Transcriptional subtyping and CD8 immunohistochemistry identifies poor prognosis stage II/III colorectal cancer patients who benefit from adjuvant chemotherapy

Purpose

Transcriptomic profiling of colorectal cancer (CRC) has led to the identification of four consensus molecular subtypes (CMS1 to 4) that have prognostic value in stage II and III disease. More recently, the Colorectal Cancer Intrinsic Subtypes (CRIS) classification system has helped to define the biology specific to the epithelial component of colorectal tumors; however, the clinical value of these classification systems in the prediction of response to standard-of-care adjuvant chemotherapy remains unknown.

Patients and Methods

Using samples from four European sites, we assembled a novel cohort of patients with stage II and III CRC (n = 156 samples) and performed transcriptomic profiling and targeted sequencing and generated a tissue microarray to enable integrated multiomics analyses. We also accessed data from two published cohorts of patients with stage II and III CRC: GSE39582 and GSE14333 (n = 479 and n = 185 samples, respectively).

Results

The epithelial-rich CMS2 subtype of CRC benefitted significantly from treatment with adjuvant chemotherapy in both stage II and III disease (P = .02 and P < .001, respectively), whereas the CMS3 subtype significantly benefitted in stage III only (P = .001). After CRIS substratification of CMS2, we observed that only the CRIS-C subtype significantly benefitted from treatment with adjuvant chemotherapy in stage II and III disease (P = .0081 and P < .001, respectively), whereas the CRIS-D subtype significantly benefitted in stage III only (P = .0034). We also observed that CRIS-C patients with low levels of CD8⁺ tumor-infiltrating lymphocytes were most at risk for relapse in both stage II and III disease (log-rank P = .0031; hazard ratio, 12.18 [95% CI, 1.51 to 98.58]).

Conclusion

Patient stratification using a combination of transcriptional subtyping and CD8 immunohistochemistry analyses is capable of identifying patients with poor prognostic stage II and III disease who benefit from adjuvant standard-of-care chemotherapy. These findings are particularly relevant for patients with stage II disease, where the overall benefit of adjuvant chemotherapy is marginal.

FKBPL Regulates Estrogen Receptor Signalling and Determines Response to Endocrine Therapy

Approximately 40% of patients with ER+ breast cancers do not respond to endocrine therapies; furthermore, most tumours eventually become resistant. We have identified a novel Hsp90 co-chaperone and immunophilin, FKBPL, that binds to Hsp90 and affects the stability and signalling of the estrogen receptor (ER) with implications for breast cancer growth and sensitivity to endocrine therapies.Using co-immunoprecipitations, we have demonstrated that FKBPL interacts within Hsp90 complexes associated with the estrogen receptor in MCF-7 cells. Cells stably overexpressing FKBPL become dependent on estrogen for their growth and even in its presence, FKBPL over-expression slows the rate of proliferation of these cells. More importantly, this dependence on estrogen, rendered FKBPL over-expressing cells dramatically more sensitive (up to 90%) to the anti-estrogens, tamoxifen and fulvestrant. Furthermore, knock-down of FKBPL using a targeted siRNA approach, dramatically increased the resistance of these cells to tamoxifen, supporting a role for FKBPL as a determinant of response to endocrine therapies.We have also identified putative estrogen responsive elements within FKBPL's promoter and show that FKBPL is upregulated in response to estrogen suggesting that FKBPL itself is an estrogen responsive gene. As FKBPL levels increased in response to estrogen, ER levels fell; implicating FKBPL in the stabilisation of ER. This is supported by data demonstrating that FKBPL over-expressing cells exhibit decreased levels of ER and cathepsin D, an estrogen responsive gene, critical to breast cancer growth, survival and invasion. Furthermore, knockdown of FKBPL using an siRNA approach increased ER and cathepsin D levels. The regulation of this ER-responsive gene supports a functional role for FKBPL in physiological ER-mediated signalling. FKBPL is also important for the stabilisation of the cyclin dependent kinase inhibitor, p21 (Jascur et al., 2005). We have seen a dramatic fall in p21 levels when FKBPL is knocked down with a targeted siRNA. Loss of p21 has been associated with a tamoxifen growth inducing phenotype and hyperphosphorylation of ER at S118, and with subsequent increased expression of ER-regulated genes. Here we show that ER phosphorylation is increased in FKBPL knockdown cells and decreased in FKBPL over-expressing cells. Together, these data support a model in which high levels of FKBPL would stabilise p21, reducing ER phosphorylation, abrogating tamoxifen-induced agonist potency and so increase sensitivity to the drug.Finally, having established that FKBPL expression may result in p21-mediated growth arrest and sensitisation to endocrine therapies, we hypothesised that FKBPL may have prognostic value that might impact upon tumour proliferative capacity and improve outcome independent of ER status. This was verified in two publically available breast cancer patient cohorts where we demonstrate that high FKBPL expression was correlated with increased overall survival and distant metastasis-free survival.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5126.

Predicting response to irinotecan/5-fluorouracil (5-FU) chemotherapy for advanced colorectal cancer based on gene expression in primary tumour

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Background: Despite improvements in the treatment of advanced colorectal cancer (CRC), there remains a subset of patients who fail to benefit from chemotherapy. The identification of predictive response markers has been limited by the relative scarcity of metastatic tumour samples for molecular analysis, prompting a need to consider surrogate models for generation of predictive markers. Methods: We performed gene expression profiling of archived formalin fixed paraffin-embedded (FFPE) colorectal primary tumours (dating from 2001–2007) from 40 patients who received irinotecan/5-FU chemotherapy as first line treatment for advanced disease. Patients were classified as responders/non-responders based on radiological response. Gene expression profiling was performed using the Almac Diagnostics Colorectal Disease Specific Array (DSA). Data was analysed using Genespring GX v7.3. Principal Components Analysis (PCA) was used to separate responding and non-responding patients based on the tumour- derived expression data. Predictive classifiers were constructed using several class prediction methods. The performance of the classifiers was assessed by leave-one-out cross-validation. Results: 37 samples passed data QC assessments for inclusion in predictive analysis. PCA using genes passing a t-test and 1.5-fold change filter demonstrated clear separation between responding and non-responding patients. Predictive modelling using the k-nearest neighbour and Support Vector Machine (SVM) algorithms with Fishers exact test as feature selection method each generated seven different predictive classifiers containing 5 to 35 genes; these had an average predictive accuracy of 80%. Predictive modelling of this dataset is ongoing and these encouraging initial results will be extended to a larger patient cohort. Conclusions: DNA microarray profiling has been used to generate gene signatures predictive of response to irinotecan/5-FU therapy in advanced CRC; importantly, these predictive signatures have been generated from FFPE colorectal primary tumour facilitating their independent validation in large patient cohorts and potential clinical implementation in the event of successful validation.

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