Integrative molecular characterisation of gallbladder cancer reveals micro-environment-associated subtypes

BACKGROUND & AIMS

Gallbladder cancer (GBC) is the most common type of biliary tract cancer, but the molecular mechanisms involved in gallbladder carcinogenesis remain poorly understood. In this study, we applied integrative genomics approaches to characterise GBC and explore molecular subtypes associated with patient survival.

METHODS

We profiled the mutational landscape of GBC tumours (whole-exome sequencing on 92, targeted sequencing on 98, in total 190 patients). In a subset (n = 45), we interrogated the matched transcriptomes, DNA methylomes, and somatic copy number alterations. We explored molecular subtypes identified through clustering tumours by genes whose expression was associated with survival in 47 tumours and validated subtypes on 34 publicly available GBC cases.

RESULTS

Exome analysis revealed TP53 was the most mutated gene. The overall mutation rate was low (median 0.82 Mut/Mb). APOBEC-mediated mutational signatures were more common in tumours with higher mutational burden. Aflatoxin-related signatures tended to be highly clonal (present in ≥50% of cancer cells). Transcriptome-wide survival association analysis revealed a 95-gene signature that stratified all GBC patients into 3 subtypes that suggested an association with overall survival post-resection. The 2 poor-survival subtypes were associated with adverse clinicopathologic features (advanced stage, pN1, pM1), immunosuppressive micro-environments (myeloid-derived suppressor cell accumulation, extensive desmoplasia, hypoxia) and T cell dysfunction, whereas the good-survival subtype showed the opposite features.

CONCLUSION

These data suggest that the tumour micro-environment and immune profiles could play an important role in gallbladder carcinogenesis and should be evaluated in future clinical studies, along with mutational profiles.

LAY SUMMARY

Gallbladder cancer is highly fatal, and its causes are poorly understood. We evaluated gallbladder tumours to see if there were differences between tumours in genetic information such as DNA and RNA. We found evidence of aflatoxin exposure in these tumours, and immune cells surrounding the tumours were associated with survival.

Abstract 386: Design and application of an 8-plex multiplex immunofluorescence panel for deep phenotypic profiling of the tumor microenvironment using InSituPlex technology

Background: The tumor microenvironment is composed of a complicated network of different cell types and activation states, the exact composition of which is important for immuno-oncology research efforts to correlate treatment options and outcome. The number of biomarkers necessary to sufficiently profile the various cellular phenotypes and elucidate contextual relationships in situ is larger than can be accommodated by standard immunohistochemistry (IHC) approaches. Furthermore, conventional IHC requires more sections, potentially exhausting tissue sample availability. To overcome these limitations, Ultivue has developed InSituPlex® technology and UltiMapper™ assays that enable biomarker multiplexing in tissue samples with an automated workflow to support high sample throughput.

Methods: An 8-plex immune-profiling panel using the InSituPlex approach was designed and tested to detect and classify T cells, macrophages, and tumor cell populations along with PD-L1 checkpoint expression in multiple tumor types. This assay was designed, developed, and tested using UltiMapper reagents and corresponding protocols. The assay was run on multiple FFPE tissue samples from breast cancer, NSCLC, and colorectal cancer (CRC) cases. Each sample was stained for the following 8 markers: CD3, CD4, CD8, CD68, FoxP3, PD-1, PD-L1, and pan-CK. Staining was performed in a single step using the Leica Biosystems BOND RX autostainer. Whole slide imaging (WSI) was performed in two steps on the ZEISS Axio Scan.Z1 slide scanner, and image analysis was performed using HALO software from Indica Labs.

Results: The 8-plex immune-profiling panel demonstrated specific biomarker staining and was verified for staining reproducibility. The 8-plex workflow was compatible across multiple tumor tissue types. The samples were characterized by cell analysis and phenotyped based on their expression of specific biomarkers. The following cell phenotypes were detected: T cells (CD3+), cytotoxic T cells (CD3+/CD8+), regulatory T cells (CD4+/FOXP3+), exhausted T cells (CD3+/PD-1+), macrophages (CD68+), and tumor cells (CK+) with a dynamic range of PD-L1 expression levels.

