Anti-tumor activity of all-trans retinoic acid in gastric-cancer: gene-networks and molecular mechanisms

BACKGROUND

Gastric-cancer is a heterogeneous type of neoplastic disease and it lacks appropriate therapeutic options. There is an urgent need for the development of innovative pharmacological strategies, particularly in consideration of the potential stratified/personalized treatment of this tumor. All-Trans Retinoic-acid (ATRA) is one of the active metabolites of vitamin-A. This natural compound is the first example of clinically approved cyto-differentiating agent, being used in the treatment of acute promyelocytic leukemia. ATRA may have significant therapeutic potential also in the context of solid tumors, including gastric-cancer. The present study provides pre-clinical evidence supporting the use of ATRA in the treatment of gastric-cancer using high-throughput approaches.

METHODS

We evaluated the anti-proliferative action of ATRA in 27 gastric-cancer cell-lines and tissue-slice cultures from 13 gastric-cancer patients. We performed RNA-sequencing studies in 13 cell-lines exposed to ATRA. We used these and the gastric-cancer RNA-sequencing data of the TCGA/CCLE datasets to conduct multiple computational analyses.

RESULTS

Profiling of our large panel of gastric-cancer cell-lines for their quantitative response to the anti-proliferative effects of ATRA indicate that approximately half of the cell-lines are characterized by sensitivity to the retinoid. The constitutive transcriptomic profiles of these cell-lines permitted the construction of a model consisting of 42 genes, whose expression correlates with ATRA-sensitivity.  The model predicts that 45% of the TCGA gastric-cancers are sensitive to ATRA. RNA-sequencing studies performed in retinoid-treated gastric-cancer cell-lines provide insights into the gene-networks underlying ATRA anti-tumor activity. In addition, our data demonstrate that ATRA exerts significant immune-modulatory effects, which seem to be largely controlled by IRF1 up-regulation. Finally, we provide evidence of a feed-back loop between IRF1 and DHRS3, another gene which is up-regulated by ATRA.

CONCLUSIONS

ATRA is endowed with significant therapeutic potential in the stratified/personalized treatment gastric-cancer. Our data represent the fundaments for the design of clinical trials focusing on the use of ATRA in the personalized treatment of this heterogeneous tumor. Our gene-expression model will permit the development of a predictive tool for the selection of ATRA-sensitive gastric-cancer patients. The immune-regulatory responses activated by ATRA suggest that the retinoid and immune-checkpoint inhibitors constitute rational combinations for the management of gastric-cancer.

Abstract P5-05-09: Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid

Background: All-trans retinoic acid (ATRA) is a promising agent in the treatment of breast cancer. In view of ATRA-based therapeutic strategies aimed at the personalized treatment of mammary tumors, we recently demonstrated that approximately 70% of estrogen-receptor-positive (ER+) breast cancer is sensitive to the anti-proliferative effects of ATRA (1). In contrast only 10-20% of the HER2-positive and triple-negative counterparts respond to the retinoid. On the basis of these data and the available basal gene-expression profiles of breast cancer cell lines and primary tumors, we developed a model consisting of 21 genes (ATRA-21) which correctly predicts ATRA-sensitivity in the context of breast cancer (2).

Aims and Approach: The present study is aimed at getting insights into the molecular mechanisms underlying the anti-tumor action of ATRA in the specific subsets of breast cancer identified. In addition, we intend to determine specific genes and gene-networks modulated by ATRA which may represent pharmacological targets for the design of rational combinations between the retinoid and unrelated therapeutic agents to be used in the personalized treatment of breast cancer. A final goal is the identification of potential bio-markers of the anti-tumor response to ATRA to be used in the clinics. To address all these points, we performed deep-sequencing experiments on a panel of sixteen cell lines recapitulating the heterogeneity of the breast cancer phenotype and characterized for their anti-proliferative response to ATRA.

Panel of Breast cancer cell lines and characteristicsCell linePhenotypeClassATRA-scoreATRA-sensitivitySKBR3LUMINALHER2+1.0yesHCC1500LUMINALER+0.7yesCAMA1LUMINALER+0.7yesMDAMB361LUMINALHER2+0.6yesHCC202LUMINALHER2+0.2noMDAMB175VIILUMINALER+0.2noZR751LUMINALER+0.1noHCC1419LUMINALHER2+0.1noHCC1599BASALTN1.0yesMB157BASALTN0.3yesMDAMB157BASALTN0.2yesHS578TBASALTN0.2yesMDAMB231BASALTN0.0noCAL851BASALTN0.0noHCC1187BASALTN0.0noMDAMB436BASALTN0.0noATRA-score = ATRA sensitivity index, the higher the score the higher is the sensitivity to ATRA. ER+ = estrogen-receptor-positive cell line. HER2+ = Her2-positive cell line.

