been shown to have a strong prognostic and predictive significance for patients' survival. Cutting-edge computational developments have made it possible to analyze complex genomic CN changes by identifying CN alterations' recurrent patterns among large cohorts of patients, named CN signatures (CNS), that are the result of cumulative chromosomic instability (CIN) processes throughout the course of cancer cells evolution. In fact, a robust methodological framework for CNS computation, along with a large compendium of CNS aetiologies have been recently published for many cancer types, notably not including MM (Drews 2022). To our knowledge, the only study that analyzes CNS in MM focused on the role of CNS in predicting chromothripsis events, but remarkably it did not include neither CNS aetiologies nor complete CNS characterization for all the discovered CNS (Maclachlan 2021). AIM: To define a novel methodological framework, based on previous studies, aimed at the identification of CNS in MM, in order to assess both the aetiologies and the biological significance of MM CNS and to evaluate their prognostic impact on MM clinical outcome. The newly extracted CNS defined at diagnosis will be also used as novel disease biomarkers, to develop an improved, aetiology-based MM patients' stratification in different molecular subtypes. METHODS: We calculated the MM genomic distributions of the six essential CN features (segment length, breakpoint per 10 Mb, breakpoint per chromosome arm, segment CN change, CN value, length of oscillating CN states) that have been previously shown to encode patterns of CN alterations, underlying the observed tumor CIN. Starting from 886 WGS generated CN profiles, included in the CoMMpass study, the above mentioned features were computed. Features were then categorized into components, by using mixture models' decomposition and CNS were finally extracted from the components, by using both a Hierarchical Dirichlet Process (HDP) and a Non-Negative Matrix Factorization (NNMF) approach. RESULTS: The main novel characteristics of the developed methodological framework aimed at CNS assessment were 1) the use of a "continuous CN value" feature, which enabled the evaluation of sub-clonal events and 2) the use of a logarithmic scale in "segment length" feature, which favored a higher resolution for categorizing focal and/or gene level CN events, that are very common in MM. Thanks to these implementations, 33 Gaussian mixture components were identified (as compared to 28 detected in Maclachlan 2021). After deriving a Sample x Component - Sum of Posteriors Matrix, the signatures were extracted by applying two parallel state-of-art approaches, namely HDP and NNMF. This allowed the extraction of 9 CNS that were characterized by their component's composition. The signature's exposure levels were correlated to well-known MM biomarkers (e.g. TP53 mut and/or del, 1q CN gain, 13q CN loss, t-IgH, hyperdiploidy), showing that all signatures correlated to at least one of the well known MM biomarkers; in particular, CN.SIG5 exposures was found to correlate to high-risk MM biomarkers (TP53 p<0.001, 1q CN gain p<0.001, t(4;14) p<0.001), thus suggesting its possible involvement in the aetiology of this peculiar genomic configuration. Finally, a survival analysis was performed in patients characterized by high exposure (4th quartile) to the CN.SIG5 (75 patients), as compared to the others (811 patients), showing a significant negative impact of this CNS on both overall (OS p<0.001)) and progression free survivals (PFS p<0.001). Cox-analysis revealed an OS HR= 1.37 p<0.001, PFS HR= 1.16, p<0.001, per 5% increase in exposure. CONCLUSION: By employing a novel bio-informatic approach, based on the use of continuous CN data for CNS extraction, 33 feature's components were identified. We observed that CN.SIG5 significantly affected patients carrying well-known high-risk genomic features, and patients highly exposed to this CNS had decreased PFS and OS. Additional characterizations are needed to unveil the biological meaning of CNS exposure; however, MM CNS, while informing on disease outcome, might be considered as new comprehensive biomarkers in this disease. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

PB1878: CROSS-TRIAL ANALYSIS OF FIXED-DURATION IBRUTINIB (I) PLUS VENETOCLAX (V) VS FLUDARABINE (F), CYCLOPHOSPHAMIDE (C), AND RITUXIMAB (R) AS FIRST-LINE TREATMENT FOR CHRONIC LYMPHOCYTIC LEUKEMIA (CLL)

