Therapeutic immunomodulation by rationally designed nucleic acids and nucleic acid nanoparticles

The immune system has evolved to defend organisms against exogenous threats such as viruses, bacteria, fungi, and parasites by distinguishing between "self" and "non-self". In addition, it guards us against other diseases, such as cancer, by detecting and responding to transformed and senescent cells. However, for survival and propagation, the altered cells and invading pathogens often employ a wide range of mechanisms to avoid, inhibit, or manipulate the immunorecognition. As such, the development of new modes of therapeutic intervention to augment protective and prevent harmful immune responses is desirable. Nucleic acids are biopolymers essential for all forms of life and, therefore, delineating the complex defensive mechanisms developed against non-self nucleic acids can offer an exciting avenue for future biomedicine. Nucleic acid technologies have already established numerous approaches in therapy and biotechnology; recently, rationally designed nucleic acids nanoparticles (NANPs) with regulated physiochemical properties and biological activities has expanded our repertoire of therapeutic options. When compared to conventional therapeutic nucleic acids (TNAs), NANP technologies can be rendered more beneficial for synchronized delivery of multiple TNAs with defined stabilities, immunological profiles, and therapeutic functions. This review highlights several recent advances and possible future directions of TNA and NANP technologies that are under development for controlled immunomodulation.

Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain

Small interfering RNAs (siRNAs) are potential therapeutic substances due to their gene silencing capability as exemplified by the recent approval by the US Food and Drug Administration (FDA) of the first siRNA therapeutic agent (patisiran). However, the delivery of naked siRNAs is challenging because of their short plasma half-lives and poor cell penetrability. In this study, we used vesicles made from bolaamphiphiles (bolas), GLH-19 and GLH-20, to investigate their ability to protect siRNA from degradation by nucleases while delivering it to target cells, including cells in the brain. Based on computational and experimental studies, we found that GLH-19 vesicles have better delivery characteristics than do GLH-20 vesicles in terms of stability, binding affinity, protection against nucleases, and transfection efficiency, while GLH-20 vesicles contribute to efficient release of the delivered siRNAs, which become available for silencing. Our studies with vesicles made from a mixture of the two bolas (GLH-19 and GLH-20) show that they were able to deliver siRNAs into cultured cancer cells, into a flank tumor and into the brain. The vesicles penetrate cell membranes and the blood-brain barrier (BBB) by endocytosis and transcytosis, respectively, mainly through the caveolae-dependent pathway. These results suggest that GLH-19 strengthens vesicle stability, provides protection against nucleases, and enhances transfection efficiency, while GLH-20 makes the siRNA available for gene silencing.

Regulation of senescence and the SASP by the transcription factor C/EBPβ

Oncogene-induced senescence (OIS) serves as an important barrier to tumor progression in cells that have acquired activating mutations in RAS and other oncogenes. Senescent cells also produce a secretome known as the senescence-associated secretory phenotype (SASP) that includes pro-inflammatory cytokines and chemokines. SASP factors reinforce and propagate the senescence program and identify senescent cells to the immune system for clearance. The OIS program is executed by several transcriptional effectors that include p53, RB, NF-κB and C/EBPβ. In this review, we summarize the critical role of C/EBPβ in regulating OIS and the SASP. Post-translational modifications induced by oncogenic RAS signaling control C/EBPβ activity and dimerization, and these alterations switch C/EBPβ to a pro-senescence form during OIS. In addition, C/EBPβ is regulated by a unique 3'UTR-mediated mechanism that restrains its activity in tumor cells to facilitate senescence bypass and suppression of the SASP.

RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition

RNA is a versatile biomaterial that can be used to engineer nanoassemblies for personalized treatment of various diseases. Despite promising advancements, the design of RNA nanoassemblies with minimal recognition by the immune system remains a major challenge. Here, an approach is reported to engineer RNA fibrous structures to operate as a customizable platform for efficient coordination of siRNAs and for maintaining low immunostimulation. Functional RNA fibers are studied in silico and their formation is confirmed by various experimental techniques and visualized by atomic force microscopy (AFM). It is demonstrated that the RNA fibers offer multiple advantages among which are: i) programmability and modular design that allow for simultaneous controlled delivery of multiple siRNAs and fluorophores, ii) reduced immunostimulation when compared to other programmable RNA nanoassemblies, and iii) simple production protocol for endotoxin-free fibers with the option of their cotranscriptional assembly. Furthermore, it is shown that functional RNA fibers can be efficiently delivered with various organic and inorganic carriers while retaining their structural integrity in cells. Specific gene silencing triggered by RNA fibers is assessed in human breast cancer and melanoma cell lines, with the confirmed ability of functional fibers to selectively target single nucleotide mutations.