Results: We exposed each cell line to ATRA (1 μM) for 24 hours and extracted total RNA which was subjected to deep sequencing. The global gene-expression data were analyzed with a number of complementary bio-informatic tools which resulted in the identification of approximately 100 genes whose expression is up- or down-regulated specifically in ATRA-sensitive luminal and/or basal cell lines. Pathway and gene-network analysis indicate a strong enrichment in the up-regulation of genes involved in the pathways modulated by interferons. These last results are consistent with the idea that ATRA exerts a strong immuno-modulatory action in breast cancer cells and represents proof of principle for the evaluation of combinations between the retinoid and check-point inhibitors in the treatment of breast cancer.

References: 1) Centritto F. et al. EMBO Mol Med. 2015 Jul;7(7):950-7. 2) Bolis M et al.. Ann Oncol. 2017 Mar 1;28(3):611-621.

Citation Format: Garattini E, Bolis M, Vallerga A, Fratelli M, Paroni G, Zanetti A, Kurosaki M, Gianni' M, Celestini V, Terao M. Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-09.

Network-guided modeling allows tumor-type independent prediction of sensitivity to all-trans-retinoic acid

Background

All-trans-retinoic acid (ATRA) is a differentiating agent used in the treatment of acute-promyelocytic-leukemia (APL) and it is under-exploited in other malignancies despite its low systemic toxicity. A rational/personalized use of ATRA requires the development of predictive tools allowing identification of sensitive cancer types and responsive individuals.

Materials and methods

RNA-sequencing data for 10 080 patients and 33 different tumor types were derived from the TCGA and Leucegene datasets and completely re-processed. The study was carried out using machine learning methods and network analysis.

Results

We profiled a large panel of breast-cancer cell-lines for in vitro sensitivity to ATRA and exploited the associated basal gene-expression data to initially generate a model predicting ATRA-sensitivity in this disease. Starting from these results and using a network-guided approach, we developed a generalized model (ATRA-21) whose validity extends to tumor types other than breast cancer. ATRA-21 predictions correlate with experimentally determined sensitivity in a large panel of cell-lines representative of numerous tumor types. In patients, ATRA-21 correctly identifies APL as the most sensitive acute-myelogenous-leukemia subtype and indicates that uveal-melanoma and low-grade glioma are top-ranking diseases as for average predicted responsiveness to ATRA. There is a consistent number of tumor types for which higher ATRA-21 predictions are associated with better outcomes.

Conclusions

In summary, we generated a tumor-type independent ATRA-sensitivity predictor which consists of a restricted number of genes and has the potential to be applied in the clinics. Identification of the tumor types that are likely to be generally sensitive to the action of ATRA paves the way to the design of clinical studies in the context of these diseases. In addition, ATRA-21 may represent an important diagnostic tool for the selection of individual patients who may benefit from ATRA-based therapeutic strategies also in tumors characterized by lower average sensitivity.

Upright, Weight-Bearing, Dynamic-Kinetic MRI of the Spine pMRI/kMRI

The purpose of this study was to demonstrate the general utility of the first dedicated magnetic resonance imaging (MRI) unit enabling upright, weight-bearing positional evaluation of the spinal column ( pMRI) during various dynamic- kinetic maneuvers ( kMRI) in patients with degenerative conditions of the spine.

This study consisted of a prospective analysis of cervical and lumbar imaging examinations. All studies were performed on a recently introduced whole body MRI system (Stand-Up™ MRI, Fonar Corp, Melville, NY). The system operates at 0.6T using an electromagnet with a horizontal field, transverse to the longitudinal axis of the patient's body. Depending upon spinal level, all examinations were acquired with either a cervical or lumbar solenoidal radiofrequency receiver coil. This unit is configured with a top/front-open design, incorporating a patient-scanning table with tilt, translation and elevation functions. The unique motorized patient handling system developed for the scanner allows for vertical (upright, weight bearing) and horizontal (recumbent) positioning of all patients. The top/front-open construction also allows dynamic-kinetic flexion and extension maneuvers of the spine. Patterns of bony and soft tissue change occurring among recumbent ( rMRI) and upright neutral positions ( pMRI), and dynamic- kinetic acquisitions ( kMRI) were sought.

Depending on the specific underlying pathologic degenerative condition, significant alterations observed on pMRI and kMRI that were either more or less pronounced than on rMRI included: fluctuating anterior and posterior disc herniations, hypermobile spinal instability, central spinal canal and spinal neural foramen stenosis and general sagittal spinal contour changes. No patient suffered from feelings of claustrophobia that resulted in termination of the examination.

