BTK mutation

P1/2, N=190, Active, not recruiting, ArQule, Inc., a subsidiary of Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc. (Rahway, NJ USA) | Trial completion date: Sep 2024 --> Sep 2025 | Trial primary completion date: Sep 2024 --> Sep 2025

Treatment of chronic lymphocytic leukemia with NX-2127 achieves >80% degradation of BTK in patients and demonstrates proof-of-concept therapeutic benefit. These data reveal an oncogenic scaffold function of mutant BTK that confers resistance across clinically approved BTK inhibitors but is overcome by BTK degradation in patients.

Re-emergent clones lacked BTK mutation and retained sensitivity to ibrutinib upon retreatment. NCT02251548.

New treatments on the horizon that attempt to maneuver around these resistance mutations can be met with new resistance mutations, creating an unmet need for patients with CLL. Novel therapies and combinations that address all forms of resistance are discussed.

This is the first study to describe the genomic landscape of patients with B-cell malignancies who were intolerant to ibrutinib and/or acalabrutinib. Here we show that the gene mutational profile of these patients at baseline or at/after disease progression is comparable with patients with relapse/refractory disease who tolerate ibrutinib and, consistent with other studies, patients with mutations in TP53, SF3B1 or ATM genes had less favorable prognosis on BTKi. Further, intolerant patients who progressed on zanubrutinib acquired new BTK mutations and/or had an increase in the frequency of BTK mutations.

Pts received 1 or more cBTKi: ibrutinib (n=44, 90%), acalabrutinib (n=10, 20%) or zanubrutinib (n=1, 2%). Whether similar resistance patterns would manifest if pirtobrutinib was utilized prior to cBTKi treatment remains uncertain. Figure 1.

Previous treatments comprised chemo-immunotherapies (FC, FCR, BR, CHLR) in 12 cases and ibrutinib in 8 cases (range, 1-3). Richter transformation was present in 2 out of 18 treated patients at 2 and 10 months after the initiation of venetoclax and one patient had progressive disease. Our data show the feasibility of NGS-based MRD assessment in a prospective cohort of patients with CLL treated with venetoclaxbased therapies.

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 ibr cohort had no prior BTKi therapy whereas 1 patient in the acala cohort had received spebrutinib, another cBTKi...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.

In this real-world cross-sectional study, BTK C481 mutations were observed in 21% of BTKi-experienced pts with CLL/SLL, all of whom had a cumulative exposure to BTKis of >36 mo. Because two-thirds of BTKi-experienced pts had <36 mo of BTKi exposure, the prevalence of BTK C481 mutations may be higher in populations with longer BTKi exposure. Further analyses of the natural history of BTK C481 mutations will help identify patients who are at risk of covalent BTKi resistance.

The majority of IR DP with BTK/PLCG2 mutations (6/8), were 100% homologous to germline IGHV unmutated, suggesting an inherent higher risk disease profile as a risk factor for acquiring BTKmt with prolonged BTKi therapy. BTK/PLCG2 mutations were enriched amongst very late progressors with 6/8 pts progressing shortly after stopping therapy at 72 mo., which is later than previously reported for relapsed/refractory CLL pts.

Preliminary data from this ongoing, first-in-human study of the novel BTK degrader BGB-16673 demonstrate a tolerable safety profile and clinical responses in heavily pretreated pts with B-cell malignancies, including those with BTKi-resistant disease. Substantial reductions in BTK protein levels in peripheral blood and tumor tissue were also observed, demonstrating proof-of-concept of a strong, on-target effect.

Background: Covalent Bruton's tyrosine kinase (BTK) inhibitors such as ibrutinib are approved for treating patients with B-cell malignancies, but their long-term efficacy is limited by toxicity related to off-target kinase inhibition and acquired resistance due to BTK C481 mutation...Changes in the level of biomarkers such as CCL3 and CCL4 chemokines and B-cell receptor pathway signaling will be evaluated prior to, during therapy, and at time of disease progression. The RP2D will be determined based on all the data generated in the study.

