PIK3CA mutations in plasma circulating tumor DNA predict survival and treatment outcomes in patients with advanced cancers

Background

Oncogenic mutations in PIK3CA are prevalent in diverse cancers and can be targeted with inhibitors of the phosphoinositide-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway. Analysis of circulating tumor DNA (ctDNA) provides a minimally invasive approach to detect clinically actionable PIK3CA mutations.

Patients and methods

We analyzed PIK3CA hotspot mutation frequency by droplet digital PCR (QX 200; BioRad) using 16 ng of unamplified plasma-derived cell-free DNA from 68 patients with advanced solid tumors (breast cancer, n = 41; colorectal cancer, n = 13; other tumor types, n = 14). Results quantified as variant allele frequencies (VAFs) were compared with previous testing of archival tumor tissue and with patient outcomes.

Results

Of 68 patients, 58 (85%) had PIK3CA mutations in tumor tissue and 43 (74%) PIK3CA mutations in ctDNA with an overall concordance of 72% (49/68, κ = 0.38). In a subset analysis, which excluded samples from 26 patients known not to have disease progression at the time of sample collection, we found an overall concordance of 91% (38/42; κ = 0.74). PIK3CA-mutated ctDNA VAF of ≤8.5% (5% trimmed mean) showed a longer median survival compared with patients with a higher VAF (15.9 versus 9.4 months; 95% confidence interval 6.7-17.1 months; P = 0.014). Longitudinal analysis of ctDNA in 18 patients with serial plasma collections (range 2-22 time points, median 5) showed that those with a decrease in PIK3CA VAF had a longer time to treatment failure (TTF) compared with patients with an increase or no change (10.7 versus 2.6 months; P = 0.048).

Conclusions

Detection of PIK3CA mutations in ctDNA is concordant with testing of archival tumor tissue. Low quantity of PIK3CA-mutant ctDNA is associated with longer survival and a decrease in PIK3CA-mutant ctDNA on therapy is associated with longer TTF.

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Testing for PIK3CA mutations in ctDNA is concordant with testing of tumor tissue.

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High PIK3CA-mutant abundance in ctDNA was associated with shorter survival.

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Increasing PIK3CA-mutant abundance in serial blood samples was associated with shorter TTF.

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Longitudinal monitoring of PIK3CA-mutant ctDNA tracked with cancer clinical course.

Multiplex KRASG12/G13 mutation testing of unamplified cell-free DNA from the plasma of patients with advanced cancers using droplet digital polymerase chain reaction

Background

Cell-free DNA (cfDNA) from plasma offers easily obtainable material for KRAS mutation analysis. Novel, multiplex, and accurate diagnostic systems using small amounts of DNA are needed to further the use of plasma cfDNA testing in personalized therapy.

Patients and methods

Samples of 16 ng of unamplified plasma cfDNA from 121 patients with diverse progressing advanced cancers were tested with a KRASG12/G13 multiplex assay to detect the seven most common mutations in the hotspot of exon 2 using droplet digital polymerase chain reaction (ddPCR). The results were retrospectively compared to mutation analysis of archival primary or metastatic tumor tissue obtained at different points of clinical care.

Results

Eighty-eight patients (73%) had KRASG12/G13 mutations in archival tumor specimens collected on average 18.5 months before plasma analysis, and 78 patients (64%) had KRASG12/G13 mutations in plasma cfDNA samples. The two methods had initial overall agreement in 103 (85%) patients (kappa, 0.66; ddPCR sensitivity, 84%; ddPCR specificity, 88%). Of the 18 discordant cases, 12 (67%) were resolved by increasing the amount of cfDNA, using mutation-specific probes, or re-testing the tumor tissue, yielding overall agreement in 115 patients (95%; kappa 0.87; ddPCR sensitivity, 96%; ddPCR specificity, 94%). The presence of ≥ 6.2% of KRASG12/G13 cfDNA in the wild-type background was associated with shorter survival (P = 0.001).

Conclusion(s)

Multiplex detection of KRASG12/G13 mutations in a small amount of unamplified plasma cfDNA using ddPCR has good sensitivity and specificity and good concordance with conventional clinical mutation testing of archival specimens. A higher percentage of mutant KRASG12/G13 in cfDNA corresponded with shorter survival.

