Global Gene Expression Profiling Studies Research Articles

Abstract LB218: A safe and highly potent anti-PD-1-IL-2c fusion that decouples efficacy and toxicity of IL-2 therapy

Abstract Interleukin 2 (IL-2) is a pivotal immune agonist for tumor immunotherapy that has produced impressive clinical efficacy in a number of cancer types. Nevertheless, its pleiotropic effect has led to prohibitory side effects and immune restraint. In contrast, the PD-1 blockade-based cancer immunotherapy has a good safety profile by targeting and sustaining the activity of tumor-antigen specific T cells within cancer tissues. To take full advantage of complementary antitumor activity of PD-1 monoclonal antibody (mAb) and IL-2 as well as supreme intratumoral T-cell-targeting property of PD-1, a bifunctional fusion protein composed of PD-1 mAb and IL-2 mutein (αPD-1-IL-2c) is designed. IL-2c is a chimeric molecule that contains a fragment from IL-15 and does not bind to IL-2 receptor alpha (IL-2Rα). αPD-1-IL-2c stimulated greater pSTAT5 activation and proliferation in PD-1+ T cells than PD-1- T cells. αPD-1-IL-2c also induced a much stronger anti-tumor immune response compared to PD-1 mAb, IL-2c, or PD-1 mAb in combination with IL-2c in multiple syngeneic models such as B16F10, CT26, and MC38. In CT26 and MC38 models, αPD-1-IL-2c achieved complete response starting from 0.3 mg/kg dosing. In B16F10 model, αPD-1-IL-2c showed greater than 70% tumor growth inhibition (TGI). Global gene expression profiling studies showed that PD-1-IL-2c treatment significantly elevated expression levels of Cd3d, Cd3e, Cd8a, Il2rα, Cxcr3, Cxcr6, Zap70, Lck, and Pdcd1 in tumor tissues compared to treatment with PD-1 mAbs or IL-2c, indicating a specific expansion and activation of T cell in the tumor microenvironment (TME). The safety profile of αPD-1-IL-2c was assessed and compared to WT IL-2 and a leading “No-α” αPD-1-IL-2 fusion protein (αPD-1-IL-2x). WT IL-2 and αPD-1-IL-2x induced significant body weight loss and severe splenomegaly when dosed at 1.25 mg/kg. In contrast, αPD-1-IL-2c dosed at 10 mg/kg did not cause appreciable body weight loss and only led to minimal splenomegaly. In summary, we have developed a safe and highly potent αPD-1-IL-2 mutein that achieves full PD-1 blockade and TME-specific T cell activation and expansion without appreciable toxicity. Citation Format: Fan Ye, Jianing Huang, Zoey Huang, Sandra Chen, Eric Liao, Ella Li, Allison Quach, Jenny Jiang, Hanna Lin, Michael Hua, Savannah Yung, Lili Cheng, Ziyang Zhong. A safe and highly potent anti-PD-1-IL-2c fusion that decouples efficacy and toxicity of IL-2 therapy [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 LB218.

HEXIM1 as a Robust Pharmacodynamic Marker for Monitoring Target Engagement of BET Family Bromodomain Inhibitors in Tumors and Surrogate Tissues.

An increasing number of BET family protein inhibitors have recently entered clinical trials. It has been reported that attempts of monitoring target engagement of the BET bromodomain inhibitor OTX015 using literature-described putative pharmacodynamic markers, such as c-Myc, BRD2, etc., failed to detect pharmacodynamic marker responses in AML patients treated at active dose and those with clinical responses. Here, we report the identification and characterization of HEXIM1 and other genes as robust pharmacodynamic markers for BET inhibitors. Global gene expression profiling studies were carried out using cancer cells and surrogate tissues, such as whole blood and skin, to identify genes that are modulated by BET family proteins. Candidate markers were further characterized for concentration- and time-dependent responses to the BET inhibitor ABBV-075 in vitro and in vivo HEXIM1 was found to be the only gene that exhibited robust and consistent modulation by BET inhibitors across multiple cancer indications and surrogate tissues. Markers such as SERPINI1, ZCCHC24, and ZMYND8 were modulated by ABBV-075 and other BET inhibitors across cancer cell lines and xenograft tumors but not in blood and skin. Significant downregulation of c-Myc, a well-publicized target of BET inhibitors, was largely restricted to hematologic cancer cell lines. Incorporating well-characterized pharmacodynamic markers, such as HEXIM1 and other genes described here, can provide a better understanding of potential efficacy and toxicity associated with inhibiting BET family proteins and informs early clinical decisions on BET inhibitor development programs. Mol Cancer Ther; 16(2); 388-96. ©2016 AACR.

