Multi-omic characterization of ILC and ILC-like cell lines as part of ILC cell line encyclopedia (ICLE) defines new models to study potential biomarkers and explore therapeutic opportunities

Invasive lobular carcinoma (ILC), the most common histological "special type", accounts for ∼10-15% of all BC diagnoses, is characterized by unique features such as E-cadherin loss/deficiency, lower grade, hormone receptor positivity, larger diffuse tumors, and specific metastatic patterns. Despite ILC being acknowledged as a disease with distinct biology that necessitates specialized and precision medicine treatments, the further exploration of its molecular alterations with the goal of discovering new treatments has been hindered due to the scarcity of well-characterized cell line models for studying this disease. To address this, we generated the ILC Cell Line Encyclopedia (ICLE), providing a comprehensive multi-omic characterization of ILC and ILC-like cell lines. Using consensus multi-omic subtyping, we confirmed luminal status of previously established ILC cell lines and uncovered additional ILC/ILC-like cell lines with luminal features for modeling ILC disease. Furthermore, most of these luminal ILC/ILC-like cell lines also showed RNA and copy number similarity to ILC patient tumors. Similarly, ILC/ILC-like cell lines also retained molecular alterations in key ILC genes at similar frequency to both primary and metastatic ILC tumors. Importantly, ILC/ILC-like cell lines recapitulated the CDH1 alteration landscape of ILC patient tumors including enrichment of truncating mutations in and biallelic inactivation of CDH1 gene. Using whole-genome optical mapping, we uncovered novel genomic-rearrangements including novel structural variations in CDH1 and functional gene fusions and characterized breast cancer specific patterns of chromothripsis in chromosomes 8, 11 and 17. In addition, we systematically analyzed aberrant DNAm events and integrative analysis with RNA expression revealed epigenetic activation of TFAP2B - an emerging biomarker of lobular disease that is preferentially expressed in lobular disease. Finally, towards the goal of identifying novel druggable vulnerabilities in ILC, we analyzed publicly available RNAi loss of function breast cancer cell line datasets and revealed numerous putative vulnerabilities cytoskeletal components, focal adhesion and PI3K/AKT pathway in ILC/ILC-like vs NST cell lines. In summary, we addressed the lack of suitable models to study E-cadherin deficient breast cancers by first collecting both established and putative ILC models, then characterizing them comprehensively to show their molecular similarity to patient tumors along with uncovering their novel multi-omic features as well as highlighting putative novel druggable vulnerabilities. Not only we expand the array of suitable E-cadherin deficient cell lines available for modelling human-ILC disease but also employ them for studying epigenetic activation of a putative lobular biomarker as well as identifying potential druggable vulnerabilities for this disease towards enabling precision medicine research for human-ILC.

ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes

Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. Fortunately, identification of mechanisms of therapeutic resistance have rapidly transformed our understanding of cancer evasion and is enabling targeted treatment regimens. When the druggable estrogen receptor (ER, ESR1 ), expressed in two-thirds of all breast cancer, is exposed to endocrine therapy, there is risk of somatic mutation development in approximately 30% of cases and subsequent treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is the expression of ER fusion proteins. ER fusions, which retain the protein's DNA binding domain, harbor ESR1 exons 1-6 fused to an in-frame gene partner resulting in loss of the 3' ER ligand binding domain (LBD). In this report we demonstrate that in no-special type (NST) and invasive lobular carcinoma (ILC) cell line models, ER fusion proteins exhibit robust hyperactivation of canonical ER signaling pathways independent of the ligand estradiol or anti-endocrine therapies such as Fulvestrant and Tamoxifen. We employ cell line models stably overexpressing ER fusion proteins with concurrent endogenous ER knockdown to minimize the influence of endogenous wildtype ER. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably the MYC pathway. The heterogeneous 3' fusion partners, particularly transcription factors SOX9 and YAP1 , evoked varying degrees of transcriptomic and cistromic activity that translated into unique phenotypic readouts. Herein we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that the loss of the LBD, the 3' fusion partner, and the cellular landscape all influence fusion activity. Therefore, it will be critical to generate additional data on frequency of the ER fusions, in the context of the clinicopathological features of the tumor.

Significance

ER fusion proteins exhibit diverse mechanisms of endocrine resistance in breast cancer cell lines representing the no special type (NST) and invasive lobular cancer (ILC) subtypes. Our emphasize upon both the shared and unique cellular adaptations imparted by ER fusions offers the foundation for further translational research and clinical decision making.

WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model

Breast cancer is categorized by the molecular and histologic presentation of the tumor, with the major histologic subtypes being No Special Type (NST) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark pathognomonic loss of E-cadherin ( CDH1 ). Few ILC cell line models are available to researchers. Here we report the successful establishment and characterization of a novel ILC cell line, WCRC-25, from a metastatic pleural effusion from a postmenopausal Caucasian woman with metastatic ILC. WCRC-25 is an ER-negative luminal epithelial ILC cell line with both luminal and Her2-like features. It exhibits anchorage independent growth and haptotactic migration towards Collagen I. Sequencing revealed a CDH1 Q706* truncating mutation, together with mutations in FOXA1, CTCF, BRCA2 and TP53 , which were also seen in a series of metastatic lesions from the patient. Copy number analyses revealed amplification and deletion of genes frequently altered in ILC while optical genome mapping revealed novel structural rearrangements. RNA-seq analysis comparing the primary tumor, metastases and the cell line revealed signatures for cell cycle progression and receptor tyrosine kinase signaling. To assess targetability, we treated WCRC-25 with AZD5363 and Alpelisib confirming WCRC-25 as susceptible to PI3K/AKT signaling inhibition as predicted by our RNA sequencing analysis. In conclusion, we report WCRC-25 as a novel ILC cell line with promise as a valuable research tool to advance our understanding of ILC and its therapeutic vulnerabilities.

