Hayley Virgil

The use of plasma cell-free methylomes offers investigators a method to monitor tumor responses to treatment noninvasively, according to findings presented during the AACR Annual Meeting 2021 in May.

 The method uses cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) to detect and classify several types of cancer early on, according to Daniel D. De Carvalho, PhD, who presented the data.

The strategy has yielded positive results and has been shown to perform well in challenging applications such as early-stage renal cell carcinoma (RCC) and intracranial tumors, even helping to differentiate between distinct intracranial tumor entities.

De Carvalho, the Helen M. Cooke associate professor in the Department of Medical Biophysics at the University of Toronto and the Canada Research Chair at the Princess Margaret Cancer Centre in Canada, further discussed the data supporting the use of cfMeDIP-seq and its potential for other low tumor burden clinical applications, such as monitoring for response and minimal residual disease (MRD).

The rationale for using plasma methylomes for cancer detection and monitoring is rooted in the fact that the cancer DNA methylation profile significantly differs from the normal tissue methylation profile, according to De Carvalho.

In one study, investigators examined DNA methylation variation in epigenetic domains in colorectal cancer (CRC) through the use of whole-genome bisulfite sequencing. By doing this, they identified a model for cancer that involved loss of epigenetic stability of well-defined genomic domains that underlies amplified methylation variability in cancer and may contribute to tumor heterogeneity.

“If you look at CpG islands…and CpG shores outside of the CpG islands, you can see a global increase in DNA methylation in cancer compared with normal [tissue] at hundreds of thousands of CpG sites,” De Carvalho said. “This provides a very rich set of biomarkers that one can use to monitor tumor DNA.”

Examining DNA Methylation Patterns to Understand Tissue of Origin Another notable area of information is the tissue of origin, De Carvalho said. A set of 500 CpG sites were utilized to identify different cancer types, including bladder, brain, breast, and colorectal tissue. Investigators were able to classify and discriminate these tissues from one another based on the DNA methylation profie alone.

As cells die and DNA is released into circulation, it is possible to capture floating cell-free DNA (cfDNA) and profile the methylome, De Carvalho said. Information content in the DNA methylation patterns can potentially be utilized to differentiate between normal tissue and cancer tissue and to differentiate the tissue of origin. Although this is an interesting concept, De Carvalho noted that several technical issues are associated with this strategy.

“[We are faced with] a major needle-in-thehaystack problem with cfDNA,” De Carvalho explained. “In the real world, what we see is that 1 cancer cell has billions of letters of DNA….Somewhere between 10 to 20 million cell-free fragments can be released by a single cell as [it dies]. If you are looking for 1 event—1 KRAS hotspot mutation, [for example]—that is just 1 fragment out of potentially 50 million fragments per cell.”

This represents a significant barrier faced with liquid biopsies, especially with regard to early detection of residual disease and monitoring in situations with low tumor burden, according to De Carvalho.

“The way for us to think about this and try to solve for this is to take advantage of the DNA methylation. We have thousands of CpG sites of differential methylation,” De Carvalho noted. “[That means we] have a lot of needles in this haystack to look for [when] looking for methylation events.”

Investigators simulated different circulating tumor DNA (ctDNA) abundance, starting from 10% down to 0.001%, so high tumor burden vs low tumor burden, respectively.3 Thousands of genome-wide markers are needed to solve the needle-in-the-haystack problem when ctDNA abundance is less than 0.1%.

Detection of ctDNA is a function of ctDNA abundance, sequencing depth, and number of features investigated. For every fold decrease in tumor DNA abundance, it is important to have the same fold increase in the number of regions that are being searched for to maintain the probability of detection, according to De Carvalho.

Another challenge faced is that the human genome is depleted of CpG sites by deamination, De Carvalho said. “If you are trying to sequence the whole genome, about half of the potential cfDNA fragments being released by the cancer cell have no CpG, and, therefore, no DNA methylation [information],” De Carvalho added.