Conclusion: The 8-plex panel revealed important immunophenotypes across multiple sample types. The assay was automated and optimized for a high-throughput workflow. By testing across multiple tissue types, this assay showcases the potential for broad application across additional cancer types. The ability to interrogate an 8-plex I/O panel on a single slide with WSI presents an attractive approach for the next generation of IHC, enabling profiling within the tumor microenvironment and sensitive detection of PD-L1 expression in cancer tissues.

Funded by NCI Contract No. 75N910D00024

Author affiliations for CGR staff: Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702

Citation Format: Alexis Wong, Mara Koerner, Katir K. Patel, Anna Potier, Stephanie Hennek, Mustapha Abubakar, Mary E. Olanich, Yelena G. Golubeva, Karun Mutreja, Scott Lawrence. Design and application of an 8-plex multiplex immunofluorescence panel for deep phenotypic profiling of the tumor microenvironment using InSituPlex technology [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 386.

PAX3-FOXO1 is essential for tumour initiation and maintenance but not recurrence in a human myoblast model of rhabdomyosarcoma

The PAX3-FOXO1 fusion gene is generated by a 2;13 chromosomal translocation and is a characteristic feature of an aggressive subset of rhabdomyosarcoma (RMS). To dissect the mechanism of oncogene action during RMS tumourigenesis and progression, doxycycline-inducible PAX3-FOXO1 and constitutive MYCN expression constructs were introduced into immortalized human myoblasts. Although myoblasts expressing PAX3-FOXO1 or MYCN alone were not transformed in focus formation assays, combined PAX3-FOXO1 and MYCN expression resulted in transformation. Following intramuscular injection into immunodeficient mice, myoblasts expressing PAX3-FOXO1 and MYCN formed rapidly growing RMS tumours, whereas myoblasts expressing only PAX3-FOXO1 formed tumours after a longer latency period. Doxycycline withdrawal in myoblasts expressing inducible PAX3-FOXO1 and constitutive MYCN following tumour formation in vivo or focus formation in vitro resulted in tumour regression or smaller foci associated with myogenic differentiation and cell death. Following regression, most tumours recurred in the absence of doxycycline. Analysis of recurrent tumours revealed a subset without PAX3-FOXO1 expression, and cell lines derived from these recurrent tumours showed transformation in the absence of doxycycline. The doxycycline-independent oncogenicity in these recurrent tumour-derived lines persisted even after PAX3-FOXO1 was inactivated with a CRISPR/Cas9 editing strategy. Whereas cell lines derived from primary tumours were dependent on PAX3-FOXO1 and differentiated following doxycycline withdrawal, recurrent tumour-derived cells without PAX3-FOXO1 expression did not differentiate under these conditions. These findings indicate that PAX3-FOXO1 collaborates with MYCN during early RMS tumourigenesis to dysregulate proliferation and inhibit myogenic differentiation and cell death. Although most cells in the primary tumours are dependent on PAX3-FOXO1, recurrent tumours can develop by a PAX3-FOXO1-independent mechanism, in which rare cells are postulated to acquire secondary transforming events that were activated or selected by initial PAX3-FOXO1 expression. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Abstract 3093: CDK4 amplification reduces sensitivity to CDK4/6 inhibition in fusion-positive rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma and includes an aggressive, PAX3-FOXO1 fusion-positive subtype. Amplification of chromosomal region 12q13-q14, which contains the CDK4 proto-oncogene, was identified in a subset of fusion-positive RMS. Other tumor types with CDK4 amplification or overexpression, including liposarcoma and neuroblastoma, are sensitive to CDK4/6 inhibition, suggesting that CDK4/6-targeted therapies may provide a new treatment strategy in fusion-positive RMS. To evaluate the role of CDK4 in chromosomal region 12q13-14 amplification in fusion-positive RMS and the potential clinical utility of CDK4/6 inhibition in this disease setting, we examined the biological consequences of CDK4 knockdown, CDK4 overexpression, and pharmacologic CDK4/6 inhibition in fusion-positive RMS in vitro and in vivo. Knockdown of CDK4 abrogated proliferation and transformation of 12q13-14-amplified and non-amplified fusion-positive RMS cells via G1-phase cell cycle arrest. This arrest was associated with reduced RB phosphorylation and E2F-responsive gene expression. Significant differences in E2F target expression, however, were not observed in RMS cells overexpressing CDK4 or in fusion-positive tumors harboring 12q13-14 amplification relative to control cells or tumors lacking amplification, respectively. Treatment with the small molecule CDK4/6 inhibitor LEE011 phenocopied CDK4 knockdown, decreasing viability, RB phosphorylation, and E2F-responsive gene expression and inducing G1-phase cell cycle arrest. All fusion-positive RMS cell lines showed sensitivity to CDK4/6 inhibition, with evidence of differential antitumor activity resulting from an inverse relationship between CDK4 expression and inhibitor vulnerability. This variable responsiveness to LEE011 was recapitulated in xenograft models of CDK4-amplified and non-amplified fusion-positive RMS. Our findings demonstrate that CDK4 is necessary for RB-E2F-mediated G1-phase cell cycle progression, proliferation, and transformation in fusion-positive RMS regardless of CDK4 amplification status. Our studies further indicate that single-agent LEE011 is active in the setting of fusion-positive RMS and suggest that CDK4 amplification may be a marker of reduced sensitivity whereas low CDK4 expression may be associated with higher susceptibility to CDK4/6 inhibition. Collectively, our data provide preclinical evidence supporting further investigation of CDK4/6-targeted therapies in treatment regimens for fusion-positive RMS.

