Robert Clarke

Robert Clarke
University of Minnesota Twin Cities | UMN · The Hormel Institute

PhD DSc

About

535
Publications
84,393
Reads
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19,484
Citations
Introduction
We develop and apply novel systems biology tools and approaches to understand drug resistance in breast cancer. Our current focus is on resistance to endocrine therapies (antiestrogens; aromatase inhibitors) and network signaling primarily among the unfolded protein response (UPR), cellular metabolism, proliferation, autophagy and apoptosis. We do translational cellular and molecular studies using patient specimens, rodent models, and cell lines. Our work is currently supported by NIH and DoD.
Additional affiliations
August 2020 - present
University of Minnesota Twin Cities
Position
  • Managing Director
January 2011 - July 2020
Georgetown University Medical Center
Position
  • Head of Faculty
July 2006 - August 2020
Georgetown University
Position
  • Managing Director
Education
January 1999 - December 1999
Queen's University Belfast
Field of study
  • Biochemistry
September 1982 - June 1986
Queen's University Belfast
Field of study
  • Biochemistry
September 1980 - June 1982
Queen's University Belfast
Field of study
  • Biochemistry

Publications

Publications (535)
Article
Full-text available
How breast cancer cells respond to the stress of endocrine therapies determines whether they will acquire a resistant phenotype or execute a cell-death pathway. After a survival signal is successfully executed, a cell must decide whether it should replicate. How these cell-fate decisions are regulated is unclear, but evidence suggests that the sign...
Article
Full-text available
While more than 70% of breast cancers express estrogen receptor-α (ER+), endocrine therapies targeting these receptors often fail. The molecular mechanisms that underlie treatment resistance remain unclear. We investigated the potential role of glucose-regulated protein 78 (GRP78) in mediating estrogen resistance. Human breast tumors showed increas...
Article
Full-text available
Antiestrogen therapy induces the unfolded protein response (UPR) in estrogen receptor-positive (ER+) breast cancer. X-box binding protein 1 (XBP1), which exists in the transcriptionally inactive unspliced form [XBP1(U)] and the spliced active form [XBP1(S)], is a key UPR component mediating antiestrogen resistance. We now show a direct link between...
Article
Full-text available
Tissue heterogeneity is both a major confounding factor and an underexploited information source. While a handful of reports have demonstrated the potential of supervised computational methods to deconvolute tissue heterogeneity, these approaches require a priori information on the marker genes or composition of known subpopulations. To address the...
Article
Full-text available
Advanced tumours are often heterogeneous, consisting of subclones with various genetic alterations and functional roles. The precise molecular features that characterize the contributions of multiscale intratumour heterogeneity to malignant progression, metastasis, and poor survival are largely unknown. Here, we address these challenges in breast c...
Article
Social isolation is associated with increased risk and mortality from many diseases, such as breast cancer. Socially isolated breast cancer survivors have a 43% higher risk of recurrence and a 64% higher risk of breast cancer-specific mortality than socially integrated survivors. Since Covid-19 has dramatically increased the incidence of social iso...
Article
Estrogen receptor positive (ER+) breast cancer is the most common breast cancer subtype. Endocrine therapies, such as selective estrogen receptor modulators (SERM) and aromatase inhibitors (AI), along with cyclin-dependent kinase 4/6 (CDK4/6) inhibitors, are the current mainstays of treatment. Despite being initially effective, the majority of adva...
Article
Estrogen receptor positive (ER+) breast cancers (BC) that do not respond to endocrine therapies exhibit lower response rates to chemotherapy than other subtypes, implying that endocrine resistance may confer cross-resistance to cytotoxic drugs and contribute to the poor responses to chemotherapy in recurrent ER+ disease. Endocrine therapies can red...
Article
Full-text available
Motivation Ideally, a molecularly distinct subtype would be composed of molecular features that are expressed uniquely in the subtype of interest but in no others – so called marker genes (MG). MG plays a critical role in the characterization, classification, or deconvolution of tissue or cell subtypes. We and others have recognized that the test s...
Article
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Reprogrammed metabolism and high energy demand are well-established properties of cancer cells that enable tumor growth. Glycolysis is a primary metabolic pathway that supplies this increased energy demand, leading to a high rate of glycolytic flux and a greater dependence on glucose in tumor cells. Finding safe and effective means to control glyco...