In conclusion, the potential relative beneficial aspects of upright, weight-bearing ( pMRI), dynamic-kinetic ( kMRI) spinal imaging on this system over that of recumbent MRI ( rMRI) include: the revelation of occult disease dependent on true axial loading, the unmasking of kinetic-dependent disease, and the ability to scan the patient in the position of clinically relevant signs and symptoms. This imaging unit also demonstrated low claustrophobic potential and yielded relatively high-resolution images with little motion/chemical-shift artifact.

Cellular and molecular determinants of all-trans retinoic acid sensitivity in breast cancer: Luminal phenotype and RARα expression

Forty-two cell lines recapitulating mammary carcinoma heterogeneity were profiled for all-trans retinoic acid (ATRA) sensitivity. Luminal and ER⁺ (estrogen-receptor-positive) cell lines are generally sensitive to ATRA, while refractoriness/low sensitivity is associated with a Basal phenotype and HER2 positivity. Indeed, only 2 Basal cell lines (MDA-MB157 and HCC-1599) are highly sensitive to the retinoid. Sensitivity of HCC-1599 cells is confirmed in xenotransplanted mice. Short-term tissue-slice cultures of surgical samples validate the cell-line results and support the concept that a high proportion of Luminal/ER⁺ carcinomas are ATRA sensitive, while triple-negative (Basal) and HER2-positive tumors tend to be retinoid resistant. Pathway-oriented analysis of the constitutive gene-expression profiles in the cell lines identifies RARα as the member of the retinoid pathway directly associated with a Luminal phenotype, estrogen positivity and ATRA sensitivity. RARα3 is the major transcript in ATRA-sensitive cells and tumors. Studies in selected cell lines with agonists/antagonists confirm that RARα is the principal mediator of ATRA responsiveness. RARα over-expression sensitizes retinoid-resistant MDA-MB453 cells to ATRA anti-proliferative action. Conversely, silencing of RARα in retinoid-sensitive SKBR3 cells abrogates ATRA responsiveness. All this is paralleled by similar effects on ATRA-dependent inhibition of cell motility, indicating that RARα may mediate also ATRA anti-metastatic effects. We define gene sets of predictive potential which are associated with ATRA sensitivity in breast cancer cell lines and validate them in short-term tissue cultures of Luminal/ER⁺ and triple-negative tumors. In these last models, we determine the perturbations in the transcriptomic profiles afforded by ATRA. The study provides fundamental information for the development of retinoid-based therapeutic strategies aimed at the stratified treatment of breast cancer subtypes.

Cytodifferentiation by retinoids, a novel therapeutic option in oncology: rational combinations with other therapeutic agents

Retinoic acid (RA) and derivatives are promising antineoplastic agents endowed with both therapeutic and chemopreventive potential. Although the treatment of acute promyelocytic leukemia with all-trans retinoic acid is an outstanding example, the full potential of retinoids in oncology has not yet been explored and a more generalized use of these compounds is not yet a reality. One way to enhance the therapeutic and chemopreventive activity of RA and derivatives is to identify rational combinations between these compounds and other pharmacological agents. This is now possible given the information available on the biochemical and molecular mechanisms underlying the biological activity of retinoids. At the cellular level, the antileukemia and anticancer activity of retinoids is the result of three main actions, cytodifferentiation, growth inhibition, and apoptosis. Cytodifferentiation is a particularly attractive modality of treatment and differentiating agents promise to be less toxic and more specific than conventional chemotherapy. This is the result of the fact that cytotoxicity is not the primary aim of differentiation therapy. At the molecular level, retinoids act through the activation of nuclear retinoic acid receptor-dependent and -independent pathways. The cellular pathways and molecular networks relevant for retinoid activity are modulated by a panoply of other intracellular and extracellular pathways that may be targeted by known drugs and other experimental therapeutics. This chapter aims to summarize and critically discuss the available knowledge in the field.

Phosphodiesterase IV Inhibition by Piclamilast Potentiates the Cytodifferentiating Action of Retinoids in Myeloid Leukemia Cells