Background: In chronic lymphocytic leukemia (CLL), despite the fact that Bruton tyrosine kinase inhibitors (BTKi) are increasingly used 1st or 2nd line therapy, and the Bcl-2 inhibitor (Bcl-2i) venetoclax +-rituximab (VEN-R) relapses, based on the good results of the MURANO trial (although it did not include BTKi–exposed patients [pts]), multicentric retrospective studies describing the real world outcomes of BTKi exposed pts under Bcl-2i treatment are still lacking. Although slightly improved as compared to other real-life series in Italy or in the US, these data indicate that VEN or VEN+R after progression, relapse or intolerance to BTKi is moderately efficient with only about 35.9 months median PFS (in spite of undetectable MRD in 26/52 available patients). TP53 abnormalities were confirmed to be an important risk factor, yet not BTK mutations, or. This work is important to help designing clinical trials aiming at improving the outcomes with next generation BTKi/Bcl-2i, or even CAR-T cells.

Our findings demonstrate that the B cell population in ibrutinib-resistant and ibrutinib sensitive CLL patients exhibit distinct transcriptional states. At the single-cell level, our findings demonstrate a systematic picture of diverse malignancy and microenvironmental changes in CLL. Overall, these findings provide an insight into the complex molecular and cellular interactions of CLL that may have a crucial role in BTKI resistance.

TMD-8-IbruR cells carrying the C481S mutation were generated by stepwise induction of increasing concentrations of Ibrutinib...In cell lines expressing C481X and pirtobrutinib resistance mutations, DZD8586 demonstrated concentration dependent anti-proliferative effects, with similar GI50s among cells carrying different BTK mutations...The Kpuu,CSF of DZD8586 in rat and monkey were 1.2 and 1.3, respectively, suggesting its excellent BBB penetration in humans. Conclusion DZD8586 is a novel non-covalent LYN/BTK dual inhibitor, which could overcome resistance mutations to the approved covalent and non-covalent BTK inhibitors, and derive clinical benefit to patients with DLBCL and CNSL by blocking both BTK-dependent and BTK-independent signaling pathways with excellent BBB penetration.

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.

Our data demonstrate the efficacy of the PKCβ inhibitor MS-553 in preclinical models of CLL including that with BTK mutations conferring BTKi resistance. These findings support continued preclinical and clinical investigation of MS-553 in CLL, and the phase 1 trial of this agent is currently underway (NCT03492125) (Blachly et al., 2022).

Twenty-three (76.7%) of the patients were on ibrutinib, while 7 (23.3%) were on acalabrutinib...Six patients (20.0%) continued on the same BTKi with addition of venetoclax, 10 (33.3%) patients were switched to venetoclax and immunotherapy (either obinutuzumab or rituximab), and 3 (10.0%) patients were started on single agent venetoclax...Three (10.0%) patients were taken to chimeric T cell receptor (CAR-T) cell therapy of which one patient had no response and was started on salvage treatment with duvelisib... Our results reveal that durable responses can be achieved by switching to venetoclax based regimens in patients with BTKi. Though the early results of the use of noncovalent BTKi in this setting aree encouraging, the durability of response is limited as new BTK mutations are selected and future therapeutic alternatives are needed for these subset of patients.

ABBV-101 is currently in phase 1 clinical trial for a variety of B-cell malignancies. ClinicalTrials.gov identifier: NCT05753501

To gain further insight into the genetic mechanisms of cBTKi resistance in a randomized population of pts with CLL, we performed next-generation sequencing (NGS) on samples from pts who had progression on zanubrutinib (zanu) or ibrutinib (ibr) in the phase 3 ALPINE study (NCT03734016; Brown et al. Of the 52 pts, most (82.6%) did not have acquired BTK or PLCG2 mutations. Among the zanu pts, 3/24 (12.5%) developed non-C481 BTK mutations. This rate was lower than that reported by Woyach et al (ICML 2023); shorter follow-up and fewer prior therapies in the ALPINE study may explain this discrepancy.