Financial support

The work was in part supported by a Susan G Komen Leadership Grant to SO (SAC160073) and NCI R01 CA252378 (SO/AVL). AVL and SO are Komen Scholars, Hillman Foundation Fellows and supported by BCRF. This project used the UPMC Hillman Cancer Center and Tissue and Research Pathology/Pitt Biospecimen Core shared resource which is supported in part by award P30CA047904. This research was also supported in part by the University of Pittsburgh Center for Research Computing, RRID:SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, which is supported by NIH award number S10OD028483. Finally, partial support was provided by the Magee-Womens Research Institute and Foundation, The Shear Family Foundation, and The Metastatic Breast Cancer Network.

FOXA1 Reprogramming Dictates Retinoid X Receptor Response in ESR1-Mutant Breast Cancer

Estrogen receptor alpha (ER/ESR1) mutations occur in 30% to 40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1-mutant breast cancer remains unclear. Our previous FOXA1 chromatin immunoprecipitation sequencing (ChIP-seq) identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1-mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome, and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1-mutant cells, FOXA1-binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1-binding sites of ESR1-mutant cells. Consistently, ESR1-mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor (TR) also showed a similar growth-promoting effect in ESR1-mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1-mutant cells and a patient-derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support the evidence for a stronger RXR response associated with FOXA1 reprograming in ESR1-mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation.

IMPLICATIONS

It provides comprehensive characterization of the role of FOXA1 in ESR1-mutant breast cancer and potential therapeutic strategy through blocking RXR activation.

RET signaling in breast cancer therapeutic resistance and metastasis

RET, a single-pass receptor tyrosine kinase encoded on human chromosome 10, is well known to the field of developmental biology for its role in the ontogenesis of the central and enteric nervous systems and the kidney. In adults, RET alterations have been characterized as drivers of non-small cell lung cancer and multiple neuroendocrine neoplasms. In breast cancer, RET signaling networks have been shown to influence diverse functions including tumor development, metastasis, and therapeutic resistance. While RET is known to drive the development and progression of multiple solid tumors, therapeutic agents selectively targeting RET are relatively new, though multiple multi-kinase inhibitors have shown promise as RET inhibitors in the past; further, RET has been historically neglected as a potential therapeutic co-target in endocrine-refractory breast cancers despite mounting evidence for a key pathologic role and repeated description of a bi-directional relationship with the estrogen receptor, the principal driver of most breast tumors. Additionally, the recent discovery of RET enrichment in breast cancer brain metastases suggests a role for RET inhibition specific to advanced disease. This review assesses the status of research on RET in breast cancer and evaluates the therapeutic potential of RET-selective kinase inhibitors across major breast cancer subtypes.

Abstract P3-08-10: Combining multiomics and histological assessment to identify patient derived xenograft models of invasive lobular carcinoma

Background Most breast cancers (~85%) are of no special histologic subtype (NST), and the most common special subtype is invasive lobular cancer (ILC). ILC accounts for 10-15% of all breast cancers, and there will be ~40,000 new cases in 2022 in the US alone. If considered an “independent” cancer type, ILC is the 6th most common cancer in women. The pathognomonic feature of ILC is loss of E-cadherin (CDH1). The resulting lack of adherens junctions causes the unique single-file growth pattern of discohesive ILC cells, which decreases the ability for detection by mammography, in turn resulting in late detection and hence larger tumors. Although ILCs show better prognostic factors than NST, patients with ILC have worse long-term outcome, which is not well understood. Additionally, ILC has historically been understudied, which is in part due to lack of appropriate research models. For example, the Cancer Cell Line Encyclopedia (CCLE) contains 54 NST cell lines but only 2 ILC cell lines, and only a limited number of patient-derived xenograft (PDX) models are evident in the published literature. There is a critical need for additional in vitro and in vivo models to study ILC biology, as well as to test targeted therapies. ILC PDX and patient derived xenograft organoids (PDXO) are particularly valuable tools to enable target validation and assess drug treatment response. Methods To identify and validate new ILC PDX models, we used Champions Oncology’s Lumin Bioinformatics to screen Champions’ collection of breast cancer models (n=126) for PDX harboring CDH1 mutation and/or low E-cadherin expression. We performed histological analysis on selected PDX models including H&E staining, and immunohistochemical assessment of E-cadherin, P120, estrogen receptor, progesterone receptor, HER2 and Ki67. Models with 2+ HER2 staining were assessed by FISH. All staining was interpreted by a certified breast pathologist. PDX tumor tissue was further used to develop PDXO models. Results Using Champions Oncology’s Lumin tool, we identified 10 putative ILC PDX models based upon CDH1 mutation, low E-cadherin mRNA expression, or clinical annotation of ILC (Table 1). Of the 10 PDX models analyzed, two cases were clinically annotated as ILC, while the remainder were classified as ‘carcinoma’ (n=5) or as NST (n=3). Histologic analysis revealed loss of E-cadherin and cytoplasmic P120 (lobular pattern) in 8/10 models assessed, and pathologic assessment confirmed these as having a lobular histology. IHC analysis classified these PDXs as 5 TNBC and 5 ER+ tumors, with none showing amplification of HER2 by FISH. All tumors demonstrated high (35%, n=1) or very high (>55%, n=9) Ki67 proliferation marker levels. We further developed PDXOs from one PDX model as proof of concept, and the resulting organoid demonstrated classic ‘grape-like’ ILC morphology. Conclusion Our study demonstrates how existing PDX banks with in-depth multi-omic and pathology analyses can be interrogated to identify models of unique histological and molecular subtypes of breast cancer. Of the PDX models selected from Champions Oncology’s breast cancer cohort, 7 models were classified as ILC either through re-classification from NST/carcinoma to ILC or confirmation of ILC histology. In addition, 1 PDX was re-classified as mixed type. Some of these models are ER+/HER- and thus have the classic molecular features of ILC. Our collaborative omics guided approach allows for reclassification of PDX models to increase available research models for unique breast cancer subtypes such as ILC which in turn will enhance translational research in unique histological subtypes of breast cancer.