Investigators set out to completely separate methylated DNA from unmethylated DNA using an approach with monoclonal antibodies.4 “When you do that, compared with the expected distribution, most of the fragments we sequenced have a high number of CpG sites,” De Carvalho noted. He emphasized that this strategy only pulls down the methylated spikings, not the unmethylated spikings.

Differentiating Cancer Types With cfMeDIP-seq Utilizing this strategy, it is possible to discriminate between different cancer types. For example, in an analysis that examined the quality control of cfMeDIP-seq to differentiate between healthy donors and patients with lung cancer, breast cancer, CRC, leukemia, RCC, or bladder cancer, disease types could be differentiated based on the plasma cfDNA methylation.

“You can see that you can have very distinct separation between the different cancer types,” De Carvalho explained. “Even if you have cancer cell lines that have no tumor microenvironment, only the methylation of the cell lines, you can see that they start to separate, as well, based on the signatures we identify in the plasma for these patients.”

A classifier was built using the original 388 plasma samples, and investigators validated an independent cohort of 199 samples. The validation set included samples from patients with lung cancer (n = 55), acute myeloid leukemia (n = 35), and pancreatic ductal adenocarcinoma (PDAC; n = 47). Notably a significant separation between the patient samples and samples from the healthy donors was observed. Moreover, even when dividing samples from patients with early-stage vs late-stage PDAC, it is possible to maintain the ability to discriminate between this disease and a healthy control sample, De Carvalho noted.

Investigators set out to further validate these findings within a cohort of patients with RCC.

The trial featured 69 plasma samples collected from patients with RCC and 14 samples collected from healthy individuals who were cancer free.

“Using the plasma cell-free methylomes, there is very good separation between the cases and the controls in this cohort,” De Carvalho said.

“Even when compared with urothelial bladder cancer, you have a very good separation between both [this disease and RCC]. Interestingly, [we used] the same feature that we identify in the plasma if we profile with urine; we still have a very good separation between the cancer cases vs the control, just based on the cell-free DNA methylome profile of urine.”

Moreover, a cross validation was performed to further evaluate the ability to discriminate between cases and controls.

When using plasma cfDNA methylomes, investigators saw favorable classification discrimination between the RCC cases and the control samples, with a mean area under the receiver operating characteristic (AUROC) of 0.990 (95% CI, 0.985-0.995).

When looking at urothelial bladder cancer cases vs RCC cases in the plasma, very good discrimination was also observed (AUROC, 0.979; 95% CI, 0.956-0.991). Additionally, when examining discrimination between the RCC cases and the control in urine samples, investigators reported a mean AUROC of 0.858 (95% CI, 0.831-0.885).

Plasma cfDNA Methylomes Allow for Noninvasive Discrimination of Intracranial Tumors? 

After establishing positive results in RCC, investigators moved on to examine the utility of cfMeDIPseq in a more difficult area: intracranial tumors. There is very little shedding of ctDNA in the plasma circulation with these tumors, according to De Carvalho. However, tissue-based DNA methylation profiling of these tumors can be utilized for molecular classification, De Carvalho explained.

“Many centers in Canada, Germany, and the United States have been using methylation profi ling from tumor DNA to classify the many different entities of intracranial tumors,” De Carvalho noted. “We tried to do the same, but with plasma cfDNA, because access to this tissue is highly invasive.”

Investigators examined 447 plasma samples, 59 of which were glioma samples. A set of features, or differential methylated regions, helped discriminate these samples from other cancer types and healthy controls. These features were hypermethylated in the plasma of patients with glioma vs the plasma of the healthy controls, and they were also hypermethylated in the tumor of the patients with glioma vs the normal cfDNA.

A similar cross validation approach that was used in the RCC study was used in the glioma samples, according to De Carvalho. “Again, we had a very strong ability to discriminate between these [samples] vs other cancer types,” De Carvalho said.

Moreover, the ability to discriminate in the patient population was maintained in patients with IDH wild-type and IDH-mutant gliomas. These abnormalities do not result in a strong disruption in the methylation profile, and one can classify between both patient subgroups; this was also true with regard to low- vs high-grade gliomas.