Background: While continuous single-agent I or I-based therapies are superior to FCR, FCR remains an efficacious fixed-duration regimen for fit patients (pts) with previously untreated CLL. CAPTIVATE (PCYC-1142; NCT02910583) is a multicenter phase 2 study of first-line treatment with the all-oral, once-daily, chemotherapy-free regimen of I+V in fit pts with CLL. Primary analysis of the CAPTIVATE Fixed Duration (FD) cohort demonstrated deep, durable responses with fixed-duration I+V (Ghia et al, ASCO 2021). Aims: We performed a cross-trial analysis to evaluate outcomes with fixed-duration I+V relative to FCR using data from the FD cohort of the CAPTIVATE study and the FCR arm of the recent E1912 study (NCT02048813; Shanafelt et al. NEJM 2019;381:432-43). Methods: This cross-trial analysis included pts with previously untreated CLL or SLL aged ≤70 y who were treated with I+V in the FD cohort of CAPTIVATE or with FCR in E1912. As pts with del(17p) were not enrolled in E1912, pts with del(17p) from CAPTIVATE were excluded from the analysis. In CAPTIVATE, pts received three 28-d cycles of I, followed by 12 cycles of I+V (I 420 mg/d orally; V ramp-up to 400 mg/d orally). In E1912, pts received six 28-d cycles of FCR (F 25 mg/m2 on days 1-3; C 250 mg/m2 on days 1-3; R 50 mg/m2 on day 1 and 325 mg/m2 on day 2 in cycle 1, then 500 mg/m2 on day 1 in cycles 2-6). PFS and OS were estimated by Kaplan-Meier method. Adjusted treatment effects for PFS, OS, and ORR were estimated by inverse probability of treatment weighting (IPTW) using propensity score (PS) which balanced treatment groups for the following baseline prognostic factors: age, sex, ECOG performance status ≥1, CLL/SLL diagnosis, time from diagnosis, advanced Rai stage, absolute lymphocyte count, beta-2 microglobulin >3.5 mg/L, and high-risk genomic features (TP53 mutated, del[11q], unmutated IGHV). AEs were evaluated using overall incidence and exposure-adjusted incidence rates (EAIRs). Results: Analysis included 136 pts without del(17p) treated with fixed-duration I+V in the CAPTIVATE FD cohort and 175 pts treated with FCR in E1912; baseline characteristics were generally well-balanced across groups, with notable differences in the proportions of pts aged ≥65 y and with baseline thrombocytopenia (Table). Median follow-up was 38.7 mo with I+V and 33.7 mo with FCR. After IPTW, PFS was improved with I+V relative to FCR (hazard ratio [HR] 0.42; 95% CI 0.25-0.71; log-rank P=0.0018; 36-mo PFS rate: 89% vs 70%), as was OS (HR 0.19; 95% CI 0.05-0.77; log-rank P=0.0084; 36-mo OS rate: 98% vs 90%). Results were generally similar in unadjusted analyses (Table). Adjusted ORRs were 96% for I+V and 85% for FCR (difference 11.2%; 95% CI 5.1–17.3; Chi-square P=0.0011). Median duration of treatment was 13.8 mo for I+V and 4.7 mo for FCR. Treatment was discontinued due to AEs in 5% and 21% of pts, respectively. Overall, grade ≥3 AEs occurred in 62% of pts with I+V and 90% with FCR. Grade ≥3 AEs in ≥5% of pts with I+V were neutropenia (36%), and with FCR were lymphopenia (67%), neutropenia (45%), leukopenia (41%), lymphocytosis (31%), anemia (18%), thrombocytopenia (18%), febrile neutropenia (16%), hypertension (6%), hyperglycemia (6%), and maculopapular rash (5%). EAIRs for grade ≥3 AEs and AEs of clinical interest of any grade were lower with I+V than with FCR (Table). Image:Summary/Conclusion: Results of this cross-trial analysis suggest superior PFS with fixed-duration I+V relative to FCR in first-line CLL. The safety profile with I+V appeared favorable relative to the safety profile of FCR, with lower AE rates and fewer discontinuations due to AEs.

Up to 8-year follow-up from RESONATE-2: first-line ibrutinib treatment for patients with chronic lymphocytic leukemia