Citation Format: Jennifer M. Atkinson, Megan Yates, Daniel D. Brown, Jagmohan Hooda, Rohit Bhargava, Paolo Schiavini, Marianna Zipeto, Steffi Oesterreich, ADRIAN V. LEE. Combining multiomics and histological assessment to identify patient derived xenograft models of invasive lobular carcinoma [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-08-10.

Abstract PD10-02: PD10-02 Novel ER fusion detection method to gain insight in fusion prevalence and endocrine resistant mechanisms

Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. The druggable estrogen receptor (ER, ESR1), overexpressed in two-thirds of all breast cancer, evolves in 30% of tumors exposed to endocrine therapy consequently resulting in treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is ER fusion proteins. ER fusions, found predominately in metastatic endocrine resistant disease, harbor ESR1 exons 1-6 fused to an in-frame gene partner due to an ESR1 intron 6 translocation break. Our lab has demonstrated that ER fusion proteins, which lack the C-terminal ligand-binding domain (LBD), recapitulate phenotypes of ER proteins harboring endocrine-resistant point mutations occurring in the LBD. Our research goals aim to 1) determine fusion prevalence and emergence, 2) understand fusion mechanisms of resistance and 3) explore alternative treatment options for our patients. The promiscuous nature of fusion partners hinders fusion detection by traditional sequencing and thus our research team has developed a novel ER fusion detection method, EnRich. The EnRich probe set (4,324 probes in total) is composed of two separate probe pools targeting at 2x tiling intronic and exonic ESR1, the upstream promoter region and select oncogenic genes. To optimize the EnRich pipeline, DNA was extracted from a frozen tumor sample and a PDX model harboring ESR1-DAB2 and ESR1-LPP fusions, respectively. ESR1-DAB2 and ESR1-LPP were accurately detected by quantifying discordant paired-end or split reads mapped to chromosome 6. In addition, liquid biopsies from 15 patients with ER positive advanced breast cancer were also assessed through EnRich to uncover unidentified ESR1 structural variants. Two patient samples were detected to harbor ESR1 fusions (ESR1-CCDC170, ESR1-AKAP12 and ESR1-YAP1) and were further validated in corresponding mRNA. These recurrent and novel fusions were supported with more than 10 reads each, indicating that the EnRich pipeline is an effective and accurate sequencing approach to understanding ER fusion prevalence. Our lab, furthermore, has studied ER fusion proteins mechanistically. We have stably overexpressed ER fusions in transgenic breast cancer cell lines engineered with shRNA targeting the endogenous wildtype ER (ESR1-WT). In this ESR1-WT depleted cellular context, we found that ER fusions (notably ESR1-SOX9 and ESR1-YAP1) demonstrate ER hyperactivation through an estrogen response element (ERE) assay compared to ESR1-WT and a truncated exon 1-6 ESR1 (ESR1∆CTD). Importantly, fusion ERE activity was robust in the absence of the ER ligand, estradiol, as well as in the presence of endocrine therapies, implying ER fusion proteins function in a ligand independent, endocrine resistant mechanism. ER fusion positive cell lines were also enriched in oncogenic phenotypes such as enhanced 3D growth, cell survival via colony formation, and migration in a wound scratch assay. These enhanced metastatic potentials of the ER fusions were observed in both invasive ductal and lobular carcinoma cell lines, albeit at varying magnitudes depending on the 3’ fusion partner and phenotype being assessed. Although the ER fusions harbored unique characteristics due to the C-terminal partner, transcriptomic profiling revealed that enhanced EMT and KRAS signaling signatures were shared among all fusions when compared to the ESR1-WT and ESR1∆CTD cell lines, which may serve as future exploitable drug targets. Comprehensive detection and functional evaluation of ER fusion proteins will provide clinicians and patients with better understanding of tumor endocrine-resistant prevalence and discovery of more effective treatment options.

Citation Format: Megan E. Yates, Tiantong Liu, Jagmohan Hooda, Sichun Yang, Riyue Bao, Jennifer M. Atkinson, ADRIAN V. LEE, Steffi Oesterreich. PD10-02 Novel ER fusion detection method to gain insight in fusion prevalence and endocrine resistant mechanisms [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-02.

Loss of E-cadherin Induces IGF1R Activation and Reveals a Targetable Pathway in Invasive Lobular Breast Carcinoma

No special-type breast cancer [NST; commonly known as invasive ductal carcinoma (IDC)] and invasive lobular carcinoma (ILC) are the two major histological subtypes of breast cancer with significant differences in clinicopathological and molecular characteristics. The defining pathognomonic feature of ILC is loss of cellular adhesion protein, E-cadherin (CDH1). We have previously shown that E-cadherin functions as a negative regulator of the IGF1R and propose that E-cadherin loss in ILC sensitizes cells to growth factor signaling that thus alters their sensitivity to growth factor-signaling inhibitors and their downstream activators. To investigate this potential therapeutic vulnerability, we generated CRISPR-mediated CDH1 knockout (CDH1 KO) IDC cell lines (MCF7, T47D, and ZR75.1) to uncover the mechanism by which loss of E-cadherin results in IGF pathway activation. CDH1 KO cells demonstrated enhanced invasion and migration that was further elevated in response to IGF1, serum and collagen I. CDH1 KO cells exhibited increased sensitivity to IGF resulting in elevated downstream signaling. Despite minimal differences in membranous IGF1R levels between wild-type (WT) and CDH1 KO cells, significantly higher ligand-receptor interaction was observed in the CDH1 KO cells, potentially conferring enhanced downstream signaling activation. Critically, increased sensitivity to IGF1R, PI3K, Akt, and MEK inhibitors was observed in CDH1 KO cells and ILC patient-derived organoids.

IMPLICATIONS

Overall, this suggests that these targets require further exploration in ILC treatment and that CDH1 loss may be exploited as a biomarker of response for patient stratification.