Preprint
Full-text available
While some forms of breast cancer are highly responsive to treatment, endocrine therapy-resistant breast cancers are disproportionately lethal. There has been significant progress in understanding how endocrine therapy-resistant strains evolve from therapy-susceptible strains of cancer, but little is understood about the proliferation of resistance...
Article
BACKGROUND: Social isolation is associated with increased risk and mortality from many diseases, such as breast cancer. Socially isolated breast cancer survivors have a 43% higher risk of recurrence and a 64% higher risk of breast cancer-specific mortality than socially integrated survivors. Since Covid-19 has dramatically increased the incidence o...
Article
Estrogen receptor-positive breast cancers constitute the majority of newly diagnosed breast cancers in patients. While commonly treated with various approved endocrine therapy strategies, these cancers can unfortunately also develop resistance to such therapies, indicating a need to explore other avenues of treatment in endocrine-resistant breast c...
Article
Full-text available
Missing values are a major issue in quantitative proteomics analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, a comparative assessment of imputation accuracy remains inconclusive, mainly because mechanisms contributing to true missing values are complex and existing evaluation methodolo...
Article
Motivation Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell subtypes. Both subtype compositions and subtype-specific expressions can vary across biological conditions. Computational deconvolution aims to dissect patterns of bulk tissue data into subtype compositions and subtype-specific expressions....
Article
Full-text available
De novo transcriptome assembly from billions of RNA-seq reads is very challenging due to alternative splicing and various levels of expression, which often leads to incorrect, mis-assembled transcripts. BayesDenovo addresses this problem by using both a read-guided strategy to accurately reconstruct splicing graphs from the RNA-seq data and a Bayes...
Preprint
Full-text available
Missing values are a major issue in quantitative proteomics analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, a comparative assessment of imputation accuracy remains inconclusive, mainly because mechanisms contributing to true missing values are complex and existing evaluation methodolo...
Article
Full-text available
Transcription factors (TFs) often function as a module including both master factors and mediators binding at cis-regulatory regions to modulate nearby gene transcription. ChIP-seq profiling of multiple TFs makes it feasible to infer functional TF modules. However, when inferring TF modules based on co-localization of ChIP-seq peaks, often many wea...
Preprint
Complex tissues are composite ecological systems whose components interact with each other to create a unique physiological or pathophysiological state distinct from that found in other tissue microenvironments. To explore this ground yet dynamic state, molecular profiling of bulk tissues and mathematical deconvolution can be jointly used to charac...
Article
Full-text available
Breast cancers characterized by expression of estrogen receptor-alpha; ESR1) represent approximately 70% of all new cases and comprise the largest molecular subtype of this disease. Despite this high prevalence, the number of adequate experimental models of ER+ breast cancer is relatively limited. Nonetheless, these models have proved very useful i...
Article
Full-text available
We determined how vitamin D receptor (VDR) is linked to disease outcome in estrogen receptor-positive (ER+) breast cancer patients treated with tamoxifen (TAM). Breast cancer patients (n = 581) in four different datasets were divided into those expressing higher (above median) and lower levels of VDR in pretreatment ER+ tumors. Across all datasets,...
Article
Full-text available
Background ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak b...
Preprint
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Data-driven differential dependency network analysis identifies in a complex and often unknown overall molecular circuitry a network of differentially connected molecular entities (pairwise selective coupling or uncoupling depending on the specific phenotypes or experimental conditions). Such differential dependency networks are typically used to a...
Preprint
Full-text available
Background: Missing values are a major issue in quantitative proteomics data analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, comparative assessment on the accuracy of existing methods remains inconclusive, mainly because the true missing mechanisms are complex and the existing evaluat...
Conference Paper
Metabolic and epigenetic reprogramming are two key hallmarks of cancer. Rapidly proliferating cancer cells often exhibit a higher and differentially reprogrammed transcriptional activity than normal cells of the same tissue. To support transcriptional reprogramming and increased transcriptional load, sustained chromatin acetylation is required to l...
Article
Full-text available
Exploring complex modularization of intracellular signal transduction pathways is critical to understanding aberrant cellular responses during disease development and drug treatment. IMPALA (Inferred Modularization of PAthway LAndscapes) integrates information from high throughput gene expression experiments and genome-scale knowledge databases to...
Article
Full-text available
Among multiple subtypes of tissue or cell, subtype-specific differentially-expressed genes (SDEGs) are defined as being most-upregulated in only one subtype but not in any other. Detecting SDEGs plays a critical role in the molecular characterization and deconvolution of multicellular complex tissues. Classic differential analysis assumes a null hy...