AbstractWe report long-term follow-up from the RESONATE-2 phase 3 study of the once-daily Bruton's tyrosine kinase inhibitor ibrutinib, which is the only targeted therapy with significant progression-free survival (PFS) and overall survival (OS) benefit in multiple randomized chronic lymphocytic leukemia (CLL) studies. Patients (≥65 years) with previously untreated CLL, without del(17p), were randomly assigned 1:1 to once-daily ibrutinib 420 mg until disease progression/unacceptable toxicity (n = 136) or chlorambucil 0.5-0.8 mg/kg ≤12 cycles (n = 133). With up to 8 years of follow-up (range, 0.1-96.6 months; median, 82.7 months), significant PFS benefit was sustained for ibrutinib vs chlorambucil (hazard ratio [HR], 0.154; 95% confidence interval [CI], 0.108-0.220). At 7 years, PFS was 59% for ibrutinib vs 9% for chlorambucil. PFS benefit was also observed for ibrutinib- vs chlorambucil-randomized patients with high-risk genomic features: del(11q) (HR, 0.033; 95% CI, 0.010-0.107) or unmutated immunoglobulin heavy chain variable region (HR, 0.112; 95% CI, 0.065-0.192). OS at 7 years was 78% with ibrutinib. Prevalence of adverse events (AEs) was consistent with previous 5-year follow-up. Ibrutinib dosing was held (≥7 days) for 79 patients and reduced for 31 patients because of AEs; these AEs resolved or improved in 85% (67 of 79) and 90% (28 of 31) of patients, respectively. With up to 8 years of follow-up, 42% of patients remain on ibrutinib. Long-term RESONATE-2 data demonstrate sustained benefit with first-line ibrutinib treatment for CLL, including for patients with high-risk genomic features. These trials were registered at www.clinicaltrials.gov as #NCT01722487 and #NCT01724346.

Primary plasma cell leukemias displaying t(11;14) have specific genomic, transcriptional, and clinical features

AbstractPrimary plasma cell leukemia (pPCL) is an aggressive form of multiple myeloma (MM) that has not benefited from recent therapeutic advances in the field. Because it is very rare and heterogeneous, it remains poorly understood at the molecular level. To address this issue, we performed DNA and RNA sequencing of sorted plasma cells from a large cohort of 90 newly diagnosed pPCL and compared with MM. We observed that pPCL presents a specific genomic landscape with a high prevalence of t(11;14) (about half) and high-risk genomic features such as del(17p), gain 1q, and del(1p32). In addition, pPCL displays a specific transcriptome when compared with MM. We then wanted to characterize specifically pPCL with t(11;14). We observed that this subentity displayed significantly fewer adverse cytogenetic abnormalities. This translated into better overall survival when compared with pPCL without t(11;14) (39.2 months vs 17.9 months, P = .002). Finally, pPCL with t(11;14) displayed a specific transcriptome, including differential expression of BCL2 family members. This study is the largest series of patients with pPCL reported so far.

Up to 6.5 years (median 4 years) of follow-up of first-line ibrutinib in patients with chronic lymphocytic leukemia/small lymphocytic lymphoma and high-risk genomic features: integrated analysis of two phase 3 studies

Genomic abnormalities, including del(17p)/TP53 mutation, del(11q), unmutated IGHV, and mutations in BIRC3, NOTCH1, SF3B1, and XPO1 predict poor outcomes with chemoimmunotherapy in chronic lymphocytic leukemia. To better understand the impact of these high-risk genomic features on outcomes with first-line ibrutinib-based therapy, we performed pooled analysis of two phase 3 studies with 498 patients randomized to receive ibrutinib- or chlorambucil-based therapy with median follow-up of 49.1 months. Ibrutinib-based therapy improved overall response rates (ORRs), complete response rates, and progression-free survival (PFS) versus chlorambucil-based therapy across all subgroups. In ibrutinib-randomized patients with versus without specified genomic features, ORR and PFS were comparable across subgroups. PFS hazard ratio (95% CI) for del(17p)/TP53 mutated/BIRC3 mutated: 1.05 (0.54–2.04); del(17p)/TP53 mutation, del(11q), and/or unmutated IGHV: 1.11 (0.69–1.77); unmutated IGHV: 1.79 (0.99–3.24); and NOTCH1 mutated 1.05 (0.65–1.69). This integrated analysis demonstrated efficacy of first-line ibrutinib-based treatment irrespective of cytogenetic and mutational risk features. Registered at ClinicalTrials.gov (NCT01722487 and NCT02264574).

The Selective Bruton Tyrosine Kinase (BTK) Inhibitor TG-1701 As Monotherapy and in Combination with Ublituximab and Umbralisib (U2) in Patients with B-Cell Malignancies

The Selective Bruton Tyrosine Kinase (BTK) Inhibitor TG-1701 As Monotherapy and in Combination with Ublituximab and Umbralisib (U2) in Patients with B-Cell Malignancies

Defining Genomic Probability of Progression to Identify Low-Risk Smoldering Multiple Myeloma