Abstract 881: Functional characterization and clinical prevalence of ESR1 fusions in advanced endocrine resistant breast cancer

Breast cancer is the most frequently diagnosed women’s cancer with one in eight women being diagnosed during her lifetime. Even within the era of novel therapeutics and improved diagnostic screening, mortality rates remain stable, with an estimated 43,600 deaths occurring in 2021 alone. Malignant transformation of breast cancer to advanced disease is the mainstay driver of mortality and is largely attributed to treatment resistance. Fortunately, identification of therapeutic resistance mechanisms has rapidly transformed our understanding of cancer evasion and is enabling personalized treatment guidance and regimens. Notably, mutations and amplifications of the estrogen receptor (ER, ESR1) remain a prominent source of endocrine therapy resistance. Two-thirds of all breast cancer are positive for ER, making it an attractive druggable target that has revolutionized patient care. Unfortunately, however, 30% of tumors exposed to endocrine therapy subsequently develop resistance. Recently identified ER fusion proteins, discovered in metastatic endocrine resistant disease, result in substitution of the C-terminal ER ligand binding domain with a variety of fused in-frame gene partners due to genomic translocations occurring at ESR1 intron 6. Our lab has demonstrated that ER fusion proteins drive robust ER hyperactivation and metastatic potential independent of ER ligand estradiol and in the presence of endocrine therapies such as Fulvestrant. Overexpression of ER fusion proteins, particularly ESR1-SOX9 and ESR1-YAP1, in invasive ductal and invasive lobular carcinoma models with endogenous ER knockdown, resulted in enhanced 3D growth, increased migration by wound scratch assay, enhanced colony formation as a proxy of survival and ER pathway hyperactivation. Targeted endogenous ER knockdown utilizing short hairpin RNA enhances fusion driven phenotypes that are unique to fusion partner proteins and cellular context. ER fusion prevalence in advanced breast cancer remains a challenge due to the promiscuous fusion partners disrupting traditional sequencing techniques. Our group has developed a novel method of ESR1 fusion detection, EnRich, which exploits the ESR1 fusion breakpoints. Importantly, we have assessed EnRich fusion discovery with the use of circulating tumor DNA (ctDNA) from non-invasive liquid biopsies. Our pilot study of 15 blood ctDNA samples detected three different ESR1 fusion gene products which have been further validated by PCR. EnRich will help us identify and monitor treatment resistance of known and novel ESR1 fusions in patient samples irrespective of treatment regime as well as in longitudinal samples collected from patients undergoing endocrine therapy. The in vitro resistant properties of fusion proteins emphasize the necessity to better detect these mutations in patients with advanced disease and determine more appropriate treatment measures.

Citation Format: Megan E. Yates, Tiantong Liu, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Functional characterization and clinical prevalence of ESR1 fusions in advanced endocrine resistant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 881.

Abstract 2690: Loss of E-cadherin induces IGF1R activation revealing a targetable pathway in invasive lobular breast carcinoma

Invasive Ductal Carcinoma (IDC) and Invasive Lobular Carcinoma (ILC) are two major subtypes of breast cancer with significant differences in their histological and molecular underpinnings. ILC has a unique loss of E-cadherin (CDH1) which we have previously demonstrated as a negative regulator of the Insulin-like Growth Factor 1 receptor (IGF1R) through a comprehensive analysis of cell line models and tumor samples. We propose that loss of E-cadherin in ILC sensitizes cells to growth factor signaling and thus alters their sensitivity to growth factor signaling inhibitors. To investigate this, we used CRISPR to generate CDH1 knockout (KO) IDC cell lines (MCF7, T47D, ZR75.1) to uncover the mechanism by which E-cadherin loss activates the IGF pathway while also assessing its targetability. CDH1 KO cells exhibited anchorage independent growth in suspension culture and altered p120 catenin localization as observed in ILC tumors. Through in vitro studies, we show increased signaling sensitivity to IGF/insulin ligands and enhanced signaling duration in CDH1 KO cells. In addition, we observed a higher migratory potential of CDH1 KO cells compared to wild type (WT) cells, which was further enhanced as a chemotactic response to IGF1 or serum. Further, this phenotype could be reversed with an IGF1R inhibitor, BMS-754807. We additionally identified an increase in Collagen I haptotaxis in the CDH1 KO cells, which was also translated into a novel invasive phenotype towards serum in the T47D CDH1 KO cells. Despite no significant differences in membranous IGF1R levels between WT and CDH1 KO cells, higher ligand-receptor interaction was observed with CDH1 KO cells, demonstrating an increased ligand-receptor complex formation upon stimulation. Our results suggest that loss of CDH1 results in an increase in IGF1 receptor availability for ligand binding which in turn allows for an enhanced downstream signaling activation. Interestingly, a physical repression of E-cadherin on IGF1R could not be demonstrated, suggesting spatial changes on the membrane following E-cadherin loss may control ligand binding. Critically, increased sensitivity to IGF1R, PI3K, AKT and MEK inhibitors was observed in CDH1 KO cells suggesting that these targets should be further explored in ILC and that CDH1 loss may be exploited as a biomarker of response, or for patient stratification to inhibitors targeting these pathways.

Citation Format: Ashuvinee Elangovan, Laura Savariau, Megan E. Yates, Jagmohan Hooda, Alison M. Nagle, Steffi Oesterreich, Jennifer M. Atkinson, Adrian V. Lee. Loss of E-cadherin induces IGF1R activation revealing a targetable pathway in invasive lobular breast carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2690.