“In increasing the number of samples from other intracranial tumor entities, such as meningioma [and others],” De Carvalho said, “you can see here that you have separation between them.”

Utilizing only the plasma cell-free methylomes, it was observed that the classifier does a fairly good job at identifying numerous intracranial tumor types, De Carvalho added.

Monitoring Response to Treatment Using ctDNA 

In addition to helping identify and classify cancer types, cfMeDIP-seq may also have potential utility in cancer management, according to De Carvalho. In a population of patients with localized head and neck squamous cell carcinoma, investigators utilized an approach that incorporated the methylome profile, mutation profile, and fragment length.

“In the patient samples compared with the healthy controls, the fragmental length of the methylated [ctDNA] starts to become [smaller] than the rest. If you look at the [patients with] healthy DNA vs the [patients with] mutant fragments…we can define the tumor based on mutation or methylation,” De Carvalho explained.

Mutations and methylation can be utilized independently to identify ctDNA, which indicates that the methylation signal allows one to quantify ctDNA as having a strong correlation between calculating the abundance based on mutation and percentage of ctDNA based on the signal of the methylome.

“Based on this, we can identify patients who are ctDNA positive vs negative and we can see a strong separation. Patients who are ctDNA negative have a much better overall survival [OS] than the [patients who are positive],” De Carvalho said.

Methylation also allows investigators to have independent prognostic markers in that methylation-specific events can be good or bad. Independent of that abundance of ctDNA, probability of OS can be calculated. Notably, patients with low methylation have a better survival than those who have a high methylation.

Lastly, cfMeDIP-seq can be monitored over time, as patients undergo treatment with different types of therapy. This can also help identify patients who have a clearance of ctDNA vs those who do not.

“Patients who are [clearing] up the ctDNA based on the methylation have a much better recurrence-free survival than the patients who do not [clear] their ctDNA. This is a very interesting application for MRD detection and monitoring of recurrence,” De Carvalho concluded.

1. De Carvalho DD. Cancer early detection, classifi cation and monitoring using plasma cell-free methylomes. Presented at: AACR Annual Meeting 2021; May 17-21, 2021; virtual.

2. Hansen KD, Timp W, Corrada Bravo H, et al. Increased methylation variation in epigenetic domains across cancer types. 

3. Shen SY, Singhania R, Fehringer G, et al. Sensitive tumour detection and classifi cation using plasma cell-free DNA methylomes. 

. 2018;563(7732):579-583. doi:10.1038/s41586-018-0703-0 

4. Shen SY, Burgener JM, Bratman SV, De Carvalho DD. Preparation of cfMeDIP-seq libraries for methylome profi ling of plasma cell-free DNA. Nat Protoc. 2019;14(10):2749-2780. doi:10.1038/s41596-019-0202-2 

5. Wilson ER, Helton N, Heath SE, et al. Genome-wide analysis of focal DNA hypermethylation in IDH-mutant AML samples. bioRxiv. Published online March 3, 2021. doi:10.1101/2021.03.03.433799 

6. Nuzzo PV, Berchuck JE, Korthauer K, et al. Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. 

. 2020;26(7):1041-1043. doi:10.1038/s41591-020-0933-1 

7. Capper D, Jones DTW, Sill M, et al. DNA methylation-based classifi cation of central nervous system tumours. 

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8. Nassiri F, Chakravarthy A, Feng S, et al. Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes. 

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9. Burgener JM, Zou J, Zhao Z, Shen SY, De Carvalho DD, Bratman SV. Comprehensive detection of ctDNA in localized head and neck cancer by genome- and methylome-based analysis. 

s. 2020;26(suppl 11):PR13. doi:10.1158/1557-3265.LiqBiop20-PR13

Articles

Th of plasma cell-free methylomes offers investigators a method to monitor tumor responses to treatment noninvasively, according to findings presented during the AACR Annual Meeting 2021.

