Toward the Scalable, Rapid, Reproducible, and Cost-Effective Synthesis of Personalized Nanomedicines at the Point of Care

Organic nanoparticles are used in nanomedicine, including for cancer treatment and some types of COVID-19 vaccines. Here, we demonstrate the scalable, rapid, reproducible, and cost-effective synthesis of three model organic nanoparticle formulations relevant to nanomedicine applications. We employed a custom-made, low-cost fluid mixer device constructed from a commercially available three-dimensional printer. We investigated how systematically changing aqueous and organic volumetric flow rate ratios determined liposome, polymer nanoparticle, and solid lipid nanoparticle sizes, size distributions, and payload encapsulation efficiencies. By manipulating inlet volumes, we synthesized organic nanoparticles with encapsulation efficiencies approaching 100% for RNA-based payloads. The synthesized organic nanoparticles were safe and effective at the cell culture level, as demonstrated by various assays. Such cost-effective synthesis approaches could potentially increase the accessibility to clinically relevant organic nanoparticle formulations for personalized nanomedicine applications at the point of care, especially in nonhospital and low-resource settings.

Abstract 1483: RNA interference seed-based approach to inhibit androgen signaling and induce prostate cancer cell death

The goal of this study is to identify RNA interference (RNAi) seed sequences that inhibit androgen signaling and induce toxicity in prostate cancer (PCa) cells. The high prevalence of acquired resistance to androgen deprivation therapy, as well as first and second generation androgen receptor (AR) antagonists, drives the development of lethal castration resistant prostate cancer (CRPC). As a result, PCa remains one of the leading causes of cancer related deaths in men. AR amplification, gain of function mutations and constitutively active splice isoforms of the AR, and the overexpression of AR coregulators, play considerable roles in promoting CRPC by sustaining AR activity in the presence of the low androgen environment and/or AR antagonists. The development of specific small molecule inhibitors of AR splice isoforms has been largely unsuccessful, and inhibitors of individual AR coregulators have not translated well into the clinic, likely due to their large number and functional redundancies. Therefore, novel therapeutic strategies for targeting androgen signaling in CRPC are necessary. Previous studies in our lab have demonstrated RNAi-mediated PCa cell death through seed region (nucleotides 2-8) complementarity of shRNA/siRNA guide strands to the 3’UTR of the AR and multiple AR coregulators and essential genes. In the current study, we used an unbiased novel seed-based shRNA screen to identify seed sequences that are toxic to different PCa cells, including CRPC cells expressing the clinically relevant constitutively active AR variant 7 (AR-V7). Common motifs were identified among toxic seed sequences, and the miRDB target prediction database was used to select those seeds that were predicted to target the AR and AR coregulators. Using RNA-seq analyses we confirmed that selected seed sequences inhibited global androgen signaling and identified potential direct targets known to be relevant to PCa. Conclusions: These studies have identified androgen signaling inhibitory sequences that have the potential to be used in RNAi-seed based therapies for PCa. The ability to inhibit the expression of the AR and multiple essential AR coregulators simultaneously with one agent, and the reduced likelihood of developed resistance, are considerable benefits of this approach.

Citation Format: Joshua M. Corbin, Maria J. Ruiz-Echevarria. RNA interference seed-based approach to inhibit androgen signaling and induce prostate cancer cell death [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 1483.

Patient-Derived Xenografts of High-Grade Serous Ovarian Cancer Subtype as a Powerful Tool in Pre-Clinical Research

(1) Background. PDX models have become the preferred tool in research laboratories seeking to improve development and pre-clinical testing of new drugs. PDXs have been shown to capture the cellular and molecular characteristics of human tumors better than simpler cell line-based models. More recently, however, hints that PDXs may change their characteristics over time have begun to emerge, emphasizing the need for comprehensive analysis of PDX evolution. (2) Methods. We established a panel of high-grade serous ovarian carcinoma (HGSOC) PDXs and developed and validated a 300-SNP signature that can be successfully utilized to assess genetic drift across PDX passages and detect PDX contamination with lymphoproliferative tissues. In addition, we performed a detailed histological characterization and functional assessment of multiple PDX passages. (3) Results. Our data show that the PDXs remain largely stable throughout propagation, with marginal genetic drift at the time of PDX initiation and adaptation to mouse host. Importantly, our PDX lines retained the major histological characteristics of the original patients' tumors even after multiple passages in mice, demonstrating a strong concordance with the clinical responses of their corresponding patients. (4) Conclusions. Our data underline the value of defined HGSOC PDXs as a pre-clinical tumor model.

