STK11 Loss Research Articles

Abstract 2205: Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment.

Abstract Background: The knowledge of actionable somatic genomic alterations present in human tumors is enabling the new era of personalized cancer treatment. The great intellectual challenge lies in linking confirmed mutations to protein function. Personalized tumor graft models (Avatars) can aid in the process of genomic analyses interpretation to ultimately move from molecular profile to medication. Methods: Using massive parallel sequencing we performed whole exome sequencing analysis of tumor and matched normal blood samples of 23 patients (pts) with advanced solid tumors (7 lung cancer, 7 pancreatic cancer, 1 neuroendocrine tumor, 2 glioblastoma, 1 uveal melanoma, 2 melanomas and 3 colon cancer) to identify putatively actionable tumor-specific genomic alterations. Avatar models generated by direct engraftment of tumor samples from the pts into immunocompromised mice were used as an in vivo platform to test proposed treatment strategies. Results: Successful exome sequencing analyses has been obtained for 21 pts (1 patient died prematurely, 1 sample was insufficient). Tumor specific mutations (Muts) and copy number variations were identified ranging from 5 to 952 and 0 to 36 respectively. All samples profiled contained clinically meaningful genomic alterations. A successful Avatar model was generated for 10 out of 17 pts. Two engraftment failures corresponded to EGFR mutant lung tumors resected while pts were receiving erlotinib, which initially grew but then regressed. Some of the most relevant drugabble alterations were: KRAS, CHEK1, FGFR2, IGF1R, MET, BRCA1, XPC, NOTCH, CREB3LB, GNA11, SMAD4 and EGFR. In occasions druggable alterations such as muts in NF1, PTPRC, PI3KA and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and accordingly treatment of the pts with these drugs was not effective. In one case, loss of STK11 lead to testing of mTOR and SRC inhibitors resulting in tumor regression both in the Avatar and in the clinic. At present time 10 pts have received a personalized treatment: 2 pts, as expected based on the Avatar model, did not response; 4 pts resulted in durable partial remissions and 4 pts are currently on treatment with disease stabilization. In one of the EGFR mutant lung pts the genomic analysis revealed traces of an acquired mutation and allowed decision making at an earlier time point, prior to relapse. Overall, there was a remarkable correlation between drug activity in the Avatar and clinical outcome in the pts, in terms of drug resistance and sensitivity. Conclusion: The detection of actionable tumor-specific genomic alterations in the clinical setting is feasible. However predicting treatment response to known oncogenes is complex and requires detailed information of how different genetic backgrounds function. Avatar models are a powerful investigational platform for therapeutic decision making and help to guide cancer treatment in the clinic. Citation Format: Elena Garralda, Keren Paz, Pedro P. López-Casas, Siân Jones, Amanda Katz, Lisa M. Kann, Fernando López-Rios, Francesca Sarno, Fátima Al-Shahrour, David Vasquez, Elizabeth Bruckheimer, Samuel V. Angiuoli, Luis A. Diaz, Alfonso Valencia, Victor E. Velculescu, David Sidransky, Manuel Hidalgo. Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment. [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 2205. doi:10.1158/1538-7445.AM2013-2205

Enchondroma resulting from loss of a Stk11-dependent switch of proliferative chondrocytes to a postmitotic fate

Stk11 (also known as liver kinase b1 (Lkb1)) is a serine-threonine protein kinase that acts upstream of the AMP-activated protein kinase (AMPK) family in coupling energy homeostasis to cell growth, proliferation and survival. Through chondrocyte-specific removal of Lkb1 activity, we showed that Stk11 is required for the normal switch of mitotic chondrocytes to a postmitotic hypertrophic chondrocyte fate. Consequently, it led to a dramatic overgrowth of the growth plate in the Stk11-mutant postnatal skeletal elements. To determine the molecular mechanisms underlying Stk11 action, we examined the mTOR pathway, which is inhibited through AMPK in growth regulation. Strikingly, rapamycin treatment of the pregnant mouse was able to rescue the delay in chondrocyte hypertrophy in Stk11-mutant embryos, suggesting that Stk11 inhibition of mTOR signaling is critical for the switch in chondrocyte fate. Since the dramatic overgrowth of the growth plate is characteristic of enchondroma, we also examined the tumorigenicity of the mutant chondrocytes both in vitro and in vivo . In contrast to wild-type chondrocytes isolated from the postnatal day-30 growth plate, Stk11-mutant chondrocytes proliferated and formed colonies in monolayer and anchorage-independent agar cultures, indicative of a neoplastic transformation in vitro . Similarly, allotransplantation of mutant chondrocytes into immune-deficient NOG mice also resulted in tumor formation in vivo . Gene Ontology analysis of gene expression profiles indicated an augmented activity of cell proliferation and cell cycle regulators within the enchondroma-chondrocyte population compared to chondrocytes in the normal growth plate. Taken together, these data demonstrated an unexpected role of Stk11 in balancing proliferative and nonproliferative hypertrophic states of chondrocyte development through the regulation of mTOR signaling. Stk11 is a known tumor suppressor; our findings raise the possibility that loss of Stk11 may play a role in human enchondroma, a possibility that we are investigating.