Abstract 956: Role of E-cadherin in progression of invasive breast lobular carcinoma

Invasive lobular carcinoma (ILC) is the second most frequently diagnosed histologic subtype of invasive breast cancer following invasive ductal carcinoma (IDC) and accounts for 15% of all cases. The hallmark of ILC is the genetic loss of E-cadherin (CDH1) causing the disruption of adherens junctions and resulting in discohesive, linear growth of ILC cells in tissues. Beyond its effects on this unique histology, there is limited data on the role of E-cadherin loss in ILC metastasis. Therefore, we generated three ILC cell lines (MDA-MB-134, SUM44PE and BCK4) with inducible E-cadherin overexpression. Using immunoblotting and immunofluorescence microscopy we confirmed E-cadherin expression, re-expression of other adherens junction proteins including α and β-catenin, and re-localization of cytoplasmic p120-catenin to the membrane. Successful cell adhesion to E-cadherin coated plates suggested formation of functional junctions. E-cadherin expression had no effect on 2D growth but did diminish cell growth in ultra-low attachment (ULA) conditions consistent with its previously described role in anoikis. We confirmed increased cell death of MM134 with E-cadherin overexpression compared to control cells when grown in ULA. Overexpression of E-cadherin failed to rescue poor migratory and invasive ability of ILC cell lines as measured by transwell assays. However, E-cadherin expression in SUM44PE lead to decreased haptotaxis to collagen I, and altered morphology from loose grape-like structure to tight sphere-like formation when embedded in collagen I.In vivo analyses revealed reduced primary tumor formation in E-cadherin-overexpression SUM44PE cells after mammary fat pad injection. Additional studies aimed at understanding E-cadherin’s effect on in vivo metastasis are ongoing.Collectively, our studies using novel cell line models will lead to an improved understanding of the hallmark loss of E-cadherin and disease mechanisms in ILC, which we hope will ultimately enable the development of more effective therapies and improve the outcome of patients with this understudied histological subtype of breast cancer.

Citation Format: Laura Savariau, Nilgun Tasdemir, Ashuvinee Elangovan, Kai Ding, Pooja Sree Tallapaneni, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Role of E-cadherin in progression of invasive breast lobular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 956.

Abstract 2864: RET as a novel therapeutic target in breast cancer brain metastases

Brain metastases (BrM) are reported in approximately 10-30% of breast cancer patients with a poor median overall survival of 8.5 months. Current therapeutic strategies are mostly limited to surgery, chemotherapy and radiotherapy, making the study of novel druggable targets and brain-permeable small molecule inhibitors an urgent clinical need.

Our lab recently reported a hybrid-capture exome RNA-sequencing study on 21 patient-matched pairs of primary breast tumors and brain metastases and identified upregulation of several receptor tyrosine kinases including RET in BrM. The ligand for RET is Glial Cell Derived Neurotrophic Factor (GDNF), which is released by astrocytes and microglia in response to neuroinflammation and brain tissue damage. Clinical BrM cell growth in ex vivo cultures was reduced by the multikinase inhibitor Cabozantinib, indicating a potential role for RET in the growth of BrM lesions. We hypothesize that the high level of brain-derived GDNF provides a permissive microenvironment for RET overexpressing breast cancer cells to form brain metastases, and will evaluate the therapeutic potential of RET targeted therapies for breast cancer BrM patients.

Our preliminary data show that in RET-overexpressing (RET-OE) breast cancer cell models, 30-minute GDNF treatment induces RET phosphorylation at two distinct tyrosine residues, along with downstream signaling illustrated by ERK1/2, AKT, and STAT3 phosphorylation. This induction was effectively abrogated after shRNA-mediated RET knockdown. We employed a phospho-kinase array to identify novel downstream targets regulated by the GDNF-RET signaling axis, and found that GDNF induces phosphorylation of multiple targets (including p27 and RSK) in RET-OE cells. Interestingly, phosphorylation of multiple Src family kinases (Lck, Lyn, Fgr) was downregulated with GDNF treatment. We will further examine these downstream targets via reverse phase protein array (RPPA).

GDNF triggers migration of RET-OE cell lines in both 2D wound scratch and 3D transwell migration assays. Additionally, we present results obtained through an ex vivo organotypic coculture system, in which RET-OE cells are cultured on top of 300-micron thick murine brain, kidney, or liver slices. RET overexpression increases colony formation compared with empty vector control, suggesting a role for RET signaling in the initial establishment of metastatic brain lesions. Differences in colonization between empty vector transfected and RET-OE cells remain minimal in kidney and liver sections, suggesting a role for RET specific to the brain microenvironment.

We will examine RET-driven brain metastasis in vivo by employing RET-OE and RET-deficient cell lines in intracranial, intracardiac, and mammary fat pad injection. These models of BrM will be randomized to RET inhibitor or vehicle treatment to evaluate the efficacy of RET-targeted therapy in the setting of breast cancer brain metastasis.

Citation Format: Simeng Liu, Geoffrey Pecar, Jagmohan Hooda, Jennifer M. Atkinson, Fangyuan Chen, Adrian V. Lee, Steffi Oesterreich. RET as a novel therapeutic target in breast cancer brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2864.

Exosomes in Breast Cancer - Mechanisms of Action and Clinical Potential

Extracellular vesicles (EV) are a heterogeneous group of cell-derived membrane vesicles comprising apoptotic bodies, microvesicles, and small EVs also called as exosomes. Exosomes when initially identified were considered as a waste product but the advancement in research techniques have provided insight into the important roles of exosomes in cell-cell communication, various biological processes and diseases, including cancer. As an important component of EVs, exosomes contain various biomolecules such as miRNAs, lipids, and proteins that largely reflect the characteristics of their parent cells. Notably, cancer cells generate and secrete many more exosomes than normal cells. A growing body of evidence suggests that exosomes, as mediators of intercellular cross-talk, play a role in tumorigenesis, cancer cell invasion, angiogenesis, tumor microenvironment (TME) formation, and cancer metastasis. As we gain more insights into the association between exosomes and cancer, the potential of exosomes for clinical use is becoming more intriguing. This review is focused on the role of exosomes in breast cancer, in terms of breast cancer biology, mechanism of action, potential as biomarkers, and therapeutic opportunities.