Analysis of TMEFF2 allografts and transgenic mouse models reveals roles in prostate regeneration and cancer

BACKGROUND

Previous results from our lab indicate a tumor suppressor role for the transmembrane protein with epidermal growth factor and two follistatin motifs 2 (TMEFF2) in prostate cancer (PCa). Here, we further characterize this role and uncover new functions for TMEFF2 in cancer and adult prostate regeneration.

METHODS

The role of TMEFF2 was examined in PCa cells using Matrigel(TM) cultures and allograft models of PCa cells. In addition, we developed a transgenic mouse model that expresses TMEFF2 from a prostate specific promoter. Anatomical, histological, and metabolic characterizations of the transgenic mouse prostate were conducted. The effect of TMEFF2 in prostate regeneration was studied by analyzing branching morphogenesis in the TMEFF2-expressing mouse lobes and alterations in branching morphogenesis were correlated with the metabolomic profiles of the mouse lobes. The role of TMEFF2 in prostate tumorigenesis in whole animals was investigated by crossing the TMEFF2 transgenic mice with the TRAMP mouse model of PCa and analyzing the histopathological changes in the progeny.

RESULTS

Ectopic expression of TMEFF2 impairs growth of PCa cells in Matrigel or allograft models. Surprisingly, while TMEFF2 expression in the TRAMP mouse did not have a significant effect on the glandular prostate epithelial lesions, the double TRAMP/TMEFF2 transgenic mice displayed an increased incidence of neuroendocrine type tumors. In addition, TMEFF2 promoted increased branching specifically in the dorsal lobe of the prostate suggesting a potential role in developmental processes. These results correlated with data indicating an alteration in the metabolic profile of the dorsal lobe of the transgenic TMEFF2 mice.

CONCLUSIONS

Collectively, our results confirm the tumor suppressor role of TMEFF2 and suggest that ectopic expression of TMEFF2 in mouse prostate leads to additional lobe-specific effects in prostate regeneration and tumorigenesis. This points to a complex and multifunctional role for TMEFF2 during PCa progression.

Abstract 2065: TMEFF2 is a novel androgen receptor co-activator in prostate cancer cells

The goal of this study is to delineate the role of a novel androgen receptor (AR) coactivator in advanced prostate cancer (PCa). While great advances have been made in the ability to detect PCa, the disease remains the second leading cause of cancer related deaths in men. The AR is a steroid nuclear receptor that serves a central function in both normal prostate cell homeostasis and in PCa; in fact, the vast majority of PCa tumors require androgens for growth. This dependency has led to the development and use of androgen deprivation therapies (ADTs) for the treatment of PCa. ADT is initially a successful form of treatment for most PCa patients; however, the majority of patients eventually relapse with castration-resistant prostate cancer (CRPC), which is currently incurable. Because sustained AR activity under androgen depleted conditions is a major contributor to the development of CRPC, identifying molecular mechanisms that contribute to AR activity in CRPC is paramount for the development of successful therapies.

Our lab has been studying the role of the transmembrane protein with epidermal-like growth factor domain and two follistatin domains 2 (TMEFF2) in PCa. While TMEFF2 gene expression is repressed by hypermethylation in multiple cancers, TMEFF2 is overexpressed in PCa and CRPC, suggesting that TMEFF2 may have a unique function in PCa. Importantly, TMEFF2 expression is activated by the androgen receptor (AR) at the level of transcription and translation, which may contribute to its overexpression in PCa. Our data presented here indicate that TMEFF2 functions in PCa cells as a coactivator of the AR. Using shRNA to stably knockdown TMEFF2 expression in androgen dependent PCa and CRPC cell lines, we demonstrate that TMEFF2 activates the basal and androgen-induced expression of multiple androgen responsive genes, including prostate-specific antigen (PSA), at the mRNA and protein level. Importantly, the knock-down of TMEFF2 does not alter AR protein levels, indicating that TMEFF2 influences AR activity. Additionally, by coimmunoprecipitation analysis, we demonstrate that TMEFF2 interacts with the AR, and western blot analyses with cellular fractionation samples indicate that TMEFF2 has the ability to translocate to the nucleus of PCa cells. Based on these results, we conclude that TMEFF2 is a novel AR coactivator in PCa. Future studies will focus on understanding the nature and biological effects of the interaction between TMEFF2 and the AR, and delineating the molecular mechanism through which TMEFF2 activates AR-mediated gene expression. Because sustained AR activity in androgen depleted conditions is a major contributor to CRPC relapse and PCa mortality, the TMEFF2-mediated AR activation mechanism may be clinically useful as a therapeutic target in CRPC.