Understanding of acquired resistance to cBTKi therapy has largely come from data on patients (pts) treated with the first-in-class cBTKi ibrutinib...In contrast, much less is known about genetic mechanisms of drug resistance in pts treated with next generation cBTKi acalabrutinib and zanubrutinib... After a median follow-up of 6.5 years (IQR 2.9-6.3), 23/48 (48%) pts developed PD (20 CLL, 3 RT). PD occurred in 17/32 (53%) R/R pts and 6/16 (38%) TN pts. Median progression-free survival was reached at 6.0 years.

In primary CLL samples, AS-1763, pirtobrutinib or ibrutinib induced a modest apoptosis...Evaluation of drug interaction models utilizing Compusyn and Synergy Finder applications predominantly indicated additive effects between AS-1763 with BCL-2 inhibitor, venetoclax as well as p53 activator APR-246... AS-1763 is a selective ncBTKi that inhibits both wild-type and mutant BTKs listed in Table 1. In CLL cells, AS-1763 was effective in inhibiting BCR pathway signaling and sensitized cells to other agents such as venetoclax. Based on these encouraging data we have initiated a clinical trial to test AS-1763 in patients with CLL and other B cell malignancies who have failed or are intolerant to at least two prior lines of systemic therapy, including cBTKi (NCT05602363 Clinical Trials.gov).

We uncovered known and novel BTK resistance mutations and demonstrated BTK scaffolding activity independent of HCK, highlighting the need for other strategies to disrupt scaffolding-mediated BCR signaling. Beyond BTK mutations, our CRISPR KO screens illustrate a map of genetic modifiers of BTKi response and point to several potential resistance biomarkers for both acala and pirto. A better understanding of resistance mechanisms in the presence and absence of BTK mutations will help augment the use of BTKi treatments in patients.

Covalent BTKi (cBTKi) including ibrutinib, acalabrutinib, and zanubrutinib, share a common resistance mechanism, acquisition of a C481 mutation in BTK. LP-168 has been well tolerated in this study, with no DLTs identified at doses up to 300 mg daily. Preliminary efficacy was observed in high risk CLL pts, including those treated with one or more BTKi. Considering safety, efficacy, and PK/PD, dose expansion will occur at 200 mg and 300 mg daily following the FDA Project Optimus guidelines to determine the recommended phase 2 dose.

BTK Cysteine 481 substitution is known to contribute to cBTKi acquired resistance to ibrutinib, acalabrutinib, and zanubrutinib. Despite this cohort representing the first relapsing CLL patients from BRUIN and presenting with frequent baseline BTK mutations, response to pirtobrutinib was high, with an ORR of 83%, and substantial clearance of BTK C481 clones. At progression, the majority of pts (56%) either acquired non-BTK mutations or did not acquire any resistance mutations in this targeted panel, suggesting alternative resistance mechanisms. A smaller group of patients (44%) displayed emergence of non-C481 clones, particularly gatekeeper T474 and kinase-impaired L528W mutations.

We used duplex sequencing, a technology that enables detection of mutations at ultra-low allelic frequencies, to identify mutations in five genes associated with drug resistance in CLL and followed their evolution in two patients who received multiple targeted therapies and ultimately developed disease progression on pirtobrutinib...In patient R001, multiple known resistance mutations in both BTK and PLCG2 appeared following progression on zanubrutinib (BTK p.L528W, p.C481S, PLCG2 S707F, L845F, R665W, and D993H). In contrast, patient R002 developed multiple BTK mutations following acalabrutinib treatment including known resistance mutations p.C481R, p.T474I and p.C481S...For example, BTK p.L528W in patient R001 increased in frequency more than 1000-fold (from CCF 0.02% to 35%), and p.T474I in patient R002 increased in CCF from 0.03% to 4.2% (more than 100-fold). Our data illuminates the evolutionary dynamics of resistant clones over the patients' disease course and under selective pressure from different targeted treatments.