Abstract LB-002: ER alpha-positive human cell line xenograft models recapitulate metastatic dissemination and endocrine response of invasive lobular breast carcinoma

Invasive lobular breast carcinoma (ILC) is the most common special histological subtype of breast cancer, accounting for 10-15% of all cases, and characterized by the loss of adherens junctions through inactivating mutations in E-cadherin. Although currently existing genetically engineered mouse models of ILC faithfully capture its dyscohesive, single-file growth and expression of estrogen receptor alpha (ER), they do not fully recapitulate all aspects of human ILC such as unique sites of metastases and endocrine response. While recent work on human ILC cell lines has proven them useful for studying ILC in vitro, there is limited data on their growth as xenografts in mice and their fidelity as in vivo models. Using dual bioluminescent and fluorescent labeled ER-positive human ILC cell lines (MDA-MB-134, SUM44PE, MDA-MB-330, BCK4), herein we characterized their growth orthotopically and at secondary sites following spontaneous or experimental metastasis. Mammary fat pad xenografts gave rise to primary tumors with single-file infiltration and cytoplasmic translocation of p120-catenin, characteristic of human ILC. The tumor microenvironment exhibited deposition of collagen fibers and infiltration by fibroblasts and neutrophils. In this orthotopic model, we observed spontaneous metastases of most cell lines to bones, brain and ovaries, closely mirroring the clinical patterns of human ILC dissemination. In contrast, experimental metastases were only observed following intravenous or intracardiac xenografts of MDA-MB-134 cells. Interestingly, tail vein injections of this cell line lead to colonization of bones and lymph nodes but not of lungs, while intracardiac injections resulted in brain, bone and lymph node metastases. Importantly, we observed high ER expression in the primary tumors and the metastatic lesions, along with a significant response to the selective ER down-regulator fulvestrant in both the mammary fat pad and intracardiac models. Ongoing work focused on genomic and transcriptional analyses of primary tumors and metastases, as well as of cell lines isolated from these lesions, will reveal additional mechanistic insights into the biology of ILC dissemination. This is the first report of ER-positive and endocrine responsive human cell line xenografts faithfully representing unique ILC features such as ovarian metastases. These versatile models will serve as an invaluable pre-clinical platform for validating candidate ILC genetic drivers and testing novel therapeutics towards translation into the clinic.

Citation Format: Nilgun Tasdemir, Laura Savariau, Julie Scott, Joseph D. Latoche, Weizhou Hou, Kyle Biery, Minji Chung, Emily A. Bossart, Sreeja Sreekumar, Daniel D. Brown, Azadeh Nasrazadani, Ye Qin, Jagmohan Hooda, Fangyuan Chen, Carlos A. Castro, Carolyn J. Anderson, Jennifer Atkinson, Peter C. Lucas, Nancy E. Davison, Adrian V. Lee, Steffi Oesterreich. ER alpha-positive human cell line xenograft models recapitulate metastatic dissemination and endocrine response of invasive lobular breast carcinoma [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 LB-002.

Abstract B58: Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA

Background: Estrogen receptor-positive (ER+) breast cancer is often intractable due to endocrine therapy resistance. Although ER basepair hotspot mutations have been well characterized in ~20-30% of endocrine-resistant disease, accumulating evidence from our group and others suggests that other genetic alterations such as ER fusions (e.g., ESR1-DAB2) could also play a role. As an important component of liquid biopsies, exosomes have recently gained much attention in the field of clinical oncology. It is well established that some species of RNA, typically microRNA and mRNA, are packaged into these small membrane-enclosed structures, which could potentially serve as a noninvasive biomarker to constantly and comprehensively monitor tumor progression and tumor cell evolution. We tested whether ESR1 fusions could be detected in exosomal RNA (exoRNA) produced by breast cancer cell lines.

Methods: Multiple methods were used to characterize exosomes isolated from cell culture media: 1) Nanoparticle tracking analysis (NTA) confirmed concentration and size of exosomes, 2) immunoblotting identified protein markers that are enriched or lacking in exosomes, 3) transmission electron microscopy validated the size and shape of exosomes. During exoRNA extraction, DNA contamination was removed by DNase treatment. Fusion-specific regions in exoRNA were amplified by standard PCR.

Results: We used breast cancer cell lines stably infected with cDNA encoding ESR1 fusions ESR1-DAB2 and ESR1-SOX9. NTA shows that our isolated exosomes had a size ranging from 30-150 nm, with the peak at 80 nm. Immunoblotting showed TSG101 and CD81 as positive markers of our exosomes, while Grp94 was negative. By RT-PCR, we identified a fusion-specific region amplified for both ESR1-SOX9 and ESR1-LPP from exoRNA for the fusion cell lines.

Conclusions: Collectively, these data indicate that multiple ESR1 fusions are detectable in breast cancer cell line-derived exoRNA.

Citation Format: Tiantong Liu, Jagmohan Hooda, Nils Ludwig, Theresa Whiteside, Jennifer M. Atkinson, Steffi Oesterreich, Adrian Lee. Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B58.

Early Loss of Histone H2B Monoubiquitylation Alters Chromatin Accessibility and Activates Key Immune Pathways That Facilitate Progression of Ovarian Cancer

Recent insights supporting the fallopian tube epithelium (FTE) and serous tubal intraepithelial carcinomas (STIC) as the tissue of origin and the precursor lesion, respectively, for the majority of high-grade serous ovarian carcinomas (HGSOC) provide the necessary context to study the mechanisms that drive the development and progression of HGSOC. Here, we investigate the role of the E3 ubiquitin ligase RNF20 and histone H2B monoubiquitylation (H2Bub1) in serous tumorigenesis and report that heterozygous loss of RNF20 defines the majority of HGSOC tumors. At the protein level, H2Bub1 was lost or downregulated in a large proportion of STIC and invasive HGSOC tumors, implicating RNF20/H2Bub1 loss as an early event in the development of serous ovarian carcinoma. Knockdown of RNF20, with concomitant loss of H2Bub1, was sufficient to enhance cell migration and clonogenic growth of FTE cells. To investigate the mechanisms underlying these effects, we performed ATAC-seq and RNA-seq in RNF20 knockdown FTE cell lines. Loss of RNF20 and H2Bub1 was associated with a more open chromatin conformation, leading to upregulation of immune signaling pathways, including IL6. IL6 was one of the key cytokines significantly upregulated in RNF20- and H2Bub1-depleted FTE cells and imparted upon these cells an enhanced migratory phenotype. These studies provide mechanistic insight into the observed oncogenic phenotypes triggered by the early loss of H2Bub1. SIGNIFICANCE: Loss of RNF20 and H2Bub1 contributes to transformation of the fallopian tube epithelium and plays a role in the initiation and progression of high-grade serous ovarian cancer.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/4/760/F1.large.jpg.