Citation Format: Joshua Corbin, Thomas Green, Maria J. Ruiz-Echevarria. TMEFF2 is a novel androgen receptor co-activator in prostate cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2065. doi:10.1158/1538-7445.AM2015-2065

Abstract 4234: Translational regulation mediates hematopoietic progenitor cell generation in embryonic stem cell culture

The development and maintenance of hematopoietic progenitors (HP) requires modulation of a network of genes that balance self-renewal, expansion and lineage commitment. Regulation by miRNAs is critical for the differentiation of progenitors along defined pathways, and requires the recruitment and coordinate interaction of RNA binding proteins that modulate translation and/or target specific transcripts for sequestration or degradation. Here we provide evidence that translational regulation by the RNA binding proteins HuR and Pum2 are critical to HP generation from murine embryonic stem (ES) cell culture and that translational regulation during HP generation enhance ex vivo proliferative capacity and transplantability of progenitors.

Translationally regulated transcript subsets in ES culture were identified by sucrose gradient polysome analysis. Ribonucleases and RNA-binding proteins comprised 12% of transcripts downregulated during ES cell differentiation to hematopoietic lineage (p=2.34 × 10-27 and 7.3 × 10-7 respectively). RNA-immunoprecipitation-sequencing (RIP-seq) using antibodies to several of the identified RNA binding proteins, followed by sequencing (Roche GS-FLX) revealed transcripts regulated by each. Pathway analysis of the transcripts associated with Pum2 in differentiated cells identified p53, p53-interacting proteins, and translation regulation Go (p=2.48×10-11). There was significant overlap with transcripts associated with HuR from undifferentiated ES (p=8.1×10-11), suggesting that the transcripts regulated by HuR in undifferentiated cells become associated with Pum2 with upon differentiation. Confocal imaging of HuR and Pum2 was consistent with this finding. Pathway analysis of DnD-associated transcripts revealed a network centered about Rac signaling and the Abl, Src and MAPK pathway via MAPKKK1–an essential pathway for stem cell self-renewal and maintenance. Consistent with the central role of translational regulation in the generation of HP, inhibition of translation using pharmacologic approaches (rapamycin, wortmannin, or clotrimazole) or siRNA (HuR, Pum2) resulted in up to three log increases in early HP derived from ES cell culture as measured by long term culture initiating cell (LTCIC) assay and the acquisition of competitive transplantability in irradiated hosts as measured by percentage chimeric animals and survival (p<0.05).

Our findings reveal a system of broad-based translational regulation of HP differentiation mediated by RNA binding proteins. The findings suggest a methodology for ex vivo expansion of marrow-derived HP and enhanced generation of ES-derived HP by coordinate regulation of specific RNA binding proteins and their associated transcripts to regulate cell differentiation.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4234.

Abstract 3059: The Tmeff2 protein functions as a tumor suppressor and interacts with Sarcosine dehydrogenase

Tmeff2 is a gene with an expression profile limited to the brain and the prostate but shown to be frequently upregulated in prostate cancer. It encodes a type I transmembrane protein with a short cytoplasmic tail containing a potential G-protein activation domain and an extracellular domain containing two follistatin (FS) modules and an epidermal growth factor-like (EGF) domain. Although these features are suggestive of a function in signal transduction, the role of the Tmeff2 in prostate cancer, or the mechanism(s) that lead to its overexpression during the disease are unclear. In the present study, we evaluated the functional role of Tmeff2 in prostate tumorigenesis.

To investigate the function of the gene, Tmeff2 was overexpressed in TRAMP C1 murine prostate cancer cells and HEK293T cells, and the effects of overexpression on cellular growth and tumorigenicity were assessed. Tmeff2 overexpression in HEK293T cells almost completely abolished the ability of these cells to form colonies in soft agar and resulted in a 20-30% reduction in proliferation rates in these and TRAMP C1 cells, indicating that the gene may function as a tumor suppressor in prostate cancer cells. Moreover, although TMEFF2 overexpression alone did not induce apoptosis, it sensitized these cell lines to staurosporine or rapamycin-induced apoptosis, causing nearly a three-fold increase in the percentage of apoptotic cells.