Inhibition of phosphodiesterase IV by N-(3,5-dichloropyrid-4-yl)-3-cyclopentyloxy-4-methoxybenzamide (piclamilast) enhances the myeloid differentiation induced by all-trans-retinoic acid (ATRA), retinoic acid receptor alpha (RARalpha), or retinoic acid receptor X agonists in NB4 and other retinoid-sensitive myeloid leukemia cell types. ATRA-resistant NB4.R2 cells are also partially responsive to the action of piclamilast and retinoic acid receptor X agonists. Treatment of NB4 cells with piclamilast or ATRA results in activation of the cAMP signaling pathway and nuclear translocation of cAMP-dependent protein kinase. This causes a transitory increase in cAMP-responsive element-binding protein phosphorylation, which is followed by down-modulation of the system. ATRA + piclamilast have no additive effects on the modulation of the cAMP pathway, and the combination has complex effects on cAMP-regulated genes. Piclamilast potentiates the ligand-dependent transactivation and degradation of RARalpha through a cAMP-dependent protein kinase-dependent phosphorylation. Enhanced transactivation is also observed in the case of PML-RARalpha. In NB4 cells, increased transactivation is likely to be at the basis of enhanced myeloid maturation and enhanced expression of many retinoid-dependent genes. Piclamilast and/or ATRA exert major effects on the expression of cEBP and STAT1, two types of transcription factors involved in myeloid maturation. Induction and activation of STAT1 correlates directly with enhanced cytodifferentiation. Finally, ERK and the cAMP target protein, Epac, do not participate in the maturation program activated by ATRA + piclamilast. Initial in vivo studies conducted in severe combined immunodeficiency mice transplanted with NB4 leukemia cells indicate that the enhancing effect of piclamilast on ATRA-induced myeloid maturation translates into a therapeutic benefit.

ST1926, a novel and orally active retinoid-related molecule inducing apoptosis in myeloid leukemia cells: modulation of intracellular calcium homeostasis

Retinoid-related molecules (RRMs) are derivatives of retinoic acid and promising antileukemic agents with a mechanism of action different from that of other common chemotherapeutics. Here, we describe a novel chemical series designed against the RRM prototype, CD437. This includes molecules with apoptotic effects in acute promyelocytic leukemia and other myelogenous leukemia cell lines, as well as ST2065, an RRM with antagonistic properties. The most interesting apoptotic agent is ST1926, a compound more powerful than CD437 in vitro and orally active in vivo on severe combined immunodeficiency (SCID) mice that received transplants of NB4 cells. ST1926 has the same mechanism of action of CD437, as indicated by the ability to trans-activate retinoic acid receptor gamma, to induce the phosphorylation of p38 and JNK, and to down-regulate the expression of many genes negatively modulated by CD437. ST1926 causes an immediate increase in the cytosolic levels of calcium that are directly related to the apoptotic potential of the RRMs considered. The intracellular calcium elevation is predominantly the result of an inhibition of the mitochondrial calcium uptake. The phenomenon is blocked by the ST2065 antagonist, the intracellular calcium chelator BAPTA (1,2 bis (2-aminophenoxy) ethane-N, N, N',N'-tetraacetic acid tetrakis (acetoxymethyl ester), and by high concentrations of calcium blockers of the dihydropyridine type, compounds that suppress ST1926-induced apoptosis.

Tyrosine kinase inhibitor STI571 potentiates the pharmacologic activity of retinoic acid in acute promyelocytic leukemia cells: effects on the degradation of RARalpha and PML-RARalpha

The 2-phenylaminopyrimidine derivative STI571 is a selective inhibitor of c-Abl, c-kit, and platelet-derived growth factor-receptor tyrosine kinases and is presently in phase II-III clinical studies. Here, this study reports on a novel pharmacologic activity of the compound, ie, enhancement of the cyto-differentiating, growth-inhibitory, and apoptogenic actions of all-trans-retinoic acid (ATRA). Whereas STI571 is not a cytodifferentiating agent by itself, the compound interacts with ATRA and enhances the myeloid maturation program set in motion by the retinoid in the PML-RARalpha(+) acute promyelocytic leukemia NB4 and the PML-RARalpha(-) myeloblastic HL60 and U937 cell lines. In addition, STI571 relieves the cyto-differentiation block observed in the ATRA-resistant cell lines, NB4.R1, NB4.306, and NB4.007. In NB4 promyelocytes, a RARalpha agonist, but not an RXR agonist, can substitute for ATRA and interact with STI571. By contrast, STI571 is unique among c-Abl-specific tyrosine kinase inhibitors in modulating the pharmacologic activity of ATRA. In NB4 cells, enhanced cyto-differentiation results in increased up-regulation of the expression of a number of genes coding for myeloid differentiation markers, including CD11b, CD11c, and some of the components of the nicotinamide adenine dinucleotide phosphate-oxidase enzymatic complex. All this is accompanied by inhibition of c-Abl tyrosine phosphorylation and retardation of the retinoid-dependent degradation of PML-RARalpha and RARalpha. Stabilization of the 2 retinoic acid receptors is likely to be the result of augmented and accelerated inhibition of the proteasome-dependent proteolytic activity observed on ATRA treatment.