Primordial germ cells as a potential shared cell of origin for mucinous cystic neoplasms of the pancreas and mucinous ovarian tumors

Mucinous ovarian tumors (MOTs) morphologically and epidemiologically resemble mucinous cystic neoplasms (MCNs) of the pancreas, sharing a similar stroma and both occurring disproportionately among young females. Additionally, MOTs and MCNs share similar clinical characteristics and immunohistochemical phenotypes. Exome sequencing has revealed frequent recurrent mutations in KRAS and RNF43 in both MOTs and MCNs. The cell of origin for these tumors remains unclear, but MOTs sometimes arise in the context of mature cystic teratomas and other primordial germ cell (PGC) tumors. We undertook the present study to investigate whether non-teratoma-associated MOTs and MCNs share a common cell of origin. Comparisons of the gene expression profiles of MOTs [including both the mucinous borderline ovarian tumors (MBOTs) and invasive mucinous ovarian carcinomas (MOCs)], high-grade serous ovarian carcinomas, ovarian surface epithelium, Fallopian tube epithelium, normal pancreatic tissue, pancreatic duct adenocarcinomas, MCNs, and single-cell RNA-sequencing of PGCs revealed that both MOTs and MCNs are more closely related to PGCs than to either eutopic epithelial tumors or normal epithelia. We hypothesize that MCNs may arise from PGCs that stopped in the dorsal pancreas during their descent to the gonads during early human embryogenesis, while MOTs arise from PGCs in the ovary. Together, these data suggest a common pathway for the development of MCNs and MOTs, and suggest that these tumors may be more properly classified as germ cell tumor variants. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Abstract B44: Early loss of monoubiquitylation of H2B alters key metabolic and immune signaling pathways promoting the progression of high-grade serous ovarian cancer

High-grade serous ovarian carcinoma (HGSOC) is the most common form of ovarian cancer, accounting for over 70% of all cases. HGSOC is frequently complicated by the inevitable development of therapeutic resistance, and thus remains an incurable disease. Recent insights supporting the fallopian tube epithelium (FTE) as a point of origin for HGSOC and the serous tubal intraepithelial carcinoma (STIC) as the precursor lesion for a majority of HGSOCs provide the necessary context to study the mechanisms that drive the development and progression of HGSOC. Understanding these key molecular processes is essential to inform the development of next-generation therapies. In this study we investigated the role of the ubiquitin ligase RNF20 and histone H2B monoubiquitylation (H2Bub1) in serous tumorigenesis. H2Bub1, catalyzed largely by RNF20, is an epigenetic mark with tumor-suppressor properties. The loss of RNF20/H2Bub1 has been linked with cancer progression. We used immunohistochemistry to characterize the expression of H2Bub1 in HGSOC and FTE precursors. We found that H2Bub1 is lost or downregulated in a large proportion of STICs and HGSOC tumors, implicating RNF20/H2Bub1 loss as an early event in serous tumorigenesis. Consistent with our findings, analysis of TCGA data shows that the majority of HGSOCs exhibit heterozygous loss of RNF20. Functionally, we demonstrated that shRNA-mediated knockdown of RNF20, with concomitant loss of H2Bub1, was sufficient to increase cell migration and clonogenic growth of immortalized FTE cells. To understand the mechanisms underlying these effects, we performed RNA-seq and proteomics profiling (RPPA) in RNF20 knockdown cells. Major changes were observed in a number of structural, metabolic (e.g., glutamine pathway), and cytokines and inflammatory signaling pathways, providing early mechanistic insights for the observed oncogenic phenotypes. In summary, our study identifies that loss of H2Bub1 is an early epigenetic event in HGSOC that rewires glutamine metabolism and certain inflammatory pathways, which may represent unique therapeutic opportunities.

Citation Format: Jagmohan Hooda, Marian Novak, Emily MacDuffie, Melissa Song, Jenny Lester, Vinita Parkash, Gordon B. Mills, Beth Y. Karlan, Moshe Oren, Ronny Drapkin. Early loss of monoubiquitylation of H2B alters key metabolic and immune signaling pathways promoting the progression of high-grade serous ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B44.

Abstract 209: The effect of heme influx on initiation and tumorigenesis of NSCLC

Heme is a central molecule for mitochondrial function and for all processes involved in oxygen utilization. Heme serves as a prosthetic group or as a cofactor for a number of oxidative phosphorylation enzymes and other oxygen-utilizing hemoproteins. Heme also directly regulates the synthesis, translocation and assembly of these enzyme complexes. Most, if not all, human cells can synthesize and uptake heme from the circulation. A number of epidemiological studies have shown that high heme intake is associated with increased risk of cancer, including lung cancer. Recent studies carried out in our lab showed intensified mitochondrial respiration and increased levels of heme and hemoproteins in non-small-cell lung cancer (NSCLC) cells. Together, these experimental and epidemiological studies strongly suggest that heme is an “oncometabolite.” To assess the status of heme metabolism in cancer cells, we performed a series of experiments in NSCLC cells and compared the results with an immortalized normal lung cell line, HBEC30KT. We used Zinc protoporphyrin, an analogue of heme to measure the level of heme uptake. We found that heme uptake as well as heme synthesis are significantly elevated in all NSCLC cells compared to HBEC. The rate of heme degradation was also measured in these cell lines. Previously, our lab demonstrated that lowering intracellular heme levels selectively decreases oxygen consumption in NSCLC cells and inhibits cell migration and colony formation. Experiments are underway to test ways to alter intracellular heme availability and characterize their effects on NSCLC tumor growth and metastasis.