Plasma Cell-Free Methylomes Offer Noninvasive Tumor Monitoring  Across Cancer Settings

Adjuvant trastuzumab (Herceptin) is showing promising long-term results in patients with HER2-positive early breast cancer, a population that is representative of most patients seen in clinical practice.¹ These updated survival data from the phase 3 SHORT-HER trial (NCT00629278) were presented during the European Society for Medical Oncology Breast Cancer Virtual Congress 2021.

“Patients classified as low/intermediate risk based on [tumor] size and nodal status represent 84.6% of the SHORT-HER study population. Long-term disease-free survival [DFS] and overall survival [OS] are superimposable between the 2 treatment arms,” Pier Franco Conte, MD, said during the presentation. “Although 1 year of trastuzumab remains a standard, deescalation of treatment is a reasonable option for a large proportion of a real-world population of [patients with] HER2-positive early breast cancer.”

Conte is a professor of oncology at the University of Padova, director of the Division of Medical Oncology at the Istituto Oncologico Veneto in Padova, and chairman of Rete Oncologica Veneta in Italy.

After a median follow-up of 8.7 years, patients who received 1 year of trastuzumab had a 5-year DFS rate of 87.9% vs 85.8% for those who received it for 9 weeks (HR, 1.09; 90% CI, 0.88-1.35). Patients had a 5-year OS rate of 95.1% in both arms (HR, 1.18; 90% CI, 0.86-1.62).

The superiority of combining 1 year of trastuzumab with adjuvant chemotherapy versus chemotherapy alone in patients with HER2-positive early breast cancer was demonstrated in the phase 3 HERA trial (NCT00045032), the NSABP B-31/NCCTG N9831 joint analysis, and the N9831 trial(NCT00005970).2-4In November 2006, trastuzumab was approved by the FDA as an adjuvant therapy for patients with HER2-positive, node-positive breast cancer as part of a treatment regimen containing doxorubicin, cyclophosphamide, and paclitaxel.

“It was very clear at the time that the choice of a 1-year duration of trastuzumab administration was based empirically and that a similar degree of benefit had already been reported with the small FinHER study with 9 weeks of trastuzumab,” Conte noted.

The SHORT-HER trial, an investigator-driven, non-inferiority study, started off with an initial sample size of 2500 patients; however, as of February 2011, it was amended to 1250 patients. The study was con-ducted across 82 investigational sites in Italy and had a recruitment period that ran from December 2007 to October 2013. The primary analysis was completed after 189 DFS events at 5.2 years of median follow-up.

The trial enrolled patients with HER2-positive, node-positive, or high-risk node-negative disease. Patients were then randomized to receive either 1 year of trastuzumab plus chemotherapy, which included 4 courses of doxorubicin and cyclophosphamide, followed by 4 courses of a taxane versus 3 courses of docetaxel combined with 9 weeks of weekly trastuzumab followed by 3 courses of fl uorouracil, epirubicin hydrochloride, and cyclophosphamide. Stratifi cation factors included hormone receptor status and nodal status. Patients 65 years or older received 80 mg of docetaxel. Eleven percent of patients who received the longer duration of trastuzumab were given paclitaxel at a dosage of 175 mg.

The overall patient population had a median age of 55 years (range, 25-78), and 64.0% were postmenopausal. Moreover, 40.6% of patients had stage I disease, 43.8% had stage II disease, and 15.2% had stage III disease. Most patients were node negative (53.5%), although 30.7% of patients had 1 to 3 positive nodes and 15.8% had at least 4 positive nodes. Additionally, 68.2% of patients had hormone receptor–positive status (FIGURE).

The DFS reported in the primary analysis of the trial showcased a HR of 1.13 (90%, CI, 0.89-1.42). Investigators reported that the probability of the shorter duration of treatment being noninferior to that of the longer duration was 78%.6 Moreover, the primary analysis identified an association between a longer duration of treatment and a longer and higher incidence of cardiac events. The incidence of grade 2 or higher cardiac events was 13.1% in the long-duration treatment arm versus 4.3% in the short-duration treatment arm.

The updated results of the study had a median follow-up of 8.7 years with 237 DFS events and 109 deaths. Investigators also examined DFS and OS outcomes with respect to risk category.

