Tatiana Lepikhova

Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei

Estrogen receptor α (ERα) is a modular protein of the steroid/nuclear receptor family of transcriptional regulators that upon binding to the hormone undergoes structural changes, resulting in its nuclear translocation and docking to specific chromatin sites. In the nucleus, ERα assembles in multiprotein complexes that act as final effectors of estrogen signaling to the genome through chromatin remodeling and epigenetic modifications, leading to dynamic and coordinated regulation of hormone-responsive genes. Identification of the molecular partners of ERα and understanding their combinatory interactions within functional complexes is a prerequisite to define the molecular basis of estrogen control of cell functions. To this end, affinity purification was applied to map and characterize the ERα interactome in hormone-responsive human breast cancer cell nuclei. MCF-7 cell clones expressing human ERα fused to a tandem affinity purification tag were generated and used to purify native nuclear ER-containing complexes by IgG-Sepharose affinity chromatography and glycerol gradient centrifugation. Purified complexes were analyzed by two-dimensional DIGE and mass spectrometry, leading to the identification of a ligand-dependent multiprotein complex comprising β-actin, myosins, and several proteins involved in actin filament organization and dynamics and/or known to participate in actin-mediated regulation of gene transcription, chromatin dynamics, and ribosome biogenesis. Time course analyses indicated that complexes containing ERα and actin are assembled in the nucleus early after receptor activation by ligands, and gene knockdown experiments showed that gelsolin and the nuclear isoform of myosin 1c are key determinants for assembly and/or stability of these complexes. Based on these results, we propose that the actin network plays a role in nuclear ERα actions in breast cancer cells, including coordinated regulation of target gene activity, spatial and functional reorganization of chromatin, and ribosome biogenesis.

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the discovery of alternative splicing events. Analysis of exon array data is more challenging than the analysis of gene expression data and there is a need for reliable quantification of exons and alternatively spliced variants. We introduce a novel, computationally efficient methodology, Multiple Exon Array Preprocessing (MEAP), for exon array data pre-processing, analysis and visualization. We compared MEAP with existing pre-processing methods, and validation of six exons and two alternatively spliced variants with qPCR corroborated MEAP expression estimates. Analysis of exon array data from head and neck squamous cell carcinoma (HNSCC) cell lines revealed several transcripts associated with 11q13 amplification, which is related with decreased survival and metastasis in HNSCC patients. Our results demonstrate that MEAP produces reliable expression values at exon, alternatively spliced variant and gene levels, which allows generating novel experimentally testable predictions.

Comparative analysis of algorithms for integration of copy number and expression data

Chromosomal instability is a hallmark of cancer, and genes that display abnormal expression in aberrant chromosomal regions are likely to be key players in tumor progression. Identifying such driver genes reliably requires computational methods that can integrate genome-scale data from several sources. We compared the performance of ten algorithms that integrate copy-number and transcriptomics data from 15 head and neck squamous cell carcinoma cell lines, 129 lung squamous cell carcinoma primary tumors and simulated data. Our results revealed clear differences between the methods in terms of sensitivity and specificity as well as in their performance in small and large sample sizes. Results of the comparison are available at http://csbi.ltdk.helsinki.fi/cn2gealgo/.

CADASIL Mutations and shRNA Silencing of NOTCH3 Affect Actin Organization in Cultured Vascular Smooth Muscle Cells

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is the most common hereditary vascular dementia caused by mutations in NOTCH3 gene. Pathology is manifested in small- and middle-sized arteries throughout the body, though primarily in cerebral white matter. Hemodynamics is altered in CADASIL and NOTCH3 is suggested to regulate actin filament polymerization and thereby vascular tone. We analyzed NOTCH3 expression and morphology of actin cytoskeleton in genetically genuine cultured human CADASIL vascular smooth muscle cells (VSMCs) (including a cell line homozygous for p. Arg133Cys mutation) derived from different organs, and in control VSMCs with short hairpin RNA (shRNA)-silenced NOTCH3. NOTCH3 protein level was higher in VSMCs derived from adult than newborn arteries in both CADASIL and control VSMCs. CADASIL VSMCs showed altered actin cytoskeleton including increased branching and node formation, and more numerous and smaller adhesion sites than control VSMCs. Alterations in actin cytoskeleton in shRNA-silenced VSMCs were similar as in CADASIL VSMCs. Severity of the alterations in actin filaments corresponded to NOTCH3 expression level being most severe in VSMCs derived from adult cerebral arteries. These observations suggest that hypomorphic NOTCH3 activity causes alterations in actin organization in CADASIL. Furthermore, arteries from different organs have specific characteristics, which modify the effects of the NOTCH3 mutation and which is one explanation for the exceptional susceptibility of cerebral white matter arteries.

Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers

Differentiated epithelial structure communicates with individual constituent epithelial cells to suppress their proliferation activity. However, the pathways linking epithelial structure to cessation of the cell proliferation machinery or to unscheduled proliferation in the context of tumorigenesis are not well defined. Here we demonstrate the strong impact of compromised epithelial integrity on normal and oncogenic Myc-driven proliferation in three-dimensional mammary epithelial organoid culture. Systematic silencing of 34 human homologs of Drosophila genes, with previously established functions in control of epithelial integrity, demonstrates a role for human genes of apico-basal polarity, Wnt and Hippo pathways and actin dynamics in regulation of the size, integrity and cell proliferation in organoids. Perturbation of these pathways leads to diverse functional interactions with Myc: manifested as a RhoA-dependent synthetic lethality and Par6-dependent effects on the cell cycle. Furthermore, we show a role for Par6G as a negative regulator of the phosphatidylinositol 3′-kinase/phosphoinositide-dependent protein kinase 1/Akt pathway and epithelial cell proliferation and evidence for frequent inactivation of Par6G gene in epithelial cancers. The findings demonstrate that determinants of epithelial structure regulate the cell proliferation activity via conserved and cancer-relevant regulatory circuitries, which are important for epithelial cell cycle restriction and may provide new targets for therapeutic intervention.

Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer

HOXB7 encodes a transcription factor that is overexpressed in a number of cancers and encompasses many oncogenic functions. Previous results have shown it to promote cell proliferation, angiogenesis, epithelial–mesenchymal transition, DNA repair and cell survival. Because of its role in many cancers and tumorigenic processes, HOXB7 has been suggested to be a potential drug target. However, HOXB7 binding sites on chromatin and its targets are poorly known. The aim of our study was to identify HOXB7 binding sites on breast cancer cell chromatin and to delineate direct target genes located nearby these binding sites. We found 1,504 HOXB7 chromatin binding sites in BT‐474 breast cancer cell line that overexpresses HOXB7. Seventeen selected binding sites were validated by ChIP‐qPCR in several breast cancer cell lines. Furthermore, we analyzed expression of a large number of genes located nearby HOXB7 binding sites and found several new direct targets, such as CTNND2 and SCGB1D2. Identification of HOXB7 chromatin binding sites and target genes is essential to understand better the role of HOXB7 in breast cancer and mechanisms by which it regulates tumorigenic processes.

Liprin-α1 is a regulator of vimentin intermediate filament network in the cancer cell adhesion machinery

PPFIA1 is located at the 11q13 region, which is one of the most commonly amplified regions in several epithelial cancers including head and neck squamous cell carcinoma and breast carcinoma. Considering the location of PPFIA1 in this amplicon, we examined whether protein encoded by PPFIA1, liprin-α1, possesses oncogenic properties in relevant carcinoma cell lines. Our results indicate that liprin-α1 localizes to different adhesion and cytoskeletal structures to regulate vimentin intermediate filament network, thereby altering the invasion and growth properties of the cancer cells. In non-invasive cells liprin-α1 promotes expansive growth behavior with limited invasive capacity, whereas in invasive cells liprin-α1 has significant impact on mesenchymal cancer cell invasion in three-dimensional collagen. Current results identify liprin-α1 as a novel regulator of the tumor cell intermediate filaments with differential oncogenic properties in actively proliferating or motile cells.

Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy

There is an unmet need for effective targeted therapies for patients with advanced head and neck squamous cell carcinoma (HNSCC). We correlated gene expression, gene copy numbers, and point mutations in 45 human papillomavirus–negative HNSCC cell lines with the sensitivity to 220 anticancer drugs to discover predictive associations to genetic alterations. The drug response profiles revealed diverse efficacy of the tested drugs across the cell lines. Several genomic abnormalities and gene expression differences were associated with response to mTOR, MEK, and EGFR inhibitors. NOTCH1 and FAT1 were the most commonly mutated genes after TP53 and also showed some association with response to MEK and/or EGFR inhibitors. MYC amplification and FAM83H overexpression associated with sensitivity to EGFR inhibitors, and PTPRD deletion with poor sensitivity to MEK inhibitors. The connection between high FAM83H expression and responsiveness to the EGFR inhibitor erlotinib was validated by gene silencing and from the data set at the Cancer Cell Line Encyclopedia. The data provide several novel genomic alterations that associated to the efficacy of targeted drugs in HNSCC. These findings require further validation in experimental models and clinical series. Mol Cancer Ther; 17(9); 2060–71. ©2018 AACR.