Preprint
Motivation Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell or tissue subtypes. Both subtype compositions and expressions in individual samples can vary across different biological states or conditions. Computational deconvolution aims to dissect patterns of bulk gene expression data into subtype com...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Motivation High-throughput RNA sequencing has revolutionized the scope and depth of transcriptome analysis. Accurate reconstruction of a phenotype-specific transcriptome is challenging due to the noise and variability of RNA-seq data. This requires computational identification of transcripts from multiple samples of the same phenotype, given the un...
Article
Full-text available
Interferon Regulatory Factors (IRFs) are key regulators of immunity, cell survival and apoptosis. IRF transcriptional activity and subcellular localization are tightly regulated by posttranscriptional modifications including phosphorylation. The IκB kinase family member IKK-ε is essential in regulating antiviral innate immunity mediated by IRFs but...
Article
Full-text available
Total metastatic burden is the primary cause of death for many cancer patients. While the process of metastasis has been studied widely, much remains to be understood. Moreover, few agents have been developed that specifically target the major steps of the metastatic cascade. Many individual genes and pathways have been implicated in metastasis but...
Conference Paper
p>Endocrine therapy is the mainstay for the treatment of estrogen-receptor positive (ER+) breast cancer. However, frequent emergence of endocrine resistance is a major clinical challenge. Cell-cell cooperation in the tumor microenvironment plays a vital role in acquiring resistance, but its role is poorly understood. We studied the interactions amo...
Article
Full-text available
Over 50% of women at a childbearing age in the United States are overweight or obese, and this can adversely affect their offspring. We studied if maternal obesity-inducing high fat diet (HFD) not only increases offspring’s mammary cancer risk but impairs response to antiestrogen tamoxifen. Female rat offspring of HFD and control diet fed dams, in...
Article
Full-text available
Genome-wide transcription factor (TF) binding signal analyses reveal co-localization of TF binding sites based on inferred cis-regulatory modules (CRMs). CRMs play a key role in understanding the cooperation of multiple TFs under specific conditions. However, the functions of CRMs and their effects on nearby gene transcription are highly dynamic an...
Presentation
We investigated the role of cellular heterogeneity in endocrine therapy resistance of Estrogen Receptor positive (ER+) breast cancers using different fluorescent-labeled sensitive and resistant ER+ BC.
Article
We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes based on bulk expression profiles. We implement an R package, deconvolution by Convex Analysis of Mixtures (debCAM) that can automatically detect tissue/cell-specific markers, determine the number of constituent sub-t...
Article
Full-text available
Dependence on the glutamine pathway is increased in advanced breast cancer cell models and tumors regardless of hormone receptor status or function. While 70% of breast cancers are estrogen receptor positive (ER+) and depend on estrogen signaling for growth, advanced ER+ breast cancers grow independent of estrogen. Cellular changes in amino acids s...
Preprint
Full-text available
Motivation: Identification of biological pathways plays a central role in understanding both human health and diseases. Although much work has previously been done to explore the biological pathways by using single omics data, little effort has been reported using multi-omics data integration, mainly due to methodological and technological limitati...
Article
Drawing on concepts from experimental biology, computer science, informatics, mathematics, and statistics, systems biologists integrate data across diverse platforms and scales of time and space to create computational and mathematical models of the integrative, holistic functions of living systems. Endocrine-related cancers are well suited to stud...
Preprint
Full-text available
Resistance to endocrine therapies remains a major challenge to the successful management of patients with estrogen receptor-positive (ER+) breast cancers. Central to the development of resistance is the adaptive reprogramming of cellular metabolism in response to treatment. Solute carriers (SLCs) play a key role in metabolic reprogramming by transp...
Article
Background: Late recurrence is characteristic of ER+ breast cancers. Despite an apparently effective adjuvant endocrine therapy, many breast cancers recur years after their initial endocrine treatment. Why some tumors recur early (<3 years) and some recur later (>5 years) is poorly understood. If systemic endocrine therapies killed all cells, recur...
Article
Endocrine therapies are commonly used to treat estrogen receptor-positive (ER+) breast cancers, which comprise 70% of all new breast cancer cases. Unfortunately, emergence of resistance to these therapies presents a major clinical challenge. Cancer cells can adapt to the dysregulation of cellular metabolism induced by endocrine therapy in order to...