“The high-risk group clearly has worse outcomes in terms of both DFS and OS, while both low- and intermediate-risk groups had very good DFS and OS estimates,” Conte said.

Patients in the low-risk group experienced a 5-year DFS of 91% in both treatment arms (HR, 0.91). In the intermediate-risk group, those treated for the longer duration had a 5-year DFS rate of 88% vs 89% of those who received the shorter duration (HR, 0.88); the 5-year DFS rates in the high-risk group for the longer and shorter treatment durations were 82% and 64%, respectively (HR, 2.06).

Additionally, the 5-year OS rate for patients in the low-risk group who received the longer duration of treatment was 97% vs 99% for patients who received the shorter duration (HR, 0.57). In the intermediate-risk group, these rates were 96% and 95%, respectively (HR, 1.14), and they were 95% and 91%, respectively, in the high-risk group (HR, 1.09).

1. Conte P, Frassoldati A, Bisagni G, et al. Nine weeks vs 1 year adjuvant trastuzumab: long term outcomes of the Short-HER randomized trial. Presented at: European Society for Medical Oncology Breast Cancer Congress 2021; May 5-8, 2021; virtual. 

2. Herceptin (Trastuzumab) in treating women with human epidermal growth factor receptor (HER) 2-positive primary breast cancer (HERA). ClinicalTrials.gov. Updated April 27, 2017. Accessed May 7, 2021. https://clinicaltrials.gov/ct2/show/NCT00045032 

3. Doxorubicin and cyclophosphamide plus paclitaxel with or without trastuzumab in treating women with node-positive breast cancer that overexpresses HER2. ClinicalTrials.gov. Updated April 29, 2021. Accessed May 7, 2021. https://clinicaltrials.gov/ct2/show/NCT00004067 

4. Doxorubicin hydrochloride, cyclophosphamide, and paclitaxel with or without trastuzumab in treating women with HER2-positive node-positive or high-risk node-negative breast cancer. ClinicalTrials.gov. Updated August 14, 2020. Accessed May 7, 2021. https://clinicaltrials.gov/ct2/ show/NCT00005970 

5. FDA approves Herceptin for the adjuvant treatment of HER2-positive node-positive breast cancer. News release. Genentech Inc. November 16, 2006. Accessed May 7, 2021. https://bit.ly/3vNSNpX 

6. Conte P, Bisagni G, Frassoldati A, et al. Final analysis of the phase III multicentric Italian study Short-HER: 9 weeks vs 1 year adjuvant trastuzumab for HER21 early breast cancer. 

. 2017;28(suppl 6):vi1vi2. doi: 10.1093/annonc/mdy414

Adjuvant trastuzumab is showing promising long-term results in patients with HER2-positive early breast cancer, a population that is representative of most patients seen in clinical practice.

Promising Long-Term Results for HER2+ Early Breast Cancer

Updated findings from the early-stage KRYSTAL-1 study (NCT03785249) showed that treatment with adagrasib (MRTX849) resulted in durable responses, broad disease control, and provided extensive predicted coverage throughout the dosing interval in patients with KRAS G12Cmutant advanced non–small cell lung cancer (NSCLC). Results were presented during the European Lung Cancer Virtual Conference 2021.

Data showed that the 600-mg, twice-daily dose of adagrasib, a selective inhibitor of KRAS G12C, yielded an overall response rate (ORR) of 43% and 45% in the trial’s phase 1/1b (n = 14) and phase 1/1b Data showed that the 600-mg, twice-daily dose of adagrasib, a selective inhibitor of KRAS G12C, yielded an overall response rate (ORR) of 43% and 45% in the trial’s phase 1/1b (n = 14) and phase 1/1b. 

The disease control rate was 100% in the phase 1/1b population and 96% in the phase 1/1b and 2 cohort. In total, 57% and 51% of patients, respectively, had stable disease. Disease progression did not occur in the phase 1/1b cohort but did occur in 2% of those in the phase 2 pooled cohort.