Nottingham Prognostic Index Plus (NPI+): a modern clinical decision making tool in breast cancer.

Background:Current management of breast cancer (BC) relies on risk stratification based on well-defined clinicopathologic factors. Global gene expression profiling studies have demonstrated that BC comprises distinct molecular classes with clinical relevance. In this study, we hypothesised that molecular features of BC are a key driver of tumour behaviour and when coupled with a novel and bespoke application of established clinicopathologic prognostic variables can predict both clinical outcome and relevant therapeutic options more accurately than existing methods.Methods:In the current study, a comprehensive panel of biomarkers with relevance to BC was applied to a large and well-characterised series of BC, using immunohistochemistry and different multivariate clustering techniques, to identify the key molecular classes. Subsequently, each class was further stratified using a set of well-defined prognostic clinicopathologic variables. These variables were combined in formulae to prognostically stratify different molecular classes, collectively known as the Nottingham Prognostic Index Plus (NPI+). The NPI+ was then used to predict outcome in the different molecular classes.Results:Seven core molecular classes were identified using a selective panel of 10 biomarkers. Incorporation of clinicopathologic variables in a second-stage analysis resulted in identification of distinct prognostic groups within each molecular class (NPI+). Outcome analysis showed that using the bespoke NPI formulae for each biological BC class provides improved patient outcome stratification superior to the traditional NPI.Conclusion:This study provides proof-of-principle evidence for the use of NPI+ in supporting improved individualised clinical decision making.

Pathobiological properties of the ubiquitin ligase Nedd4L in melanoma

A recent global gene expression profiling study unexpectedly showed that activated oncogenic NRAS may recruit neural precursor cell expressed, developmentally downregulated 4L (Nedd4L; a human homologue of Nedd4-2) in cultured melanoma cells. However, whether Nedd4L was expressed in melanoma tissues or participated in melanoma carcinogenesis remains to be clarified. Here, we investigated the expression status of Nedd4L in human melanocytes, benign nevi and melanoma tissue specimens and subsequently attempted to determine the role of Nedd4L in melanoma cell growth. Immunohistochemical staining revealed that Nedd4L was not present in any non-tumorous melanocytes or in 18 benign nevi tissues, but it was detected in 34 of 79 cutaneous melanomas and 9 of 32 nodal metastatic melanomas. Downregulation of Nedd4L significantly reduced the growth of cultured G361 melanoma cells in vitro. Moreover, exogenous Nedd4L expression significantly promoted the growth of A2058 melanoma cells in vivo in a xenograft assay. The present findings indicate that Nedd4L expression may be increased to facilitate tumour growth in many melanomas.

Total Survivin and acetylated Survivin correlate with distinct molecular subtypes of breast cancer

Global gene expression profiling studies led to the recent classification of breast cancer into 4 distinct molecular subtypes including luminal, human epidermal growth factor receptor 2 enriched, basal like, and unclassified. Here, we used immunohistochemistry to evaluate expression of the antiapoptotic protein Survivin and its recently described acetylated form, Survivin acetyl129, in normal breast tissue and in 226 primary breast tumors of different molecular subtypes. Correlation of Survivin expression with molecular markers and its impact on patient outcomes were analyzed. Eighty-four percent of basal-like tumors expressed high levels of total Survivin, whereas 52% of luminal tumors expressed high levels of acetylated Survivin (P < .001). Overall survival (91%) for tumors expressing low levels of total Survivin was better than that for tumors expressing high levels of total Survivin (72%, P = .02), whereas the reverse was true for tumors expressing acetylated Survivin. In hierarchical cluster analysis, total Survivin clustered with basal marker expression, whereas acetylated Survivin clustered with luminal marker expression. In multivariate analysis, high total Survivin expression was an independent predictor of worse overall survival in patients with breast cancer (relative risk, 11; P < .01). These data indicate that high levels of total Survivin predict poor outcome in patients with grade 3 invasive ductal carcinoma and correlate directly with a basal-like phenotype. In contrast, high expression of the acetylated form of the protein associates with a favorable outcome and preferentially correlates with luminal-type tumors. Survivin likely has different functions in distinct breast cancer subtypes, and diagnostic strategies that incorporate immunohistochemical markers that detect both Survivin forms may help better strategize patient risk and direct therapy.