Ibrutinib is a first-line drug for the treatment of B-cell malignancies...More importantly, 15-271 has a longer half-life and better bioavailability in vivo. The development strategy of compound 15-271 can be a general procedure for the optimization of other PROTACs.

The C481S and C481R mutations eliminated the anti-proliferative effects of covalent inhibitors ibrutinib, acalabrutinib, and zanubrutinib, whereas the V416L, T474I, and L528W mutations had variable effects on the covalent inhibitors. By contrast, the non-covalent inhibitors pirtobrutinib, vecabrutinib, and fenebruitnib maintained activity against C481S but displayed partially reduced potency against the C481R mutation and dramatically reduced potency against the V416L, T474I, and L528W mutations...These degrader molecules may also have utility in earlier lines of therapy due to their ability to suppress scaffold-mediated BTK signaling. Phase 1a/b trials of NX-5948 and NX-2127 in patients with relapsed or refractory B-cell malignancies are ongoing (NX-5948: NCT05131022; NX-2127: NCT04830137).

With regard to treatment, 56% received Brutone tyrosine kinase (BTK) inhibitors, others received Bcl-2 inhibitor venetoclax (31%) or PI3K inhibitor idelalisib (13%). This interim analysis points to the dynamic and complex nature of genomic alterations in CLL, with implications for disease progression and therapeutic responses. Our findings highlight the importance of longitudinal genomic monitoring to uncover evolving mutational profiles and their clinical implications.

Background: There remains an unmet need for patients with aggressive disease refractory to both Bruton Tyrosine Kinase inhibitors (BTKi) and Venetoclax...Two patients received acalabrutinib and obinutuzumab, one patient had a sustained partial response while the other died due to POD. One patient was started on vecabrutinib and died due to POD. A total of 17 double refractory CLL patients were identified between 2016 and 2021. The median age was 66 years (range 47–80 years), and 10 (58.8%) patients were female. At the time of double refractory status, 15 (88.2%) patients had unmutated IgHV disease, 11 (64.7%) had 17p deletion, while 9 (52.9%) had complex karyotype identified on the CLL fluorescence in situ hybridization (FISH) test.

main study Substudy patients treated with VenR (n = 194) patients treated with BR (n = 195) patients retreated with VenR (n = 25) Baseline characteristics mean age, years (SD) 63.9 (10.5) 64.4 (9.6) 65.8 (8.3) Number of prior cancer therapy, n (%) 1 111 (57.2) 117 (60.0) 0 (0.0) 2 58 (29.9) 43 (22.1) 20 (80.0) ≥3 25 (12.9) 35 (17.9) 5 (20.0) del(17p) and/or TP53 mutation (aCGh), n (%) mutated 53 (27.3) 55 (28.2) 14 (56.0) unmutated 104 (53.6) 98 (50.3) 9 (36.0) unknown 37 (19.1) 42 (21.5) 2 (8.0) Genomic complexity, n (%) n = 48 n = 46 n = 20 3–4 34 (70.8) 29 (63.0) 3 (15.0) ≥5 14 (29.2) 17 (37.0) 8 (40.0) iGhV, n (%) n = 180 n = 180 n = 23 mutated 53 (29.4) 51 (28.3) 2 (8.7) unmutated 123 (68.3) 123 (68.3) 21 (91.3) unknown 4 (2.2) 6 (3.3) 0 (0.0) efficacy results median follow-up, months 85.7 85.7 33.4 Best oRR, % 93.3 67.7 72.0 umRD at eoCT of main study, n (%) 121 (62.4) 26 (13.3) 16 (64.0) umRD at eoCT of substudy, n (%) N/a N/a 8 (32.0) umRD at eoT of main study, n (%) 83 (70.3)* N/a 14 (56.0) umRD at eoT of substudy, n (%) N/a N/a 0 (0.0) median pFS, months (95% Ci) 54.7 17.0 23.3 (52.3, 59.9) (15.5, 21.7) (15.6, 24.3) 3-year oS rate, % (95% Ci) 88.4 78.9 53.1 (83.8, 93.0) (72.8, 84.9) (25.1, 81.0) *patients who completed 2 years of Ven without pD (n = 118) aCGh: array comparative genomic hybridization; BR: bendamustine- rituximab; Ci: confidence interval; del(17p): deletion in chromosome 17p; eoCT: end of combination treatment; eoT: end of treatment; iGhV immu- noglobulin heavy chain gene; oRR: overall response rate; oS: overall sur- vival; pD: progressive disease; pFS: progression free survival; SD: standard deviation; TP53: tumor protein p53; umRD: undetectable minimal residual disease; Ven(R): venetoclax-(rituximab) cBTKi pre-treated CLL pts treated with pirtobrutinib monotherapy in the phase 1/2 BRUIN trial (NCT03740529) who subsequently developed disease progression (PD) were included in this analysis...Pts received one or more of the following cBTKi: ibrutinib (n = 44, 90%), acalabrutinib (n = 10, 20%), or zanubrutinib (n = 1, 2%)... Pts who progressed on pirtobrutinib showed clearance of BTK C481 clones and the emergence or outgrowth of non-C481 clones, particularly gatekeeper T474 and kinase-impaired L528W mutations, as well as other VUS. Many acquired BTK mutations were shown to pre-exist at baseline at low VAF, reflecting emergence on prior cBTKi. Importantly, these baseline kinase domain BTK mutations did not preclude pirtobrutinib efficacy.