Pharmacokinetic (PK) data indicated that adagrasib yielded a C

 of 2.63 µg/mL, which is 2- to 5-fold above the target threshold for the full dosing interval. More-over, investigators found that the C

 PK parameter was best matched to nonclinical antitumor activity. Additionally, the extensive volume of distribution was predicted based on nonclinical studies.

“The observed steady-state concentration was above the target threshold for the full dosing interval,” lead study author Gregory J. Riely, MD, PhD, vice chair of clinical research in the Department of Medicine at Memorial Sloan Kettering Cancer Center in New York, New York, said in a virtual presentation during the meeting. “We also observed low peak to trough ratio at 1.27 and a half-life of 24 hours.”

Adagrasib is a covalent inhibitor of KRAS G12C that irreversibly and selectively binds KRAS G12C in its inactive guanosine diphosphate (GDP)–bound state, according to Riely. The agent has been optimized for desired properties, demonstrating high selectivity for KRAS G12C mutations over wild-type and favorable PK properties, including oral bioavailability, a half-life of approximately 24 hours, and extensive tissue distribution.

By maintaining a continuous exposure to adagrasib above the target threshold, investigators theorized, inhibition of KRAS-dependent signaling will be enabled for the complete dosing interval, which could maximize depth and duration of the agent’s antitumor activity.

"KRAS G12C mutations act as an oncogenic driver and occur in approximately 14% of patients with NSCLC,” Riely said. “The KRAS protein cycles between GTP-on and GDP-off states and has a protein resynthesis of approximately 24 hours.”

To be eligible for enrollment, patients had to have KRAS G12C–mutant unresectable or metastatic NSCLC following progression on or after treatment with a PD-1/PD-L1 inhibitor in combination with or following chemotherapy.

In the phase 1, dose-escalation portion of the trial, investigators examined various once-daily doses of adagrasib: 150, 300, 600, and 1200 mg. They also looked at 600 mg given twice daily, which moved to the expansion phase and became the recommended phase 2 dose. Clinical findings indicated that the 600-mg, twice-daily dose of adagrasib in the phase 1/1b portion had a clinical benefit rate of 96%.

The phase 1b section looked at adagrasib alone and combined with pembrolizumab (Keytruda), afatinib (Gilotrif), and cetuximab (Erbitux). The phase 2 portion looked at adagrasib alone in patients with NSCLC (n = 61), colorectal cancer, and other solid tumors.

The primary end points of the phase 1b study consisted of safety, maximum-tolerated dose, PK, and the recommended phase 2 dose, as well as ORR in the phase 2 portion.

Secondary end points in the phase 1b portion included ORR, duration of response, progression-free survival, and overall survival. Secondary outcome measures in the phase 2 portion included safety.

Most patients across all phases were current or former smokers (89% and 95%, respectively) and had nonsquamous histology (100% and 96%). Patients had an average of 3 (range, 1-9) and 2 (range, 1-9) prior lines of therapy, respectively, and the majority of patients had previously received a PD-1/PD-L1 inhibitor (89% and 92%).

After a median follow-up of 9.6 months, 5 of 6 responders remain on treatment, which has been ongoing for more than 11 months. The median time to response was 1.5 months, and the median duration of treatment was 8.2 months (range, 1.4 to 13.1+).

“We see some clear evidence that we’re inhibiting KRAS signaling. The gene set enrichment analysis [identified] downregulation of KRAS signaling and downregulation of MYC, E2F, G2M, and MTORC1,” Riely explained. “We’re seeing a trend, but it’s hard to determine significance based on this small number of samples.”

Investigators also conducted a preliminary analysis examining comutations with KRAS G12C. Baseline next-generation sequencing reports were reviewed in order to conduct the analysis for all patients with NSCLC who had available mutation data. Notably, patients who had KRAS G12C mutations and an STK11 comutation experienced an ORR of 64%, although there were no apparent trends with KEAP1, TP53, or other common mutations and response rate (TABLE1).