Somatic mutations of STK11 gene in human papillomavirus positive and negative penile cancer

BackgroundHuman papillomavirus (HPV) infection accounts for about 40-50% of all cases of penile carcinoma suggesting that other factors, including host genetic status, are involved in neoplastic transformation. In this perspective, STK11 gene, which has been found frequently mutated in HPV-related cervical carcinoma, has been analyzed in HPV-positive and HPV-negative invasive penile cancers to establish its mutational status and the possible correlation of HPV infection with specific genetic alterations.MethodsGenomic DNAs extracted from 26 cases of penile squamous cell carcinoma were analyzed for genetic alterations in the exons 1 to 9 of STK11 gene by quantitative real-time PCR. Ratios of potentially deleted and non-deleted exons were indicative of specific loss of STK11 coding regions. DNA samples of 5 cancer cases were subjected to standard PCR amplification of STK11 exons 1 to 9 and analyzed for somatic mutations by direct nucleotide sequencing analysis.ResultsHeterozygous deletions of STK11 exon 1 and 2 were identified in 2 out of 14 HPV-positive (14.3%) and 1 out of 12 HPV-negative cases (8.3%). Complete nucleotide sequencing analysis of exons 1 to 9 showed a single nucleotide change upstream the exon 2 coding region in 1 out of 5 penile carcinoma samples.ConclusionsThe present results suggest that single nucleotide mutations and/or deletions of STK11 gene are rare events in penile cancer. Moreover, no significant association was observed between STK11 alterations and HPV infection in these tumors.

Next-generation sequencing (NGS) to identify actionable genomic changes in common and rare solid tumors: The FMI experience with the initial 50 consecutive patients.

10590 Background: Solid tumor (ST) oncology has been transformed by the linkage of genomic changes with targeted therapeutics. Unfortunately, most STs still have no alteration detected with currently available assays. Thus, more informative testing platforms are needed to analyze genomic changes in FFPE biopsy samples often limited by tumor size, heterogeneity and ploidy. Methods: We reviewed the genomic profiles of the first 50 clinical specimens received by our CLIA lab (Foundation Medicine) and analyzed by our NGS assay (Ross J. ASCO 2011). 182 genes known altered in STs and 14 genes known rearranged in STs were included. Genomic alterations were categorized as “actionable” if linked to an approved therapy in the ST under study or another ST (e.g. ALK rearrangement in lung or breast cancer, respectively), a known or suspected contraindication to a given therapy (e.g. KRAS G12D in colorectal cancer) or a clinical trial linked to the alteration (e.g. mTOR inhibition in a tumor with STK11 loss). Results: Fifty tumor specimens were received from 50 patients (median age 54, F/M=30/20) representing 35 sites. Two samples failed analysis and 6 had no detectable genomic alteration. Among 16 primary tumor types, lung (n=15), colorectal (n=7), sarcoma (n=5), breast and esophageal/gastric (n=4 each) were most common. We reported 135 genomic alterations (mean 2.8, range 0-6) unequivocally involved in oncogenesis and 69 actionable alterations. At most, 29 of these (42%) would have been detected by current assays (138% increase with NGS). Thirty seven patients had one or more actionable alterations (range 1-4) detected by NGS (74%, 95% CI 60-85%) versus only 21 (42%, 95% CI 28-57%) in whom changes would have been detected by current assays. Conclusions: Use of a broad, comprehensive NGS assay identifies an unprecedented number of actionable genomic alterations across a variety of STs from routine FFPE samples. This assay can serve as a paradigm for improving access to approved therapies in STs, minimizing use of ineffective therapies and enhancing enrollment in rationally chosen trials. Ongoing and planned trials will study the impact on several efficacy endpoints.

LKB1 signaling in mesenchymal cells required for suppression of gastrointestinal polyposis

Germline mutations in STK11 (also known as LKB1) are found in individuals with Peutz-Jeghers syndrome (PJS) manifesting with gastrointestinal polyps that contain a prominent stromal component. Epithelia in polyps of Stk11(+/-) mice can retain a functional copy of Stk11 (refs. 2,3), and loss of heterozygosity is not an obligate feature of human polyps, raising the possibility of non-epithelial origins in tumorigenesis. Here we show that either monoallelic or biallelic loss of murine Stk11 limited to Tagln-expressing mesenchymal cells results in premature postnatal death as a result of gastrointestinal polyps indistinguishable from those in PJS. Stk11-deficient mesenchymal cells produced less TGFbeta, and defective TGFbeta signaling to epithelial cells coincided with epithelial proliferation. We also noted TGFbeta signaling defects in polyps of individuals with PJS, suggesting that the identified stromal-derived mechanism of tumor suppression is also relevant in PJS.