Citation Format: Mary E. Olanich, Wenyue Sun, Stephen M. Hewitt, Zied Abdullaev, Svetlana D. Pack, Frederic G. Barr. CDK4 amplification reduces sensitivity to CDK4/6 inhibition in fusion-positive rhabdomyosarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3093. doi:10.1158/1538-7445.AM2015-3093

CDK4 Amplification Reduces Sensitivity to CDK4/6 Inhibition in Fusion-Positive Rhabdomyosarcoma

PURPOSE

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma and includes a PAX3- or PAX7-FOXO1 fusion-positive subtype. Amplification of chromosomal region 12q13-q14, which contains the CDK4 proto-oncogene, was identified in an aggressive subset of fusion-positive RMS. CDK4/6 inhibitors have antiproliferative activity in CDK4-amplified liposarcoma and neuroblastoma, suggesting CDK4/6 inhibition as a potential therapeutic strategy in fusion-positive RMS.

EXPERIMENTAL DESIGN

We examined the biologic consequences of CDK4 knockdown, CDK4 overexpression, and pharmacologic CDK4/6 inhibition by LEE011 in fusion-positive RMS cell lines and xenografts.

RESULTS

Knockdown of CDK4 abrogated proliferation and transformation of 12q13-14-amplified and nonamplified fusion-positive RMS cells via G1-phase cell-cycle arrest. This arrest was mediated by reduced RB phosphorylation and E2F-responsive gene expression. Significant differences in E2F target expression, cell-cycle distribution, proliferation, or transformation were not observed in RMS cells overexpressing CDK4. Treatment with LEE011 phenocopied CDK4 knockdown, decreasing viability, RB phosphorylation, and E2F-responsive gene expression and inducing G1-phase cell-cycle arrest. Although all fusion-positive cell lines showed sensitivity to CDK4/6 inhibition, there was diminished sensitivity associated with CDK4 amplification and overexpression. This variable responsiveness to LEE011 was recapitulated in xenograft models of CDK4-amplified and nonamplified fusion-positive RMS.