“As many know, comutations in STK11 and KEAP1 are thought to predict lack of benefit from immunotherapy,” Riely said. “We decided to look at response rate in this cohort of patients.”

Regarding safety for all patients treated at the 600-mg, twice-daily dose (n = 110), the most common all-grade, treatment-related adverse effects (TRAEs) included nausea (54%), diarrhea (51%), vomiting (35%), and fatigue (32%). Grade 3/4 TRAEs included fatigue (6%), increased alanine aminotransferase (5%), aspartate aminotransferase (5%), and QT prolongation (3%). There were 2 grade 5 TRAEs: pneumonitis, which developed in a patient with recurrent pneumonitis, and cardiac failure. In total, TRAEs led to discontinuation in 4.5% of patients.

“Adagrasib is a KRAS G12C–selective covalent inhibitor with a long half-life and extensive predictive target coverage throughout the dosing interval,” Riely concluded. “[It] is well tolerated and provides durable response and broad disease control to [this patient population].”

1. Riely GJ, Ignatius Ou SH, Rybkin II, et al. KRYSTAL-1: Activity and pre-liminary pharmacodynamic (PD) analysis of adagrasib (MRTX849) in pa-tients (pts) with advanced non-small-cell lung cancer (NSCLC) harboring KRASG12C mutation. Presented at: European Lung Cancer Virtual Confer-ence 2021; March 25-27, 2021. Abstract 99O_PR

Updated findings from the early-stage KRYSTAL-1 study showed that treatment with adagrasib resulted in durable responses, broad disease control, and provided extensive predicted coverage throughout the dosing interval in patients with KRAS G12Cmutant advanced non–small cell lung cancer.

Adagrasib Reveals Efficacy in  KRAS  G12CMutated NSCLC

A combination of zandelisib (ME-401) and zanubrutinib (Brukinsa) induced significant responses, including several complete responses (CRs) in patients with relapsed or refractory chronic lymphocytic leukemia (CLL) and other B-cell lymphomas in a phase 1b study (NCT02914938), the results of which were presented during the 2021 European Hematology Association Annual Congress.

Patients were treated with a 60-mg dose of zandelisib on an intermittent schedule starting with cycle 1 and an 80-mg dose of zanubrutinib twice daily. 

Results from the trial indicate that after a median follow-up of 6.6 months for all patients (range, 0.6-21.3; Group A, median follow-up = 3.6 months; Group B, median follow-up = 6.6 months), those with follicular lymphoma (n = 8), CLL and small lymphocytic lymphoma (SLL; n = 5), marginal zone lymphoma (MZL; n = 2), and mantle cell lymphoma (MCL; n = 1) had a complete response (CR) rate of 100%. Additionally, CRs and CRs with incomplete hematologic recovery occurred in 25% of those with follicular lymphoma, and 40% of those with CLL. Notably, there were no responders within the diffuse large B-cell lymphoma (DLBCL)/ high-grade B-cell lymphomas (HGBCL) subgroup (n = 2).

“Responses were observed in all patients with indolent B-cell non-Hodgkin lymphoma histologies and CLL,” according to Jacob Soumerai, MD, a clinical investigator in lymphoma, Medicine, at Massachusetts General Hospital, and an assistant professor of medicine at Harvard Medical School. “Among 13 patients treated in group B, 8 remain on treatment [with] an ongoing treatment response, 4 came off [treatment] due to progression, and 1 came off to do grade 3 alanine aminotransferase [ALT] elevation.”

Dual inhibition of PI3Kδ and BTK pathways has demonstrated synergistic activity that is notable, even at suboptimal concentrations. The strategy could work to even overcome resistance to monotherapies, both acquired and existing. This formed the rationale for leveraging an innovative dosing schedule with the PI3Kδ inhibitor zandelisib in combination with the oral BTK inhibitor zanubrutinib, with the intent to improve the tolerability of a dual targeted approach, as well as offer improved responses.

The phase 1b, multi-cohort study enrolled patients with an ECOG performance status of 0-2 who had progressed on 1 or more prior therapies for a B-cell malignancy. Patients were required to have measurable disease and have received no prior PI3K or BTK inhibitor therapies.