Abstract 4361: Role of Rab GTPases and endosomal adaptor proteins in oncogenic RAS induced formation of perinuclear signaling complexes (PSCs)

Oncogenic RAS signaling leads to neoplastic transformation in immortalized cells and oncogene induced senescence in primary cells. Our laboratory has found that in both primary and immortalized cells oncogenic RAS induces constitutive perinuclear re-localization of p-ERK, CK2, and the MAPK scaffolding protein, KSR1. KSR1 binds to p-ERK and CK2, forming assemblies that we call “perinuclear signaling complexes” (PSCs). We observe PSCs in all cancer cell lines tested and in KRasG12V-driven mouse lung tumors, indicating that PSC formation is an important and integral characteristic of tumor cells. Our results show that KSR1 is essential for PSCs, as RNAi-mediated depletion of KSR1 or knockout of KSR1 disrupted their formation. We also demonstrated a key role for endosomal trafficking in this localized RAS signaling, as pharmacological inhibition of endocytosis prevented PSC formation. Furthermore, Rab11A, a Rab GTPase involved in trafficking of recycling endosomes, is required for establishment of PSCs and co-localizes with a pool of cellular CK2 and KSR1, but not p-ERK. Moreover, Rab11A knockdown caused decreased proliferation and survival of A549 cells (human KRAS mutant non-small cell lung adenocarcinoma). Our results demonstrate that there may be at least two classes of PSC-containing endosomes, p-ERK bound endosomes and CK2 bound endosomes. We are currently attempting to identify Rab GTPases that may differentiate these two kinds of PSC containing endosomes. Jongsma et al. (Cell, 2016) have shown that endosomes associated with the ubiquitin adaptor proteins EPS15, Tollip or TAXBP1 localize to the perinuclear region via the signaling adaptor, SQSTM1 (p62), which is tethered to the ER. We found that Tollip knockdown in A549 cells disrupted the CK2 bound endosomes but not p-ERK bound endosomes. Tollip knockdown also decreased cell proliferation and cell survival, while increasing apoptosis and autophagy. Whether other adaptor proteins are involved in RAS-mediated PSC formation remains to be determined. Growth factors (GF) also transiently induced PSCs in normal cells with delayed kinetics (4-6 hr). Our findings indicate that transformed cells sustain this novel late phase of GF signaling, localizing RAS pathway kinases to a nuclear-proximal compartment to drive tumorigenesis. We propose that PSCs are hallmarks of cancer cells and may represent useful biomarkers for cancer diagnosis and therapeutic responses.

Citation Format: Srikanta Basu, Sandip K. Basu, Jacqueline Salotti, Peter F. Johnson. Role of Rab GTPases and endosomal adaptor proteins in oncogenic RAS induced formation of perinuclear signaling complexes (PSCs) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4361.

A RAS-CaMKKβ-AMPKα2 pathway promotes senescence by licensing post-translational activation of C/EBPβ through a novel 3'UTR mechanism

Oncogene-induced senescence (OIS) is an intrinsic tumor suppression mechanism that requires the p53 and RB pathways and post-translational activation of C/EBPβ through the RAS-ERK cascade. We previously reported that in transformed/proliferating cells, C/EBPβ activation is inhibited by G/U-rich elements (GREs) in its 3′UTR. This mechanism, termed “3′UTR regulation of protein activity” (UPA), maintains C/EBPβ in a low-activity state in tumor cells and thus facilitates senescence bypass. Here we show that C/EBPβ UPA is overridden by AMPK signaling. AMPK activators decrease cytoplasmic levels of the GRE binding protein HuR, which is a key UPA component. Reduced cytoplasmic HuR disrupts 3′UTR-mediated trafficking of Cebpb transcripts to the peripheral cytoplasm – a fundamental feature of UPA – thereby stimulating C/EBPβ activation and growth arrest. In primary cells, oncogenic RAS triggers a Ca⁺⁺-CaMKKβ-AMPKα2-HuR pathway, independent of AMPKα1, that is essential for C/EBPβ activation and OIS. This axis is disrupted in cancer cells through down-regulation of AMPKα2 and CaMKKβ. Thus, CaMKKβ-AMPKα2 signaling constitutes a key tumor suppressor pathway that activates a novel UPA-cancelling mechanism to unmask the cytostatic and pro-senescence functions of C/EBPβ.