In order to assess the molecular mechanism(s) by which Tmeff2 may suppress cellular growth and tumorigenicity, we screened Tmeff2 affinity complexes by mass spectrometry to search for candidate functional partner(s) of Tmeff2. Our results showed an interaction with Sarcosine Dehydrogenase (SARDH) an enzyme involved in the metabolism of sarcosine. This interaction was further confirmed by co-immunoprecipitation analysis. Importantly, sarcosine has recently been described as a biomarker for prostate cancer as it was shown to be highly increased in prostate and metastatic prostate cancer. In addition, it may also play a role in the biology of the cancer since it promotes cell invasion when added to benign prostate epithelial cells.

In summary, the results presented here suggest that Tmeff2 functions as a tumor suppressor for prostate cancer. Its interaction with SARDH may represent a mechanism by which Tmeff2 modulates tumorigenicity by altering the levels of sarcosine. Further analyses are necessary to determine the value of Tmeff2 as a prognostic marker.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3059.

Characterization of a general stabilizer element that blocks deadenylation-dependent mRNA decay

mRNA degradation is a regulated process that can play an important role in determining the level of expression of specific genes. The rate at which a specific mRNA is degraded depends largely on specific cis-acting sequences located throughout the transcript. cis-Acting destabilizer sequences that promote increased rates of decay have been identified in several short-lived mRNAs. However, little is known about elements that promote stability, known as stabilizer elements (STEs), and how they function. The work presented here describes the characterization of a STE in the PGK1 transcript. The PGK1 stabilizer element (P-STE) has been delineated to a 64-nucleotide sequence from the coding region that can stabilize a chimeric transcript containing the instability elements from the 3'-untranslated region of the MFA2 transcript. The P-STE is located within the PGK1 coding region and functions when located in the translated portion of the transcript and at a minimum distance from the 3'-untranslated region. These results further support the link between translation and mRNA degradation. A conserved sequence in the TEF1/2 transcript has been identified that also functions as a STE, suggesting that this sequence element maybe a general stability determinant found in other yeast mRNAs.

Should we kill the messenger? The role of the surveillance complex in translation termination and mRNA turnover

Eukaryotes have evolved conserved mechanisms to rid cells of faulty gene products that can interfere with cell function. mRNA surveillance is an example of a pathway that monitors the translation termination process and promotes degradation of transcripts harboring premature translation termination codons. Studies on the mechanism of mRNA surveillance in yeast and humans suggest a common mechanism where a "surveillance complex" monitors the translation process and determines whether translation termination has occurred at the correct position within the mRNA. A model will be presented that suggests that the surveillance complex assesses translation termination by monitoring the transition of an RNP as it is converted from a nuclear to a cytoplasmic form during the initial rounds of translation.

The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs

The nonsense-mediated mRNA decay pathway is an example of an evolutionarily conserved surveillance pathway that rids the cell of transcripts that contain nonsense mutations. The product of the UPF1 gene is a necessary component of the putative surveillance complex that recognizes and degrades aberrant mRNAs. Recent results indicate that the Upf1p also enhances translation termination at a nonsense codon. The results presented here demonstrate that the yeast and human forms of the Upf1p interact with both eukaryotic translation termination factors eRF1 and eRF3. Consistent with Upf1p interacting with the eRFs, the Upf1p is found in the prion-like aggregates that contain eRF1 and eRF3 observed in yeast [PSI+] strains. These results suggest that interaction of the Upf1p with the peptidyl release factors may be a key event in the assembly of the putative surveillance complex that enhances translation termination, monitors whether termination has occurred prematurely, and promotes degradation of aberrant transcripts.

Translating old drugs into new treatments: ribosomal frameshifting as a target for antiviral agents

Programmed ribosomal frameshifting is used by many viruses to regulate the production of structural and enzymatic proteins. Altering the frameshifting efficiencies disrupts the virus life cycle and eliminates or reduces virus production. Ribosomal frameshifting therefore provides a unique target on which antiviral agents can function. This article describes a series of rapid assay strategies that have been developed and used to identify potential antiviral agents that target programmed -1 ribosomal frameshifting.