Abstract 4933: Functional properties of PPFIA1, located at the 11q13 amplification region, in epithelial cancer cells.

PPFIA1 (liprin α1) is a member of the liprin (LAR protein-tyrosine phosphatase-interacting protein) family and is located at the 11q13 amplification region, which is one of the most common amplicons in multiple epithelial cancers. In squamous cell carcinoma of head and neck (HNSCC), this amplification occurs in 30-50% of the cases. In epithelial cancers, the size and structure of 11q13 amplicon is complex and consists of multiple amplicon cores that differ between different tumor types. In HNSCC, the amplicon core contains 10 genes that are amplified in cases with 11q13 amplification. This region contains well-established oncogenes, such as CCND1 and CTTN (cortactin), yet the role of several genes in this region is unknown. Our aim is to study the role of PPFIA1, which has recently been found to be involved in cell motility, modeling of the cell edge dynamics and axon guidance. PPFIA1 is amplified and overexpressed in several epithelial cancers, but the role of it is controversial. PPFIA1 is required for breast and cervical cancer cell invasion, but in contrast depletion of it results in increased invasion of HNSCC cells. We have overexpressed liprin α1 and cortactin in HNSCC cells with no 11q13 amplification and related phenotypes have been analysed in in vitro assays. Migration assays using matrigel coated inserts have shown that overexpression of cortactin increases invasive properties of the HNSCC cells with no 11q13 amplicon whereas liprin α1 has an opposite effect. We have also shown that liprin α1 localizes with cortactin in same vesicular structures, but they do not show physical interaction. Our aim is now to explore the molecular mechanisms behind these findings to assess the role of liprin α1 in vesicular transport and cell motility. We are also carrying out immunoprecipitation and mass spectrometry analyses to identify novel interaction partners for this protein. Our study will provide novel information on the potential specialized functions of liprin α1 in different epithelial cancers, which is likely to improve our understanding on the functional role of 11q13 amplification in malignant potential of cancer cells. Citation Format: Henna Pehkonen, Tatiana Lepikhova, Riku Louhimo, Nina Peitsaro, Misa Imai, Rafael Martinez, Juha Kleftsrom, Sampsa Hautaniemi, Outi Monni. Functional properties of PPFIA1, located at the 11q13 amplification region, in epithelial cancer cells. [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 4933. doi:10.1158/1538-7445.AM2013-4933

Abstract 2192: Functional genomic screen to identify candidates capable of modulating invasive properties of HNSCC

Head and neck squamous cell carcinomas (HNSCC) contain a heterogeneous population of cancer cells some of which is explained by ongoing mutations that occur due to genetic instability and environmental factors. Not all of the cancer cells have a similar ability to drive tumor formation. To identify genes capable of modulating invasive properties in head and neck squamous cell carcinoma (HNSCC), we have compared copy number profiles (244K aCGH) of 12 primary and metastatic cancer cell lines obtained from patients with HNSCC of tongue and larynx. A specific pattern of copy number gains and losses was present in each cell line studied. Majority of the changes occurred in both the primary tumor and corresponding metastasis, but some amplifications, such as 10q21.1., 11q22, and 17p12 occurred more frequently in metastatic cancers. To determine whether any genes located at the amplicons input to metastatic potential of HNSCC we are performing a systematic loss-of-function survey. First, we examined the cell growth and invasive properties of primary and metastatic cell lines in vitro and in vivo. We then set up a genetic screen using highly metastatic cell lines in in vitro invasion assay system. pLKO1 shRNA library targeting genes located at identified amplified regions in invasive cells were transduced into the selected cell lines and transduced cell lines were subjected to transwell invasion assay. Several genes targeted for amplification and capable of modulating invasive properties of HNSCC in vitro have been selected for further validation in vivo. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2192.