Oncogenic RAS-Induced Perinuclear Signaling Complexes Requiring KSR1 Regulate Signal Transmission to Downstream Targets

The precise characteristics that distinguish normal and oncogenic RAS signaling remain obscure. Here, we show that oncogenic RAS and BRAF induce perinuclear relocalization of several RAS pathway proteins, including the kinases CK2 and p-ERK1/2 and the signaling scaffold KSR1. This spatial reorganization requires endocytosis, the kinase activities of MEK-ERK and CK2, and the presence of KSR1. CK2α colocalizes with KSR1 and Rab11, a marker of recycling endosomes, whereas p-ERK associates predominantly with a distinct KSR1-positive endosomal population. Notably, these perinuclear signaling complexes (PSC) are present in tumor cell lines, mouse lung tumors, and mouse embryonic fibroblasts undergoing RAS-induced senescence. PSCs are also transiently induced by growth factors (GF) in nontransformed cells with delayed kinetics (4-6 hours), establishing a novel late phase of GF signaling that appears to be constitutively activated in tumor cells. PSCs provide an essential platform for RAS-induced phosphorylation and activation of the prosenescence transcription factor C/EBPβ in primary MEFs undergoing senescence. Conversely, in tumor cells, C/EBPβ activation is suppressed by 3'UTR-mediated localization of Cebpb transcripts to a peripheral cytoplasmic domain distinct from the PSC region. Collectively, our findings indicate that sustained PSC formation is a critical feature of oncogenic RAS/BRAF signaling in cancer cells that controls signal transmission to downstream targets by regulating selective access of effector kinases to substrates such as C/EBPβ.Significance: In addressing the long-standing question of the difference between normal and oncogenic RAS pathway signaling, this study shows that oncogenic RAS specifically triggers constitutive endocytosis-dependent movement of effector kinases to a perinuclear region, thereby creating connections to unique downstream targets such as the core prosenescence and the inflammatory regulatory transcription factor C/EBPβ. Cancer Res; 78(4); 891-908. ©2017 AACR.

Abstract A19: A Ras-Arf-Egr-C/EBPβ axis underlying oncogene-induced senescence and cancer

In normal cells, persistent oncogenic Ras activation triggers senescence, an intrinsic tumor suppression mechanism that protects cells from malignant transformation. Oncogene-induced senescence (OIS) is dependent on tumor suppressors such as p19/p14Arf, and loss of those genes facilitates transformation by oncogenic Ras. We previously reported that C/EBPβ, a transcription factor that has both pro- and anti-oncogenic functions, contributes to OIS in primary fibroblasts. Notably, C/EBPβ is down-regulated in H- or K-RasV12-transformed NIH 3T3 cells in a manner that requires loss of p19Arf. The potential role of C/EBPβ down-regulation in RasV12-induced transformation prompted us to investigate the mechanisms of Cebpb gene transcription. Here we show that Cebpb is an early growth factor-induced gene whose induction is suppressed by H-RasV12 in NIH 3T3 cells and p19Arf-/- MEFs. The early growth response (Egr) transcription factors are also down-regulated by H-RasV12 in these cells. Over-expression of any of Egr proteins (Egr1-4) restored C/EBPβ levels in 3T3Ras cells. Interestingly, Egrs induce growth arrest and senescence in 3T3Ras cells in a manner that is only partially dependent on reactivation of C/EBPβ. Egr1-4 proteins stimulated transcription from a promoter-reporter construct containing ∼3 kb of the Cebpb 5' flanking region. The proximal Cebpb promoter contains several putative Egr binding motifs, and mutating three of these sites disrupted Egr-mediated transactivation of the Cebpb promoter. Chromatin immunoprecipitation assays showed that ectopically expressed and endogenous Egrs bind to the Cebpb proximal promoter. Furthermore, microarray data from Oncomine show a strong correlation between CEBPB and EGR expression in human tumor samples, regardless of whether C/EBPβ levels increase or decrease in tumors compared to normal tissue. Since CEBPB and EGRs are down-regulated in lung adenocarcinomas and their elevated expression is associated with a better prognosis in lung cancer patients (Prognoscan), we over-expressed Egrs in A549 lung adenocarcinoma cells, which carry a KRAS mutation. Ectopic Egr2-4 induced CEBPB mRNA expression and dramatically suppressed cell proliferation. Collectively, our data indicate that decreased Egr levels account for oncogenic Ras-induced down-regulation of C/EBPβ in certain transformed cells, and restoration of Egrs induces growth arrest and C/EBPβ expression. Our findings identify the Egr-C/EBPβ axis as an important pathway in determining the cellular response (transformation or senescence) to oncogenic Ras-Arf signaling.