Characterizing the patterns of clonal selection in circulating tumor DNA from patients with colorectal cancer refractory to anti-EGFR treatment

INTRODUCTION

KRAS and EGFR ectodomain-acquired mutations in patients with metastatic colorectal cancer (mCRC) have been correlated with acquired resistance to anti-EGFR monoclonal antibodies (mAbs). We investigated the frequency, co-occurrence, and distribution of acquired KRAS and EGFR mutations in patients with mCRC refractory to anti-EGFR mAbs using circulating tumor DNA (ctDNA).

PATIENTS AND METHODS

Sixty-two post-treatment plasma and 20 matching pretreatment archival tissue samples from KRAS (wt) mCRC patients refractory to anti-EGFR mAbs were evaluated by high-sensitivity emulsion polymerase chain reaction for KRAS codon 12, 13, 61, and 146 and EGFR 492 mutations.

RESULTS

Plasma analyses showed newly detectable EGFR and KRAS mutations in 5/62 [8%; 95% confidence interval (CI) 0.02-0.18] and 27/62 (44%; 95% CI 0.3-0.56) samples, respectively. KRAS codon 61 and 146 mutations were predominant (33% and 11%, respectively), and multiple EGFR and/or KRAS mutations were detected in 11/27 (41%) cases. The percentage of mutant allele reads was inversely correlated with time since last treatment with EGFR mAbs (P = 0.038). In the matching archival tissue, these mutations were detectable as low-allele-frequency clones in 35% of patients with plasma mutations after treatment with anti-EGFR mAbs and correlated with shorter progression-free survival (PFS) compared with the cases with no new mutations (3.0 versus 8.0 months, P = 0.0004).

CONCLUSION

Newly detected KRAS and/or EGFR mutations in plasma ctDNA from patients refractory to anti-EGFR treatment appear to derive from rare, pre-existing clones in the primary tumors. These rare clones were associated with shorter PFS in patients receiving anti-EGFR treatment. Multiple simultaneous mutations in KRAS and EGFR in the ctDNA and the decline in allele frequency after discontinuation of anti-EGFR therapy in a subset of patients suggest that several resistance mechanisms can co-exist and that relative clonal burdens may change over time. Monitoring treatment-induced genetic alterations by sequencing ctDNA could identify biomarkers for treatment screening in anti-EGFR-refractory patients.

Survival advantage observed with the use of metformin in patients with type II diabetes and colorectal cancer

BACKGROUND

Patients with type II diabetes mellitus (DM) have an increased risk of adenomatous colorectal (CRC) polyps and CRC cancer. The use of the anti-hyperglycemic agent metformin is associated with a reduced incidence of cancer-related deaths.

METHODS

We retrospectively evaluated the medical records of 4758 patients seen at a single institution and determined that 424 patients were identified by their physicians as having type II DM and CRC cancer. Data were subsequently acquired determining the subject's age, body mass index (BMI), and disease date of diagnosis, stage, site of cancer, treatment, and survival.

RESULTS

Patients with type II DM and CRC cancer treated with metformin as one of their diabetic medications had a survival of 76.9 months (95% CI=61.4-102.4) as compared with 56.9 months in those patients not treated with metformin (95% CI=44.8-68.8), P=0.048. By using a multivariable Cox regression model adjusted for age, sex, race, BMI, and initial stage of disease, we demonstrated that type II diabetic patients treated with metformin had a 30% improvement in overall survival (OS) when compared with diabetic patients treated with other diabetic agents.

CONCLUSION

Colorectal cancer patients with DM treated with metformin as part of their diabetic therapy appear to have a superior OS.

Survival advantage associated with palliative oophorectomy in patients with metastatic colorectal cancer (CRC) to the ovaries (mCRC-O): A single institution retrospective analysis

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Background: The ovaries are an uncommon site for secondary spread from metastatic CRC. We hypothesize that palliative oophorectomy improves survival among patients with mCRC-O.

Methods: We undertook a single institution IRB-approved (DR-09-623) retrospective evaluation of women with mCRC-O from 2001-2008; 110 pts with ovarian metastases and follow-up information for survival analysis were identified out of 3,776 female pts with CRC (2.9%). Survival data was calculated from the date of diagnosis of ovarian metastases (by pathology or radiology) to date of death.