Peptidyl-transferase inhibitors have antiviral properties by altering programmed -1 ribosomal frameshifting efficiencies: development of model systems

The effects of two peptidyl-transferase inhibitors, anisomycin and sparsomycin, on ribosomal frameshifting efficiencies and the propagation of yeast double-stranded RNA viruses were examined. At sublethal doses in yeast cells these drugs specifically alter the efficiency of -1, but not of +1, ribosomal frameshifting. These compounds promote loss of the yeast L-A double-stranded RNA virus, which uses a programmed -1 ribosomal frameshift to produce its Gag-Pol fusion protein. Both of these drugs also change the efficiency of -1 ribosomal frameshifting in yeast and mammalian in vitro translation systems, suggesting that they may have applications to control the propagation of viruses of higher eukaryotes, which also use this translational regulatory mechanism. Our results offer a new set of antiviral agents that may potentially have a broad range of applications in the clinical, veterinary, and agricultural fields.

Making sense of nonsense in yeast

Messenger RNA (mRNA) degradation is a process that plays an important role in the regulation of gene expression and can be linked to translation. Study of the nonsense-mediated mRNA decay pathway has greatly aided our understanding of the link between these processes. Evidence indicates that this pathway regulates the abundance of both aberrant and wild-type transcripts. Factors involved in this pathway have been identified and recent results indicate that they might also be involved in modulating translation. Here, we discuss the mechanism of nonsense-mediated mRNA decay in the yeast Saccharomyces cerevisiae and the potential role that this pathway can have on the regulation of gene expression.

Utilizing the GCN4 leader region to investigate the role of the sequence determinants in nonsense-mediated mRNA decay

In the yeast Saccharomyces cerevisiae, premature translation termination promotes rapid degradation of mRNAs. Accelerated decay requires the presence of specific cis-acting sequences which have been defined as downstream elements. It has been proposed that the role of the downstream element may be to promote translational reinitiation or ribosomal pausing. The GCN4 gene produces an mRNA that contains four short upstream open reading frames (uORFs) preceding the GCN4 protein-coding region in which translational initiation and reinitiation events occur. It was anticipated that these uORFs would function in a manner analogous to nonsense codons, promoting rapid degradation of the mRNA. However, the GCN4 transcript was not degraded by the nonsense-mediated mRNA decay pathway. We have investigated the role of the leader region of the GCN4 transcript in an effort to identify possible sequence elements that inactivate this decay pathway. We show that the GCN4 leader region does not harbor a downstream element needed to promote mRNA decay. In addition, using hybrid GCN4-PGK1 transcripts, we demonstrate that if a translational reinitiation signal precedes a downstream element, the mRNA will no longer be sensitive to nonsense-mediated decay. Furthermore, we demonstrate that the downstream element is functional only after a translational initiation and termination cycle has been completed but is unable to promote nonsense-mediated mRNA decay if it is situated 5' of a translational initiation site. Based on these results, the role of the downstream element will be discussed.

Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay

In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3' of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3' of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5' of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3' of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3' of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed.

Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover

Several lines of evidence indicate that the processes of mRNA turnover and translation are intimately linked and that understanding this relationship is critical to elucidating the mechanism of mRNA decay. One clear example of this relationship is the observation that nonsense mutations can accelerate the decay of mRNAs in a process that we term nonsense-mediated mRNA decay. The experiments described here demonstrate that in the yeast Saccharomyces cerevisiae premature translational termination within the initial two-thirds of the PGK1 coding region accelerates decay of that transcript regardless of which of the stop codons is used. Nonsense mutations within the last quarter of the coding region have no effect on PGK1 mRNA decay. The sequences required for nonsense-mediated mRNA decay include a termination codon and specific sequences 3' to the nonsense mutation. Translation of two-thirds of the PGK1 coding region inactivates the nonsense-mediated mRNA decay pathway. This observation explains why carboxyl-terminal nonsense mutations are resistant to accelerated decay. Characterization of the decay of nonsense-containing HIS4 transcripts yielded results mirroring those described above, suggesting that the sequence requirements described for the PGK1 transcript are likely to be a general characteristic of this decay pathway. In addition, an analysis of the decay intermediates of nonsense-containing mRNAs indicates that nonsense-mediated mRNA decay flows through a pathway similar to that described for a class of wild-type transcripts. The initial cleavage event occurs near the 5' terminus of the nonsense-containing transcript and is followed by 5'-->3' exonucleolytic digestion. A model for nonsense-mediated mRNA decay based on these results is discussed.