Citation Format: Jacqueline Salotti, Krisada Sakchaisri, Peter F. Johnson. A Ras-Arf-Egr-C/EBPβ axis underlying oncogene-induced senescence and cancer. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr A19. doi: 10.1158/1557-3125.RASONC14-A19

Fibroblast growth factor 2 causes G2/M cell cycle arrest in ras-driven tumor cells through a Src-dependent pathway

We recently reported that paracrine Fibroblast Growth Factor 2 (FGF2) triggers senescence in Ras-driven Y1 and 3T3^Ras mouse malignant cell lines. Here, we show that although FGF2 activates mitogenic pathways in these Ras-dependent malignant cells, it can block cell proliferation and cause a G2/M arrest. These cytostatic effects of FGF2 are inhibited by PD173074, an FGF receptor (FGFR) inhibitor. To determine which downstream pathways are induced by FGF2, we tested specific inhibitors targeting mitogen-activated protein kinase (MEK), phosphatidylinositol 3 kinase (PI3K) and protein kinase C (PKC). We show that these classical mitogenic pathways do not mediate the cytostatic activity of FGF2. On the other hand, the inhibition of Src family kinases rescued Ras-dependent malignant cells from the G2/M irreversible arrest induced by FGF2. Taken together, these data indicate a growth factor-sensitive point in G2/M that likely involves FGFR/Ras/Src pathway activation in a MEK, PI3K and PKC independent manner.

Abstract B24: A p19Arf-Egr-C/EBPβ axis underlying oncogene-induced senescence and tumor suppression

Cellular senescence is an intrinsic tumor suppression mechanism that protects cells from neoplastic transformation by activated oncogenes. As such, strategies to enhance senescence could be a promising avenue for cancer prevention. The transcription factor (TF) CCAAT/enhancer binding protein β (C/EBPβ) is induced and post-translationally activated by oncogenic Ras signaling in primary mouse embryonic fibroblasts (MEFs) and cooperates with RB:E2F to implement RasV12-induced senescence. In contrast, immortalized cells lacking the tumor suppressor p19Arf, such as NIH 3T3 murine fibroblasts, bypass senescence and are transformed by RasV12. Our lab previously showed that C/EBPβ expression is down-regulated in association with RasV12 transformation of NIH 3T3 cells. Furthermore, p19Arf acts in a p53-independent manner to maintain C/EBPβ levels in RasV12-expressing fibroblasts. Thus, C/EBPβ functions as part of an Arf-dependent tumor suppressor network activated by oncogenic stress. The opposing effects of oncogenic Ras on Cebpb expression in primary MEFs and immortalized NIH 3T3 cells prompted us to investigate the mechanisms that regulate Cebpb gene transcription. The early growth response (Egr) family of zinc-finger TFs is composed of 4 members, Egr-1-4. Here we show that Egrs are also down-regulated in RasV12-transformed NIH 3T3 cells (3T3Ras) and their ectopic expression restores C/EBPβ levels. Over-expression of any of the Egr proteins causes growth arrest and senescence in 3T3Ras cells in a manner that is partially dependent on reactivation of C/EBPβ. Egr proteins stimulate transcription from a promoter-reporter construct containing ∼3 kb of the Cebpb 5' flanking region. The proximal Cebpb promoter contains several putative Egr binding motifs, and mutating three of these sites disrupts Egr-mediated transactivation of the Cebpb reporter. Chromatin immunoprecipitation assays showed that ectopically expressed and endogenous Egrs bind to the Cebpb proximal promoter. In addition, serum stimulation of normal NIH 3T3 cells induces C/EBPβ mRNA and protein levels, which peak between 2-5 hours and coincide with transient induction of Egr proteins. Moreover, Egrs are only weakly induced by serum in 3T3Ras cells compared to their robust induction in the parental cells, with the exception of Egr-4 which was not detected in either cell line. Thus, decreased Egr levels can account for RasV12-induced down-regulation of C/EBPβ in transformed fibroblasts. Furthermore, microarray data from Oncomine show a strong correlation between CEBPB and EGR expression in human tumor samples. Collectively, our findings identify the Egr-C/EBPβ axis as a critical pathway in determining the cellular response (transformation or senescence) to oncogenic Ras-p19Arf signaling.