Results: Median age of patients was 49 years (range 19-82); median duration of follow-up was 49 months. Twenty patients were identified from 1,758 female patients with CRC seen at our institution from 2001-2004 (1.1%) and ninety patients identified from 2,018 female CRC patients from 2005-2008 (4.5%). KRAS mutation was present in the primary tumor in 23 of 43 (54%). Sixteen evaluable patients who received systemic chemotherapy with mCRC-O and other sites of metastatic disease were identified; five (31%) had a mixed radiographic response (progression in the ovarian metastases with disease response in other sites of metastases). Seventy-one (64.5%) patients had metastatic disease at the time of initial presentation; 39 (35.5%) had completely resected stage II or III CRC with mCRC-O occurring at a later date. 86 (78.2%) underwent unilateral or bilateral oophorectomy for treatment of their disease. Patients who had metastatic disease at presentation and underwent oophorectomy had a median survival of 39.4 months versus 18.2 months for those with ovarian metastases left in situ (p < 0.0001); patients who developed ovarian relapse after prior colectomy and subsequently underwent oophorectomy had a median survival of 50 months versus 12 months for those patients who did not (p = 0.001). Patients with mCRC-O and peritoneal metastases had a significantly worse survival (p = 0.003).

Conclusions: This single institution retrospective data analysis suggests that women with colorectal cancer metastatic to the ovaries may derive a survival benefit from palliative oophorectomy.

No significant financial relationships to disclose.

Retrospective evaluation of patients with colorectal cancer (CRC) and type II non-insulin-dependent diabetes (NIDDM)

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Background: Patients with NIDDM have an increased risk of colorectal adenomas and CRC possibly mediated through the insulin growth factor receptor pathway. Metformin is associated with anticancer efficacy in preclinical models and a lower risk of cancer mortality in patients with NIDDM. We undertook to evaluate the difference in outcome in NIDDM patients with CRC based upon their medications taken for glycemic control.

Methods: We conducted an IRB-approved (DR09-0719) retrospective analysis of 4,758 patients seen at a single institution (University of Texas M. D. Anderson) with CRC between the years of 2005-2008, to determine the prevalence of NIDDM in this patient population, in addition to determining whether patient survival differs based upon their diabetic therapy.

Results: 425 out of 4,758 CRC patients (8.9%) were identified as having NIDDM. Gender, male:female 283:142 (67%, 33%), age, mean 62 years (range 31-91), stage I/II/III/IV 37:55:175:158 (8.7%, 12.9%, 41.2%, 37.2%). Overall survival (OS) for the 397 patients with follow-up data available, by univariable Kaplan Meier analysis, was 63.7 months (95% confidence interval (CI), 52.3-75.5). Patients with NIDDM and CRC treated with metformin as one of their diabetic medications had a survival of 76.9 months (95% CI, 61.4-102.4) as compared to 56.9 months in those patients not treated with metformin (95% CI, 44.8- 68.8), p = 0.048. By using a Cox regression model adjusted for age, sex, race, body mass index, and initial stage of disease we demonstrated that NIDDM patients treated with metformin had a 30% improvement in OS when compared to NIDDM patients treated with other diabetic agents. There was a non-statistically significant trend toward higher complete and minor pathologic response rate (≤ 10% residual tumor) in NIDDM patients with rectal cancer receiving chemoradiation who were treated with metformin when compared to those who were not (14/19, 74% vs. 9/19, 47%, p = 0.09).

Conclusions: In this analysis the use of metformin in NIDDM patients with CRC was associated with an improved overall survival. While these results are consistent with the findings in other solid tumors they will need to be validated in other colorectal cancer data sets.

No significant financial relationships to disclose.

Clinical and pharmacokinetic (PK) findings in a phase I study of 7-t-butyldimethylsilyl-10-hydroxycamptothecin (AR-67) in patients with refractory solid tumors