On an average, 1% of monoclonal gammopathy of undermined significance (MGUS) and 10% of smoldering Multiple Myeloma (SMM) progress to symptomatic MM every year within the first five years of diagnosis. The probability of progression significantly decreases for SMM patients after first 5 years. However, a distinct subset of SMM patients progress within 2 years and are re-classified as high-risk patients based on risk markers such as 20/2/20 or certain genomic features. Although recent studies have evaluated the high-risk genomic features for SMM but genomic background of SMM patients who do not progress to MM after long-term follow-up (>= 5 years) has not been described.Here, we evaluated transcriptomic and genomic changes enriched in non-progressor (NP) (no progression after 5 years of follow-up) precursor conditions (N=31) with those progressed within short period of time (N=71) and compared them with changes observed in newly diagnosed MM (N=192). Additionally, using transcriptome, epigenome and whole genome profiling we also studied additional unique samples from 18 patients at their precursor stage as well as when progressed to MM.Overall, we have observed significantly lower mutational load for NP SMM from progressor SMM (median SNV 4900 vs. 7881 p < 3e-04) with high sensitivity (0.83) and specificity (0.65) to separate NP from progressors. We have further developed a deep learning model by using more than 4500 genome wide features using ten-fold cross validation. This model indicated that not only the load but also the patterns of mutations (type, location, frequency) are different between two conditions. We also found that NP samples have significantly lower heterogeneity (p < 0.05). However, progressed samples showed similar mutational load and heterogeneity at precursor stage and MM. Among CNA differences, absence of gain or deletion of chr8 (not involving MYC region) were strong predictor of NP (OR=7.2 95% CI 2.2-24). Focal genomic loss was also significantly lower for NP (p=0.004) which was also reflected by low genome scar score (GSS) (p=0.07). Structural variant and copy number signature analysis also showed that NPs were showing significantly low exposure to non-clustered variable size genomic deletions. We observed similar frequency of primary translocations [t(11;14), t(4;14), and t(14;16)] in both progressor and NP samples as well as newly diagnosed MM. MYC translocation with any partner was not observed in NP samples, whereas 37% of progressor samples had a MYC translocations (OR=12.8). Adding all these differences including chr8 CNAs, MYC translocations, mutation burden, GSS, focal deletions, all driver mutations as well as primary translocations into recursive partitioning model to predict non-progressor SMM, we have identified a simple genomic model only involving chr8 CN changes and overall mutational burden to achieve a high sensitivity (0.82) and specificity (74%).Our transcriptomic analysis measured the distance between progressor and NP SMM as well as MM and found that NP SMM has greater difference with MM which is closer to progressor SMM. We quantified transcriptomic heterogeneity by using molecular degree of perturbation. This analysis showed that consistent with DNA changes, DNA repair pathway and MYC target genes are expressed similarly in NP SMM as in normal plasma cells compared to progressor SMM. Epigenomic analysis yielded 75 SEs regions differentially utilized between precursor and symptomatic MM stage using paired samples. The targeted genes included BMP6, PRDM1, STAT1, SERTAD2 and RAB21 and possibly regulating genes related to oncogenic KRAS activities.In conclusion, we define genomic characterization of non-progressor SMM and our results now provide the basis to develop molecular definition of SMM as well as risk driving features. DisclosuresMunshi: Janssen: Consultancy; Pfizer: Consultancy; Legend: Consultancy; Novartis: Consultancy; Adaptive Biotechnology: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Takeda: Consultancy; Abbvie: Consultancy; Karyopharm: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Bristol-Myers Squibb: Consultancy.

Ras-p53 genomic cooperativity as a model to investigate mechanisms of innate immune regulation in gastrointestinal cancers.

Despite increasingly thorough mechanistic understanding of the dominant genetic drivers of gastrointestinal (GI) tumorigenesis (e.g., Ras/Raf, TP53, etc.), only a small proportion of these molecular alterations are therapeutically actionable. In an attempt to address this therapeutic impasse, our group has proposed an innovative extreme outlier model to identify novel cooperative molecular vulnerabilities in high-risk GI cancers which dictate prognosis, correlate with distinct patterns of metastasis, and define therapeutic sensitivity or resistance. Our model also proposes comprehensive investigation of their downstream transcriptomic, immunomic, metabolic, or upstream epigenomic cellular consequences to reveal novel therapeutic targets in previously “undruggable” tumors with high-risk genomic features. Leveraging this methodology, our and others’ data reveal that the genomic cooperativity between Ras and p53 alterations is not only prognostically relevant in GI malignancy, but may also represent the incipient molecular events that initiate and sustain innate immunoregulatory signaling networks within the GI tumor microenvironment, driving T-cell exclusion and therapeutic resistance in these cancers. As such, deciphering the unique transcriptional programs encoded by Ras-p53 cooperativity that promote innate immune trafficking and chronic inflammatory tumor-stromal-immune crosstalk may uncover immunologic vulnerabilities that could be exploited to develop novel therapeutic strategies for these difficult-to-treat malignancies.