Citation Format: Jacqueline Salotti, Krisada Sakchaisri, Peter Johnson. A p19Arf-Egr-C/EBPβ axis underlying oncogene-induced senescence and tumor suppression. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B24.

Paternal preconceptional irradiation, population mixing and solid tumors in the children of radiation workers (England)

OBJECTIVE

To investigate whether there was an increased incidence of solid tumors among offspring of male radiation workers at the Sellafield nuclear installation in Cumbria, northwest England and whether paternal preconceptional irradiation was associated with the risk of solid tumors.

METHODS

A cohort study of 266,710 live births in Cumbria, 1950-1991, followed up to age 25 years on the end of 1991.

RESULTS

Children of radiation workers had a non-significantly increased risk of solid tumors (RR= 1.5, 95% CI: 0.9-2.4, p = 0.09), determined largely by an increased risk of cancers excluding leukemias, lymphomas, brain, spinal and gender-specific tumors (RR= 1.9, 95% CI: 1.0-3.3, p = 0.05), which was partly explained by differing patterns of parental migration (adjusted RR= 1.7, 95% Cl: 0.8-3.2, p = 0.50). Within children of radiation workers there was no evidence of an increased risk with increasing paternal preconception dose of external radiation (hazard ratio per 100 mSv for all solid tumors=0.6, 95% CI: 0.1-1.8, p = 0.52).

CONCLUSIONS

Any observed excess of solid tumors in children of radiation workers may be partly explained by population mixing. Fathers' occupational exposure to radiation before conception was not found to be risk factor for solid tumors in their children.

Stillbirths in relation to the coastline of Cumbria, 1950-89

The nuclear installation at Sellafield, in west Cumbria in the north of England, has discharged radioactive waste into the Irish Sea since 1952. The objective of this paper was to investigate whether women living near to the coast in Cumbria had an increased risk of having stillborn children. A retrospective cohort analysis was carried out using all 259,050 births (4017 stillbirths) to women normally resident in Cumbria during 1950-89, allowing for year of birth, social class and birth order using (i) comparison of observed and expected numbers of stillbirths in distance bands relative to the coast, (ii) comparison of cumulative observed and expected numbers of stillbirths by distance from the coast, and (iii) logistic regression analysis of stillbirth risk in relation to distance from the coast. Comparison of observed and expected numbers of stillbirths in distance bands within 10 km of the coast did not provide evidence of an excess risk of stillbirth closer to the coast. The comparison of the cumulative observed and expected numbers of stillbirths within 10 km of the coast supported this result. Logistic regression analysis of all births in Cumbria showed that distance from the coast did not significantly influence stillbirth risk (P > 0.05). There was no evidence to suggest an increased risk of stillbirth in mothers resident nearer to the coast.

Stillbirth rates around the nuclear installation at Sellafield, North West England: 1950-1989

BACKGROUND

The aim of the study was to investigate whether proximity to the nuclear installation at Sellafield, in Cumbria, North West of England, increases the risk of stillbirth in the resident population. The cohort consisted of all 256066 live and 4034 stillbirths to mothers usually domiciled in Cumbria, 1950-1989.

METHODS

The study was a retrospective cohort analysis allowing for year of birth, social class and birth order using: (i) Poisson probability mapping, (ii) comparison of cumulative observed and expected numbers of stillbirths by distance from Sellafield, (iii) logistic regression of stillbirth risk in relation to distance and direction from Sellafield.

RESULTS

Poisson probability mapping of stillbirths within 25 km of Sellafield provided no evidence to suggest that proximity to Sellafield increased the risk of stillbirth, either overall or in any specific direction. Comparison of the cumulative observed and expected numbers of stillbirths also showed no increased risk with proximity to Sellafield. Logistic regression analysis of all Cumbrian births supported these results, showing, in particular, that distance from Sellafield did not significantly influence stillbirth risk (P = 0.30). Although there was significant variation in stillbirth risk with direction (P = 0.0004), this was due to stillbirths in areas much further than 25 km from Sellafield. There was no significant effect with distance from Sellafield within any of six directional sectors (P > 0.05).

CONCLUSIONS

There was no evidence to suggest that proximity to Sellafield increases the risk of stillbirth in the resident population.