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Background: AR-67 is a 3rd generation camptothecin analog selected for development based on the high in vitro stability of its pharmacologically active lactone form and high potency in preclinical models. This report describes the initial phase I study of intravenous AR-67 in adults with refractory solid tumors. Methods: AR-67 was infused over 1 hour for 5 days of a 21-day cycle using an accelerated titration phase I trial design. PK was performed on the 1st and 4th day of cycle 1. AR-67 was assayed with a validated chromatography method. Toxicity and response were assessed using NCI CTC (v3) grading scale and RECIST. Results: In total, 26 patients were treated at 9 dose levels (mg/m2/day): 1.2 (n=2), 1.67 (n=3), 2.34 (n=3), 3.2 (n=3); 4.5 (n=1), 6.3 (n=1), 7.5 (n=7), 8.9 (n=4) and 12.4 (n=2). Median age 62 (range 31–79), 15M/11F, median prior therapies 3 (range 1 to 6). Tumor types included: colorectal (8), non-small cell lung (NSCLC) (4), small cell lung (3), soft tissue sarcoma, (3), head and neck (2), prostate (2), and other (4). 21 subjects completed 2 or more cycles of therapy, 5 subjects received 1 cycle of therapy and had rapid disease progression (1 received 2d of drug prior to PD), 1 subject is still under treatment after 9 cycles. DLTs were observed in 5 patients: 2 of 2 at 12.4 mg/m2/day (Gr 4 febrile neutropenia, Gr 3 fatigue); 2 of 4 at 8.9 mg/m2/day (Gr 4 thrombocytopenia), 1 of 7 at 7.5 mg/m2/day (Gr 4 thrombocytopenia). Common C1 worst-grade drug related toxicities (CTC I/II % vs III/IV %): Hg (27/8), WBC (11/19), ANC (19/8), platelets (19/12), fatigue (15/8) insomnia (8/0), flushing (15//0), constipation (8/0), nausea (23/0), ALT elevation (12/0), hiccups (8/0). Antitumor activity, assessed by development of PR and SD, was observed in NSCLC, SCLC, colon and bladder cancer. The lactone form was predominant in plasma (>85% of AUC) at all time points. Clearance was constant with increasing dose and exposure (AUC) correlated with toxicity. Conclusions: AR-67 has superior lactone stability compared to approved analogs, has a predictable toxicity profile that did not include diarrhea and has activity in NSCLC. The RP2D is 7.5 mg/m2/day for 5 days of a 21-day cycle. This work was supported by R21-CA-123867 and Arno Therapeutics.

[Table: see text]

Pharmacokinetics (PK) of the highly lipophilic and blood stable camptothecin AR-67 (7-t-butyldimethylsilyl-10- hydroxycamptothecin) in adult patients with solid malignancies

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Background: Camptothecin analogs possess a labile lactone ring, which readily undergoes a pH dependent, albeit reversible, hydrolysis in plasma to yield a carboxylate moiety. The latter is considered inactive due to its electronegative charge that impedes transport into cells. Furthermore, the carboxylate is cleared rapidly and causes toxicity in eliminating organs due to lactonation. AR-67 is a highly lipophilic 3rd generation analog with superior stability of its lactone form in preclinical models. This report describes the PK of AR-67 in patients with refractory solid tumors enrolled in a phase I study. Methods: AR-67 was infused over 1 hr for 5 days every 21-days. PK was performed on the 1st and 4th day of cycle 1. Blood, plasma, and urine were collected (0–24 hrs) from 26 patients (see 09-AB-30336-ASCOAM) treated at 9 dose levels: 1.2–12.4 (mg/m2/day). AR-67 carboxylate and lactone were assayed with a validated chromatography method. Results: AR-67 was detectable at all dose levels. Blood concentrations mirrored those in plasma and were superimposable when adjusted by the hematocrit. AR-67 concentration peaked at the end of the 1-hr infusion and declined biexponentially with a terminal t1/2 of 1.4 hr (plasma lactone). A linear relationship was observed between dose and AUC. The lactone clearance on Day 1 was 16.6 (±5.5) vs. 19.6 (±6.3) L/hr/m2 on Day 5. The carboxylate clearance was ∼ 6-fold higher. Lactone was the major form in all samples and its area under the time vs. concentration curve (AUC) was 85.5% (range 74.0%-94.1%) of the total AUC. Urine (0–24 hr) contained 2.5% (0.3%-6.7%) of the dose on Day 1 vs. 2.7% (0.9–11.1%) on Day 4. Extensive metabolite peaks were not observed in plasma, blood, or urine samples. Plasma protein binding of the carboxylate was 90% (range 80%-96%) vs. 95% (range 90%-98%) for the lactone. Conclusions: AR-67 is a lipophilic camptothecin with a unique PK profile. Unlike other clinically approved analogs with lower lactone stability (35%-65%), over 85% of the AR-67 AUC is in the active lactone form. This high lactone-low carboxylate exposure coupled with the apparently limited metabolism of AR-67 may result in increased activity and decreased toxicity.

[Table: see text]