Citation Format: Sagar Sohoni, Md Maksudul Alam, Chantal Vidal, Jagmohan Hooda, Li Zhang. The effect of heme influx on initiation and tumorigenesis of NSCLC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 209.

Measurement of Heme Synthesis Levels in Mammalian Cells

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in various molecular and cellular processes such as gene transcription, translation, cell differentiation and cell proliferation. The biosynthesis levels of heme vary across different tissues and cell types and is altered in diseased conditions such as anemia, neuropathy and cancer. This technique uses [4-(14)C] 5-aminolevulinic acid ([(14)C] 5-ALA), one of the early precursors in the heme biosynthesis pathway to measure the levels of heme synthesis in mammalian cells. This assay involves incubation of cells with [(14)C] 5-ALA followed by extraction of heme and measurement of the radioactivity incorporated into heme. This procedure is accurate and quick. This method measures the relative levels of heme biosynthesis rather than the total heme content. To demonstrate the use of this technique the levels of heme biosynthesis were measured in several mammalian cell lines.

Enhanced heme function and mitochondrial respiration promote the progression of lung cancer cells

Lung cancer is the leading cause of cancer-related mortality, and about 85% of the cases are non-small-cell lung cancer (NSCLC). Importantly, recent advance in cancer research suggests that altering cancer cell bioenergetics can provide an effective way to target such advanced cancer cells that have acquired mutations in multiple cellular regulators. This study aims to identify bioenergetic alterations in lung cancer cells by directly measuring and comparing key metabolic activities in a pair of cell lines representing normal and NSCLC cells developed from the same patient. We found that the rates of oxygen consumption and heme biosynthesis were intensified in NSCLC cells. Additionally, the NSCLC cells exhibited substantially increased levels in an array of proteins promoting heme synthesis, uptake and function. These proteins include the rate-limiting heme biosynthetic enzyme ALAS, transporter proteins HRG1 and HCP1 that are involved in heme uptake, and various types of oxygen-utilizing hemoproteins such as cytoglobin and cytochromes. Several types of human tumor xenografts also displayed increased levels of such proteins. Furthermore, we found that lowering heme biosynthesis and uptake, like lowering mitochondrial respiration, effectively reduced oxygen consumption, cancer cell proliferation, migration and colony formation. In contrast, lowering heme degradation does not have an effect on lung cancer cells. These results show that increased heme flux and function are a key feature of NSCLC cells. Further, increased generation and supply of heme and oxygen-utilizing hemoproteins in cancer cells will lead to intensified oxygen consumption and cellular energy production by mitochondrial respiration, which would fuel cancer cell proliferation and progression. The results show that inhibiting heme and respiratory function can effectively arrest the progression of lung cancer cells. Hence, understanding heme function can positively impact on research in lung cancer biology and therapeutics.

The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation

BACKGROUND

Hypoxia is associated with many disease conditions in humans, such as cancer, stroke and traumatic injuries. Hypoxia elicits broad molecular and cellular changes in diverse eukaryotes. Our recent studies suggest that one likely mechanism mediating such broad changes is through changes in the cellular localization of important regulatory proteins. Particularly, we have found that over 120 nuclear proteins with important functions ranging from transcriptional regulation to RNA processing exhibit altered cellular locations under hypoxia. In this report, we describe further experiments to identify and evaluate the role of nuclear protein relocalization in mediating hypoxia responses in yeast.

RESULTS

To identify regulatory proteins that play a causal role in mediating hypoxia responses, we characterized the time courses of relocalization of hypoxia-altered nuclear proteins in response to hypoxia and reoxygenation. We found that 17 nuclear proteins relocalized in a significantly shorter time period in response to both hypoxia and reoxygenation. Particularly, several components of the SWI/SNF complex were fast responders, and analysis of gene expression data show that many targets of the SWI/SNF proteins are oxygen regulated. Furthermore, confocal fluorescent live cell imaging showed that over 95% of hypoxia-altered SWI/SNF proteins accumulated in the cytosol in hypoxic cells, while over 95% of the proteins were nuclear in normoxic cells, as expected.

CONCLUSIONS

SWI/SNF proteins relocalize in response to hypoxia and reoxygenation in a quick manner, and their relocalization likely accounts for, in part or in whole, oxygen regulation of many SWI/SNF target genes.

Hypoxia elicits broad and systematic changes in protein subcellular localization

Oxygen provides a crucial energy source in eukaryotic cells. Hence, eukaryotes ranging from yeast to humans have developed sophisticated mechanisms to respond to changes in oxygen levels. Regulation of protein localization, like protein modifications, can be an effective mechanism to control protein function and activity. However, the contribution of protein localization in oxygen signaling has not been examined on a genomewide scale. Here, we examine how hypoxia affects protein distribution on a genomewide scale in the model eukaryote, the yeast Saccharomyces cerevisiae. We demonstrate, by live cell imaging, that hypoxia alters the cellular distribution of 203 proteins in yeast. These hypoxia-redistributed proteins include an array of proteins with important functions in various organelles. Many of them are nuclear and are components of key regulatory complexes, such as transcriptional regulatory and chromatin remodeling complexes. Under hypoxia, these proteins are synthesized and retained in the cytosol. Upon reoxygenation, they relocalize effectively to their normal cellular compartments, such as the nucleus, mitochondria, endoplasmic reticulum, and cell periphery. The resumption of the normal cellular locations of many proteins can occur even when protein synthesis is inhibited. Furthermore, we show that the changes in protein distribution induced by hypoxia follow a slower trajectory than those induced by reoxygenation. These results show that the regulation of protein localization is a common and potentially dominant mechanism underlying oxygen signaling and regulation. These results may have broad implications in understanding oxygen signaling and hypoxia responses in higher eukaryotes such as humans.