A review of the biological and clinical characteristics of luminal‐like oestrogen receptor‐positive breast cancer

Global gene expression profiling (GEP) studies of breast cancer have identified distinct biological classes with different clinical and therapeutic implications. Oestrogen receptor (ER) has been found to be a central marker of the molecular signature. GEP studies have consistently recognized a molecularly distinct class of tumours that is characterized by high-level expression of ER and other biomarkers recognized to be characteristic of normal luminal cells of the breast. This class is the largest of the GEP-defined molecular subclasses, comprising 60-70% of breast cancer cases. Moreover, it has been proposed that this group of tumours is composed of at least two subclasses distinguished by differing GEP profiles. At present, there is no consensus on the definition of the luminal subclasses and, in clinical practice, luminal-like tumours and ER-positive tumours are frequently considered to be the same. A better understanding of the biological features of luminal tumours could lead to their improved characterization and consistent identification. In this review, we explore the concept and definitions of the luminal-like class of breast carcinoma and their contribution to our understanding of their molecular features, clinical significance and therapeutic implications.

Genomic approaches for the understanding of aging in model organisms

Aging is one of the most complicated biological processes in all species. A number of different model organisms from yeast to monkeys have been studied to understand the aging process. Until recently, many different age-related genes and age-regulating cellular pathways, such as insulin/IGF-1-like signal, mitochondrial dysfunction, Sir2 pathway, have been identified through classical genetic studies. Parallel to genetic approaches, genome-wide approaches have provided valuable insights for the understanding of molecular mechanisms occurring during aging. Gene expression profiling analysis can measure the transcriptional alteration of multiple genes in a genome simultaneously and is widely used to elucidate the mechanisms of complex biological pathways. Here, current global gene expression profiling studies on normal aging and age-related genetic/environmental interventions in widely-used model organisms are briefly reviewed.

Metaplastic breast carcinoma: tumour histogenesis or dedifferentiation?

Global gene expression profiling studies have classified breast cancer into molecular classes, some of which show similarity to normal mammary cells (ie luminal and basal subtypes) with a subsequent histogenetic implication that reinforced the perception that the phenotype of breast cancer reflects the cell of origin. However, it remains to be determined whether phenotypic changes are the result of malignant transformation of particular cancer stem cells (histogenesis) or specific genetic hits occurring at various stages of carcinogenesis (dedifferentiation). We sought to test the hypothesis that dedifferentiation may be the more likely explanation using in vivo clinical data. Our findings support the hypothesis that at least some metaplastic carcinomas are derived from phenotypic transition from conventional mammary adenocarcinoma either at the in-situ, primary invasive stage or at a distant metastatic site. This observation argues against the cell of origin theory (histogenesis) for breast carcinogenesis and favours the concept of tumour dedifferentiation at later stages.

RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype

Global gene expression profiling studies have classified breast cancer into a number of distinct biological and molecular classes with clinical relevance. The heterogeneous luminal group, which is largely characterised by oestrogen receptor (ER) expression, appears to contain distinct subgroups with differing behaviour. In this study, we analysed 47,293 gene transcripts in 128 invasive breast carcinomas (BC) using Artificial Neural Networks and a cross-validation analysis in combination with an ensemble sample classification to identify genes that can be used to subclassify ER+ luminal tumours. The results were validated using immunohistochemistry on TMAs containing 1,140 invasive breast cancers. Our results showed that the RERG gene is one of the highest ranked genes to differentiate between ER+ luminal-like and ER- non-luminal cancers based on a 10-fold external cross-validation analysis with an average classification accuracy of 89%. This was confirmed in our protein expression studies that showed RERG positive associations with markers of luminal differentiation including ER, luminal cytokeratins (CK19, CK18 and CK7/8) and FOXA1 (P = 0.004) and other markers of good prognosis in BC including small size, lower histologic grade and positive expression of androgen receptor, nuclear BRCA1, FHIT and cell cycle inhibitors p27 and p21. RERG expression was inversely associated with the proliferation marker MIB1 (P = 0.005) and p53. Strong RERG expression showed an association with longer breast cancer specific survival and distant metastasis free interval in the whole series as well as in the ER+ luminal group and these associations were independent of other prognostic variables. In conclusion, we used novel bioinformatics methods to identify candidate genes to characterise ER+ luminal-like breast cancer. RERG gene is a key marker of the luminal BC class and can be used to separate distinct prognostic subgroups.