A 6 + 6 trial design was implemented, with 2 treatment dose schedules utilized over the course of the study. All patients were treated with a pneumocystis jiroveci pneumonia prophylaxis. Additionally, patients were treated until they experienced disease progression, drug intolerance, or withdrawal of consent.

Group A, which included 7 patients, was given 60 mg of oral zandelisib daily for 8 weeks, followed by days 1 to 7 of each subsequent 28-day cycle, plus 160 mg of oral zanubrutinib twice daily. Over the 28-day dose-limiting toxicity (DLT) period, 1 patient with DLBCL was not evaluable for DLT due to a grade 3 adverse effect (AE) on day 1 because of treatment with a prior therapy. No other DLTs were observed in this cohort.

At cycle 2, 1 patient who developed grade 3 elevated aspartate aminotransferase (AST)/ ALT and grade 3 rash discontinued treatment due to the rash AE. Additionally, 1 other patient experienced grade 3 AST/ALT and discontinued to undergo transplant. With these findings in mind, investigators increased the DLT observation period to 56 days.

In group B (n = 13), patients received 60 mg of oral zandelisib daily on days 1 through 7 of each 28-day cycle starting at cycle 1, as well as a twice daily dose of zanubrutinib of 80 mg. During the DLT period of 56 days, 1 patient with HGBCL was not evaluable due to disease progression on day 14, and 2 patients developed grade 3 elevated AST/ALT in cycle 2. Although 1 patient is receiving ongoing treatment on the study, another patient discontinued due to recurrence of grade 3 ALT increase. Based on these findings, investigators opened disease-specific expansion cohorts using the Group B dosing schedule.

Among the patients enrolled on the study, the median age was 70 years old (range, 44-85), with an even split between male and female patients. Additionally, patients had received a median of 2 prior therapies (range, 1-8), with 55% of patients having undergone 2 or more therapies prior to enrolling on the study. Thirty percent of patients were refractory to rituximab (Rituxan), and 30% had tumor bulk that was greater than 55 mm.

Imaging scans were given on months 3, 7, 13, and then every 6 months until progression, with reported responses based on Lugano criteria and International Workshop on CLL guidelines. Two patients with DLBCL and HGBCL did not receive on therapy scans, as 1 developed clinically progressive disease and the other needed to discontinue early due to an AE from a prior therapy.

In terms of safety, the most common grade 3 or higher treatment-emergent AEs (TEAEs) in group A included neutropenia (43%), ALT increase (29%), AST increase (29%), and thrombocytopenia (29%). Common all grade TEAEs included neutropenia (57%), thrombocytopenia (57%), and diarrhea (43%). In group B, the most common grade 3 or higher TEAEs included neutropenia (23%), ALT increase (15%), and AST increase (15%), with any grade TEAEs including neutropenia (46%), AST increase (23%), thrombocytopenia (23%), and diarrhea (23%).

“We are currently enrolling expansion cohorts for follicular lymphoma and MCL [utilizing the group B regimen],” Soumerai concluded.

Soumerai JD, Jagadeesh D, Salman HS, et al. Tolerability and efficacy of the combination of PI3KΔ inhibitor zandelisib (ME-401) and BTK inhibitor zanubrutinib in patients with relapsed or refractory (R/R) B-cell malignancies: initial results. Presented at 2021 European Hematology Association Annual Congress; June 9-17, 2021; Virtual. Abstract S214.

A combination of zandelisib and zanubrutinib induced significant responses, including several complete responses in patients with relapsed or refractory chronic lymphocytic leukemia and other B-cell lymphomas in a phase 1b study, the results of which were presented during the 2021 European Hematology Association Annual Congress.

Hayley Virgil | Authors

Articles

Plasma Cell-Free Methylomes Offer Noninvasive Tumor Monitoring Across Cancer Settings

Promising Long-Term Results for HER2+ Early Breast Cancer

Adagrasib Reveals Efficacy in KRAS G12CMutated NSCLC

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