Our data demonstrate the efficacy of the PKCβ inhibitor MS-553 in preclinical models of CLL, including BTK inhibitor resistant disease. These findings support continued preclinical and clinical investigation of MS-553 in CLL, and the phase 1 trial of this agent is currently underway (NCT03492125) [7].

73 patients had only one BTKi (ibrutinib (IBR), 64; acalabrutinib (ACA), 9). 12 pts had multiple BTKis, 8 with two drugs with IBR first followed by ACA (Nf3, 37.5%), vecabrutinib (Nf1, 12.5%), and PIR (Nf4, 50.0%); and 4 with three or more drugs... Our retrospective report summarizes mutations detected during BTKi treatment and shows that BTK L528W can occur during both covalent and non-covalent BTK inhibitor therapy. Four of six patients who progressed on PIR had T474 mutations. In addition, our results may suggest that activating mutations in RAS/RAF/MAPK pathway are related to BTKi resistance.

Our findings demonstrate that the B cell population in ibrutinib-resistant and ibrutinib sensitive CLL patients exhibit distinct transcriptional states. At the single-cell level, our findings demonstrate a systematic picture of diverse malignancy and microenvironmental changes in CLL. Overall, these findings provide an insight into the complex molecular and cellular interactions of CLL that may have a crucial role in BTKI resistance.

Novel, non-C481 BTK mutations have been described, including BTK L528W, which has been reported in patients treated with ibrutinib, zanubrutinib, and pirtobrutinib (Maddocks, JAMA Oncol. This is the largest dataset characterizing the incidence and patterns of BTK and PLCG2 mutations in patients with CLL treated with ibrutinib. BTK C481 mutations are the most frequently occurring mutations. PLCG2 mutations occur across the gene at a low incidence per locus (<5%).

Introduction: The drug-resistant mechanisms of the first-generation Bruton’s tyrosine kinase (BTK) inhibitor, ibrutinib, has been extensively explored in Chronic Lymphocytic Leukemia (CLL) patients. Integrated multi-omics were performed in our zanubrutinib-resistant CLL patients’ cohort. BTK Cys481 and Leu528 were two main BTK resistant mutations in zanubrutinib resistant CLL patients. Due to spatial heterogeneity and clonal evolution among patients, deep targeted-gene NGS and ddPCR should be used comprehensively to evaluate the emergence of resistant clones.