Article
Full-text available
Approximately 30% of aromatase-inhibitor–resistant, estrogen receptor–positive patients with breast cancer benefit from treatment with estrogen. This enigmatic estrogen action is not well understood and how it occurs remains elusive. Studies indicate that the unfolded protein response and apoptosis pathways play important roles in mediating estroge...
Article
Full-text available
Resistance to endocrine therapy remains a clinical challenge in the treatment of estrogen receptor positive (ER+) breast cancer. We investigated if adding a traditional Asian herbal mixture consisting of 12 herbs, called Jaeumkanghwa-tang (JEKHT), to tamoxifen (TAM) therapy might prevent resistance and recurrence in the ER+ breast cancer model of 7...
Preprint
Full-text available
Tissue/cell-specific marker genes (MGs) are defined as being exclusively and consistently expressed in a particular tissue/cell subtype across varying conditions. Detecting MGs plays a critical role in molecularly characterizing and conferring tissue/cell subtypes. Unfortunately, classic differential analysis assumes a convenient statistical distri...
Article
Full-text available
Therapeutic targeting of estrogen receptor-α (ERα) by the anti-estrogen tamoxifen is standard of care for premenopausal breast cancer patients and remains a key component of treatment strategies for postmenopausal patients. While tamoxifen significantly increases overall survival, tamoxifen resistance remains a major limitation despite continued ex...
Chapter
The unfolded protein response (UPR) is an adaptive mechanism to maintain protein homeostasis by decreasing the accumulation of unfolded proteins in the endoplasmic reticulum (EnR) of cells. EnR stress activates three distinct sensors, namely, inositol requiring protein 1 alpha (IRE1-α), activating transcription factor 6 (ATF6), and protein kinase R...
Chapter
The translation and appropriate folding of proteins is critical for the maintenance of cellular function. This process is tightly controlled, and it can create a significant energy demand, particularly in secretory cells. Inadequate folding of proteins, as may occur with an insufficient energy supply, can cause unfolded, misfolded, or damaged prote...
Chapter
Tumors expressing either estrogen receptor-alpha (ER; ESR1) and/or the progesterone receptor (PR) represent the most prevalent breast cancer molecular subtype. Patients diagnosed with this form of breast cancer are generally treated with a drug that targets estrogen receptor action. While these drugs are highly effective in improving overall surviv...
Chapter
XBP1 is a critical determinant of several outcomes following activation of the unfolded protein response (UPR). This UPR gene is initially transcribed as an unspliced mRNA but can subsequently be spliced by the endoribonuclease activity of IRE1α induced by activation of GRP78 in response to endoplasmic reticulum stress. Both the unspliced (XBP1-U)...
Chapter
Full-text available
We have used RNA interference (RNAi) screening technology to reveal unknown components of biological signaling pathways including survival mechanisms of estrogen-independent breast cancer cell growth and cancer cell resistance to immune attack. In this chapter, a detailed protocol describing the use of RNAi screening to identify factors important f...
Book
This volume presents state-of-the-art information on each of the arms of the unfolded protein response (UPR), how their activation/repression are regulated, integrated, and coordinated, how UPR components affect cancer cell biology and responsiveness to therapeutic interventions, and how UPR components/activities offer potentially novel targets for...
Article
Full-text available
The post-natal mammary gland undergoes repeated cycles of proliferation and cell death, most notably when the fully differentiated (lactating) gland dedifferentiates to a pre-lactation state. Accumulation of milk proteins in the secretory epithelium creates the stress signal that triggers this process (involution). How this stress is perceived, and...
Preprint
Full-text available
While the two major types of cells in the brain are known to be glia and neuron, the true ratio of glia to neurons in the brain remains a mystery. One of recent studies reveals that the ratio of glia to neurons in the brain varies from one region to another, sometimes dramatically. Here we report a study that applies UNsupervised DecOnvolution vers...
Article
The majority of breast tumors express estrogen receptors (ER), and are treated with endocrine therapy (ET) drugs to target ERs and estrogen (E2) biosynthesis in the management of early and metastatic ER + breast cancer. However, ∼50% of patients receiving an ET exhibit either intrinsic (de novo) resistance or acquire resistance to these treatments...
Article
The cell-cell interactions that occur within the breast tumor microenvironment are critical determinants of cancer cell fate. In the face of treatment, the theory of clonal evolution dominates current thinking. Thus, individual cells acquire a mutation(s) that provides a selection advantage where Darwinian selection acts at the single-cell level. W...