Identification of uniquely expressed transcription factors in highly purified B‐cell lymphoma samples

Transcription factors (TFs) are critical for B-cell differentiation, affecting gene expression both by repression and transcriptional activation. Still, this information is not used for classification of B-cell lymphomas (BCLs). Traditionally, BCLs are diagnosed based on a phenotypic resemblance to normal B-cells; assessed by immunohistochemistry or flow cytometry, by using a handful of phenotypic markers. In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), providing a new powerful means for the classification, prediction of survival, and response to treatment of lymphomas. However, most GEP studies have typically been performed on whole tissue samples, containing varying degrees of tumor cell content, which results in uncertainties in data analysis. In this study, global GEP analyses were performed on highly purified, flow-cytometry sorted tumor-cells from eight subgroups of BCLs. This enabled identification of TFs that can be uniquely associated to the tumor cells of chronic lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), hairy cell leukemia (HCL), and mantle cell lymphoma (MCL). The identified transcription factors influence both the global and specific gene expression of the BCLs and have possible implications for diagnosis and treatment.

Gene Expression Profiling and Cellular Distribution of Molecules with Altered Expression in the Hippocampal CA1 Region after Developmental Exposure to Anti-Thyroid Agents in Rats

To determine whether developmental hypothyroidism causes permanent disruption of neuronal development, we first performed a global gene expression profiling study targeting hippocampal CA1 neurons in male rats at the end of maternal exposure to anti-thyroid agents on weaning (postnatal day 20). As a result, genes associated with nervous system development, zinc ion binding, apoptosis and cell adhesion were commonly up- or down-regulated. Genes related to calcium ion binding were up-regulated and those for myelination were often down-regulated. We, then, examined immunohistochemical cellular distribution of Ephrin type A receptor 5 (EphA5) and Tachykinin receptor (Tacr)-3, those selected based on the gene expression profiles, in the hippocampal formation at the adult stage (11-week-old) as well as at the end of exposure. At weaning, both EphA5- and Tacr3-immunoreactive cells with strong intensities appeared in the pyramidal cell layer or stratum oriens of the hippocampal CA1 region. Although the magnitude of the change was decreased at the adult stage, Tacr3 in the CA1 region showed a sustained increase in expressing cells until the adult stage after developmental hypothyroidism. On the other hand, EphA5-expressing cells did not show sustained increase at the adult stage. The results suggest that developmental hypothyroidism caused sustained neuronal expression of Tacr3 in the hippocampal CA1 region, probably reflecting a neuroprotective mechanism for mismigration.

Transcript Profiling During Fiber Development Identifies Pathways in Secondary Metabolism and Cell Wall Structure That May Contribute to Cotton Fiber Quality

A global gene expression profiling study at different stages of fiber development was undertaken on two cotton species cultivated for fiber, Gossypium hirsutum (L.) and G. barbadense (L.). A large proportion of the genome was expressed during both fiber elongation and subsequent secondary cell wall thickening. There was a major shift in abundance of transcripts for gene regulation, cell organization and metabolism between fiber elongation and fiber thickening that was fundamentally similar in both species. Each stage had its own distinctive features represented by specific metabolic and regulatory genes, a number of which have been noted previously. Many of the genes expressed in the fibers were of a similar type and developmental expression to those seen in other fiber-producing plants, indicating a conservation of mechanisms of cell elongation and wall thickening across diverse plant genera. Secondary metabolism and pectin synthesis and modification genes were amongst the most statistically significant differentially expressed categories between the two species during fiber elongation. The gene profiles of the fiber thickening stage, however, were almost identical between the two species, suggesting that their different final fiber quality properties may be established at earlier stages of fiber development. Expression levels of representative phenylpropanoid and pectin modification genes showed high correlations with specific fiber properties in an inter-specific cotton recombinant inbred line (RIL) population, supporting a role in determining fiber quality.

Triple-negative/basal-like breast cancer: review

Breast cancer comprises a heterogeneous group of diseases that vary in morphology, biology, behaviour and response to therapy. Triple-negative (TN) breast cancer is a subtype of tumours with aggressive clinical behaviour which currently lacks effective targeted therapies. The majority of TN breast cancers possess a basal phenotype and show varying degrees of basal marker expression (basal-like tumours). The importance of recognising these tumours came to light largely as the result of global gene expression profiling studies that categorised breast cancer into distinct molecular classes. These studies showed that basal-like tumours are molecularly different from hormone receptors and HER2 positive tumours. Although both TN and basal-like tumours share many molecular and morphological features, equating both tumour classes may be misleading. A better understanding of the molecular and histopathological features of TN and basal-like cancers is of paramount importance, in particular for unravelling the heterogeneous nature of these tumour subgroups and for the identification of prognostic biomarkers, ideal systemic therapy regimens and novel therapeutic targets for these aggressive tumours. In this review, we discuss the difference between TN and basal-like tumours, pathological and clinical features of basal-like cancer and hence explore the criteria that can be used to identify these tumours in routine practice.

