Bart Burington

CD40 Pathway Activation Status Predicts Response to CD40 Therapy in Diffuse Large B Cell Lymphoma

A 15-gene expression signature predicts whether a patient with diffuse large B cell lymphoma will respond to dacetuzumab, a therapeutic antibody. Matching Treatment to Tumor If physicians could predict the future, it would take the guess work out of designing the right treatment regimen for every patient’s cancer. The results presented by Burington et al. move us closer to clearing the crystal ball for diffuse large B cell lymphomas, a common type of non-Hodgkin’s lymphoma in which a cell surface receptor, CD40, presents a seemingly attractive target for therapy. Although stimulation of CD40 by ligand binding can cause apoptosis of B cells—a trait that one would predict to be desirable for a B cell lymphoma drug—it can also induce undesirable proliferation of some lymphoma cells. This murky paradox makes it unclear when to prescribe dacetuzumab, a CD40-targeted therapeutic monoclonal antibody. The authors have now identified a 15-gene expression signature that signals the biochemical status of a lymphoma, thus clarifying whether it can be subdued by anti-CD40 therapy. The authors collected an array of cell lines derived from non-Hodgkin’s lymphomas that show a range of sensitivity to anti-CD40 therapy. By assessing gene expression before and after CD40 stimulation and creating a score that reflected CD40 pathway activation, Burington et al. found that cell lines with higher baseline activation of the CD40 pathway tended to be unresponsive to anti-CD40 stimulation. The researchers then identified a group of 15 active genes whose expression in formalin-fixed tissue (as would be obtained from patients) correctly predicted susceptibility to anti-CD40 treatment 77% of the time, a result verified in another set of cells lines and by quantitative polymerase chain reaction (PCR). Next, in a real-world test of the utility of this 15-gene predictor, tumor tissue samples from 39 patients who had been treated with dacetuzumab were scored for CD40 pathway activation with the new gene signature. A large majority (88%) of the patients predicted by the gene signature to be resistant to therapy in fact did not respond to therapy, showing a median progression-free survival of 40 days; 67% of those predicted to respond to dacetuzumab did so, with median progression-free survival extended to 169 days. These results encourage further testing in a prospective clinical trial designed to examine the ability of the 15-gene signature to predict which lymphoma patients will benefit from dacetuzumab treatment. If this index proves useful, it can be added to the catalog of prognostic tools at the service of the oncologist as they match drug to patient—without the need of a crystal ball. The primary function of B cells, critical components of the adaptive immune response, is to produce antibodies against foreign antigens, as well as to perform isotype class switching, which changes the heavy chain of an antibody so that it can interact with different repertoires of effector cells. CD40 is a member of the tumor necrosis factor superfamily of cell surface receptors that transmits survival signals to B cells. In contrast, in B cell cancers, stimulation of CD40 signaling results in a heterogeneous response in which cells can sometimes undergo cell death in response to treatment, depending on the system studied. We found an association between sensitivity to CD40 stimulation and mutation of the tumor suppressor p53 in a panel of non-Hodgkin’s lymphoma cell lines. Consistent with p53’s tumor suppressor role, we found that higher levels of intrinsic DNA damage and increased proliferation rates, as well as higher levels of BCL6, a transcriptional repressor proto-oncogene, were associated with sensitivity to CD40 stimulation. In addition, CD40 treatment–resistant cell lines were sensitized to CD40 stimulation after the introduction of DNA-damaging agents. Using gene expression analysis, we also showed that resistant cell lines exhibited a preexisting activated CD40 pathway and that an mRNA expression signature comprising CD40 target genes predicted sensitivity and resistance to CD40-activating agents in cell lines and mouse xenograft models. Finally, the gene signature predicted tumor shrinkage and progression-free survival in patients with diffuse large B cell lymphoma treated with dacetuzumab, a monoclonal antibody with partial CD40 agonist activity. These data show that CD40 pathway activation status may be useful in predicting the antitumor activity of CD40-stimulating therapeutic drugs.

Estimating duration in partnership studies: issues, methods and examples

Background and objectives Understanding the time course of sexual partnerships is important for understanding sexual behaviour, transmission risks for sexually transmitted infections (STI) and development of mathematical models of disease transmission. Study design The authors describe issues and biases relating to censoring, truncation and sampling that arise when estimating partnership duration. Recommendations for study design and analysis methods are presented and illustrated using data from a sexual-behaviour survey that enrolled individuals from an adolescent-health clinic and two STD clinics. Survey participants were queried, for each of (up to) four partnerships in the last 3 months, about the month and year of first sex, the number of days since last sex and whether partnerships were limited to single encounters. Participants were followed every 4 months for up to 1 year. Results After adjustment for censoring and truncation, the estimated median duration of sexual partnerships declined from 9 months (unadjusted) to 1.6 months (adjusted). Similarly, adjustment for censoring and truncation reduced the bias in relative risks for the effect of age in a Cox model. Other approaches, such as weighted estimation, also reduced bias in the estimated duration distribution. Conclusion Methods are available for estimating partnership duration from censored and truncated samples. Ignoring censoring, truncation and other sampling issues results in biased estimates.