CONCLUSIONS

Our data demonstrate that CDK4 is necessary but overexpression is not sufficient for RB-E2F-mediated G1-phase cell-cycle progression, proliferation, and transformation in fusion-positive RMS. Our studies indicate that LEE011 is active in the setting of fusion-positive RMS and suggest that low CDK4-expressing fusion-positive tumors may be particularly susceptible to CDK4/6 inhibition.

A call to ARMS: targeting the PAX3-FOXO1 gene in alveolar rhabdomyosarcoma

INTRODUCTION

Expression of fusion oncoproteins generated by recurrent chromosomal translocations represents a major tumorigenic mechanism characteristic of multiple cancers, including one-third of all sarcomas. Oncogenic fusion genes provide novel targets for therapeutic intervention. The PAX3-FOXO1 oncoprotein in alveolar rhabdomyosarcoma (ARMS) is presented as a paradigm to examine therapeutic strategies for targeting sarcoma-associated fusion genes.

AREAS COVERED

This review discusses the role of PAX3-FOXO1 in ARMS tumors. Besides evaluating various approaches to molecularly target PAX3-FOXO1 itself, this review highlights therapeutically attractive downstream genes activated by PAX3-FOXO1.

EXPERT OPINION

Oncogenic fusion proteins represent desirable therapeutic targets because their expression is specific to tumor cells, but these fusions generally characterize rare malignancies. Full development and testing of potential drugs targeted to these fusions are complicated by the small numbers of patients in these disease categories. Although efforts to develop targeted therapies against fusion proteins should continue, molecular targets that are applicable to a broader tumor landscape should be pursued. A shift of the traditional paradigm to view therapeutic intervention as target-specific rather than tumor-specific will help to circumvent the challenges posed by rare tumors and maximize the possibility of developing successful new treatments for patients with these rare translocation-associated sarcomas.

Identification of FUSE-binding protein 1 as a regulatory mRNA-binding protein that represses nucleophosmin translation

Nucleophosmin (NPM/B23) is a multifunctional oncoprotein whose protein expression levels dictate cellular growth and proliferation rates. NPM is translationally responsive to hyperactive mammalian target of rapamycin (mTOR) signals, but the mechanism of this regulation is not understood. Using chimeric translational reporters, we found that the 3' untranslated region (UTR) of the NPM messenger (m)RNA is sufficient to mediate its translational modulation by mTOR signalling. We show that far upstream element (FUSE)-binding protein 1 (FBP1) interacts specifically with the 3' UTR of NPM to repress translation. Overexpression of FBP1 resulted in translational repression of NPM mRNAs, whereas depletion of FBP1 caused a dramatic increase in NPM translation and resulted in enhanced overall cell proliferation. Thus, we propose that FBP1 is a key regulator of cell growth and proliferation through its ability to selectively bind the NPM 3' UTR and repress NPM translation.

The effects of removing the GAT domain from E. coli GMP synthetase

E. coli GMP synthetase (GMPS) catalyzes the conversion of XMP to GMP. Ammonia, generated in the amino-terminal glutamine amidotransferase (GAT) domain, is transferred by an unknown mechanism to the ATP-pyrophosphatase (ATPP) domain, where it attacks a highly reactive adenyl-XMP intermediate, leading to GMP formation. To study the structural requirements for the activity of E. coli GMPS, we used PCR to generate a protein expression construct that contains the ATPP domain as well as the predicted dimerization domain (DD). The ATPP/DD protein is active in solution, utilizing NH (4) (+) as an NH(3) donor. Size-exclusion chromatography demonstrates a dimeric mass for the ATPP/ DD protein, providing the first evidence in solution for the structural organization of the intact GMPS. Kinetic characterization of the ATPP/DD domain protein provides evidence that the presence of the GAT domain can regulate the activity of the ATPP domain.