Cutaneous Melanoma: Fishing with Chips

DNA microarray technology is a versatile platform that allows rapid genetic analysis to take place on a genome-wide scale and has revolutionized the way cancers are studied. This platform has enabled researchers to characterize mechanisms central to tumorigenesis and understand important molecular events in the multi-step tumor progression model of cutaneous melanoma and other cancers. In melanoma, multiple global gene expression profiling studies using various DNA microarray platforms and various experimental designs have been performed. Each study has been able to capture and characterize either the involvement of a novel pathway or a novel cause-effect-relationship. The use of microarrays to define subclasses, to identify differentially regulated genes within a mutational context to analyze epigenetically regulated genes has resulted in an unprecedented understanding of the biology of cutaneous melanoma that may lead to more accurate diagnosis, more comprehensive prognosis, prediction and more effective therapeutic interventions. Related DNA microarray platforms like array-comparative genomic hybridization (CGH) have also been instrumental to identify many non-random chromosomal alterations; however, studies identifying validated targets as a result of CGH are limited. Thus, there exists significant opportunity to discover novel melanoma genes and translate such discoveries into meaningful clinical endpoints. In this review, we focus on various DNA microarray-based studies performed in cutaneous melanoma and summarize our current understanding of the genetics and biology of melanoma progression derived from accumulating genomic information.

Compound K Enhances Insulin Secretion with Beneficial Metabolic Effects in db/db Mice

Compound K (CK) is a final metabolite of panaxadiol ginsenosides. Although Panax ginseng is known to have antidiabetic activity, the active ingredient is not yet fully identified. In our preliminary studies, panaxadiol ginsenosides showed insulin secretion stimulating activity. Therefore, it would be interesting to know whether and how CK has antidiabetic activity. In in vitro studies using HIT-T15 cells and primary cultured islets, CK enhanced the insulin secretion in a concentration-dependent manner. This effect, however, was completely abolished in the presence of diazoxide (K+ channel opener) or nifedipine (Ca2+ channel blocker). Insulin secretion stimulating activity of a single oral CK administration was also confirmed with an oral glucose tolerance test (OGTT) using ICR mice. From these studies, we may conclude that CK lowered the plasma glucose level by stimulating insulin secretion and this action was presumably associated with an ATP-sensitive K+ channel. In a long-term study using C57BL/KsJ db/ db mice, CK treatment significantly decreased the fasting blood glucose levels in a dose-dependent fashion. OGTT revealed that CK improved glucose tolerance with increased insulin levels 30 min after the glucose challenge. Concurrently, CK treatment prevented the destruction of islets and preserved more insulin. Next, to gain insight into the extra-pancreatic molecular mechanism of CK, we performed a global gene expression profiling study in the liver and adipose tissues. According to DNA microarray analysis, CK shifted glucose metabolism from hepatic glucose production to hepatic glucose utilization in the liver and improved insulin sensitivity through enhancing plasma adiponectin levels, resulting in overexpression of genes for adipogenesis and glucose transporter in the adipose tissue. Taken together, we may suggest that CK could be developed as a therapeutic tool in type 2 diabetic patients with disability of insulin secretion and/or insulin resistance.

Regulation of Tissue-Specific and Extracellular Matrix-Related Genes by a Class I Histone Deacetylase

Class I histone deacetylases (HDACs) repress transcription by deacetylating histones and have been shown to play crucial roles in mouse, Xenopus, zebrafish, and C. elegans development. To identify the molecular networks regulated by a class I HDAC in a multicellular organism, we carried out a global gene expression profiling study using C. elegans embryos, and identified tissue-specific and extracellular matrix (ECM)-related genes as major HDA-1 targets. Ectopic expression of HDA-1 or C. elegans cystatin, an HDA-1 target identified from the microarray, significantly perturbed mammalian cell invasion. Similarly, RNAi depletion or overexpression of human HDAC-1 also affected cell migration. These findings suggest that HDA-1/HDAC-1 may play a critical, evolutionarily conserved role in regulating the extracellular microenvironment. Because human HDACs are targets for cancer therapy, these findings have significant implications in cancer treatment.

DNA Microarrays: Implications for Clinical Medicine

DNA microarrays are capable of measuring the expression of thousands of genes in a single assay. This technology has led to an explosion in global gene expression profiling studies, allowing researchers to more fully explore a multitude of complex biological systems ranging from the yeast cell cycle to the progression of cancer. By analyzing collections of these global profiles, the molecular underpinnings of biological phenomena are being unraveled. It is the goal of this review to address the basic principles of the technology and methodology employed in gene expression profiling with DNA microarrays, and then to highlight recent studies with particular importance for clinical medicine, focusing on cancer.