Statistical techniques to construct assays for identifying likely responders to a treatment under evaluation from cell line genomic data.

BackgroundDeveloping the right drugs for the right patients has become a mantra of drug development. In practice, it is very difficult to identify subsets of patients who will respond to a drug under evaluation. Most of the time, no single diagnostic will be available, and more complex decision rules will be required to define a sensitive population, using, for instance, mRNA expression, protein expression or DNA copy number. Moreover, diagnostic development will often begin with in-vitro cell-line data and a high-dimensional exploratory platform, only later to be transferred to a diagnostic assay for use with patient samples. In this manuscript, we present a novel approach to developing robust genomic predictors that are not only capable of generalizing from in-vitro to patient, but are also amenable to clinically validated assays such as qRT-PCR.MethodsUsing our approach, we constructed a predictor of sensitivity to dacetuzumab, an investigational drug for CD40-expressing malignancies such as lymphoma using genomic measurements of cell lines treated with dacetuzumab. Additionally, we evaluated several state-of-the-art prediction methods by independently pairing the feature selection and classification components of the predictor. In this way, we constructed several predictors that we validated on an independent DLBCL patient dataset. Similar analyses were performed on genomic measurements of breast cancer cell lines and patients to construct a predictor of estrogen receptor (ER) status.ResultsThe best dacetuzumab sensitivity predictors involved ten or fewer genes and accurately classified lymphoma patients by their survival and known prognostic subtypes. The best ER status classifiers involved one or two genes and led to accurate ER status predictions more than 85% of the time. The novel method we proposed performed as well or better than other methods evaluated.ConclusionsWe demonstrated the feasibility of combining feature selection techniques with classification methods to develop assays using cell line genomic measurements that performed well in patient data. In both case studies, we constructed parsimonious models that generalized well from cell lines to patients.

Abstract 2376: Improved progression-free survival (PFS) in patients with short tumor telomere length: Subgroup analysis from a randomized phase II study of the telomerase inhibitor imetelstat as maintenance therapy for advanced NSCLC .

Tumor regrowth after chemotherapy may be driven by growth of tumor ‘stem cells’. Telomerase, required for indefinite replication, is upregulated both in putative ‘stem cells’ and bulk tumor cells. Imetelstat, a lipidated 13-mer oligonucleotide, is a potent and specific inhibitor of telomerase. A randomized phase II study was conducted to assess whether imetelstat, given as maintenance therapy, prolongs PFS in advanced NSCLC: results for the primary and secondary endpoints are reported separately. NSCLC cell lines and other tumor cells with short telomeres appear to be more sensitive to imetelstat in vitro than those with long telomeres. A planned exploratory analysis to determine PFS as a function of tumor telomere length (TL) was performed. Tumor TL was assessed in archival tumor specimens from pts by quantitative PCR (qPCR). TL data were available for 57 of the 116 pts accrued in the clinical trial. PFS was evaluated in patients grouped into the shortest 1/2, shortest 1/3 and shortest 1/4 of TL. In 19 pts with the shortest 1/3 TL measured by qPCR, imetelstat maintenance increased PFS with a HR in favor of the imetelstat arm of 0.32 (95% CI 0.1 to 1.0), p=0.042 (un-stratified log rank). Median PFS was 4.0 months for the imetelstat-treated short TL sub-group and 1.5 months for the control short TL sub-group. In the 38 pts with the longest 2/3 TL HR was 0.83 (95% CI 0.36 to 1.9). Results in the group with the shortest 1/4 of TL were similar to the shortest 1/3 TL group, and in the shortest 1/2 group, results were consistent but attenuated, indicating that a smaller subset may contain patients with the most potential to benefit. In the control arm, short TL was associated with shorter median PFS (1.48 months) compared to patients with long TL (2.7 months), suggesting that short TL has a negative prognostic value. These findings suggest that imetelstat given as maintenance therapy prolongs PFS in pts with advanced NSCLC whose tumors have short telomeres as measured by qPCR. The data are consistent with the hypothesis that clinical benefit from telomerase inhibition is greater in patients with tumors possessing short telomeres. Prospective confirmation of these results in solid tumors and hematologic neoplasms is planned. Citation Format: Alberto Chiappori, Ekaterina Bassett, Bart Burington, Tatjana Kolevska, David R. Spigel, Steven Hager, Mark Rarick, Shirish Gadgeel, Normand Blais, Joachim Von Pawel, Lowell Hart, Hui Wang, Kevin Eng, Martin Reck, Joan Schiller. Improved progression-free survival (PFS) in patients with short tumor telomere length: Subgroup analysis from a randomized phase II study of the telomerase inhibitor imetelstat as maintenance therapy for advanced NSCLC . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2376. doi:10.1158/1538-7445.AM2013-2376