Toward a Better Understanding of Bioassays for the Development of Biopharmaceuticals by Exploring the Structure-Antibody-Dependent Cellular Cytotoxicity Relationship in Human Primary Cells

Pharmaceutical manufacturing relies on rigorous methods of quality control of drugs and in particular of the physico-chemical and functional characterizations of monoclonal antibodies. To that end, robust bioassays are very often limited to reporter gene assays and the use of immortalized cell lines that are supposed to mimic immune cells such as natural killer (NK) cells to the detriment of primary materials, which are appreciated for their biological validity but are also difficult to exploit due to the great diversity between individuals. Here, we characterized the phenotype of the peripheral blood circulating cytotoxic cells of 30 healthy donors, in particular the repertoire of cytotoxic markers, using flow cytometry. In parallel, we characterized the antibody-dependent cellular cytotoxicity (ADCC) effector functions of these primary cells by measuring their cytolytic activity against a cancer cell-line expressing HER2 in the presence of trastuzumab and with regards to FCGR3A genotype. We could not establish a correlation or grouping of individuals using the data generated from whole peripheral blood mononuclear cells, however the isolation of the CD56-positive population, which is composed not only of NK cells but also of natural killer T (NKT) and γδ-T cells, as well as subsets of activated cytotoxic T cells, monocytes and dendritic cells, made it possible to standardize the parameters of the ADCC and enhance the overall functional avidity without however eliminating the inter-individual diversity. Finally, the use of primary CD56+ cells in ADCC experiments comparing glycoengineered variants of trastuzumab was conclusive to test the limits of this type of ex vivo system. Although the effector functions of CD56+ cells reflected to some extent the in vitro receptor binding properties and cytolytic activity data using NK92 cells, as previously published, reaching a functional avidity plateau could limit their use in a quality control framework.

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway

Cell cycle is a cellular process that is subject to stringent control. In contrast to the wealth of knowledge of proteins controlling the cell cycle, very little is known about the molecular role of lncRNAs (long noncoding RNAs) in cell-cycle progression. By performing genome-wide transcriptome analyses in cell-cycle-synchronized cells, we observed cell-cycle phase-specific induction of >2000 lncRNAs. Further, we demonstrate that an S-phase-upregulated lncRNA, SUNO1, facilitates cell-cycle progression by promoting YAP1-mediated gene expression. SUNO1 facilitates the cell-cycle-specific transcription of WTIP, a positive regulator of YAP1, by promoting the co-activator, DDX5-mediated stabilization of RNA polymerase II on chromatin. Finally, elevated SUNO1 levels are associated with poor cancer prognosis and tumorigenicity, implying its pro-survival role. Thus, we demonstrate the role of a S-phase up-regulated lncRNA in cell-cycle progression via modulating the expression of genes controlling cell proliferation.

Small-molecule MDM2 antagonists attenuate the senescence-associated secretory phenotype

Processes that have been linked to aging and cancer include an inflammatory milieu driven by senescent cells. Senescent cells lose the ability to divide, essentially irreversibly, and secrete numerous proteases, cytokines and growth factors, termed the senescence-associated secretory phenotype (SASP). Senescent cells that lack p53 tumor suppressor function show an exaggerated SASP, suggesting the SASP is negatively controlled by p53. Here, we show that increased p53 activity caused by small molecule inhibitors of MDM2, which promotes p53 degradation, reduces inflammatory cytokine production by senescent cells. Upon treatment with the MDM2 inhibitors nutlin-3a or MI-63, human cells acquired a senescence-like growth arrest, but the arrest was reversible. Importantly, the inhibitors reduced expression of the signature SASP factors IL-6 and IL-1α by cells made senescent by genotoxic stimuli, and suppressed the ability of senescent fibroblasts to stimulate breast cancer cell aggressiveness. Our findings suggest that MDM2 inhibitors could reduce cancer progression in part by reducing the pro-inflammatory environment created by senescent cells.

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

CD133 is widely used as a marker for stem/progenitor cells in many organ systems. Previous studies using in vitro stem cell assays have suggested that the CD133-expressing prostate basal cells may serve as the putative prostate stem cells. However, the precise localization of the CD133-expressing cells and their contributions to adult murine prostate homeostasis in vivo remain undetermined. We show that loss of function of CD133 does not impair murine prostate morphogenesis, homeostasis and regeneration, implying a dispensable role for CD133 in prostate stem cell function. Using a CD133-CreER(T2) model in conjunction with a fluorescent report line, we show that CD133 is not only expressed in a fraction of prostate basal cells, but also in some luminal cells and stromal cells. CD133(+) basal cells possess higher in vitro sphere-forming activities than CD133(-) basal cells. However, the in vivo lineage tracing study reveals that the two cell populations possess the same regenerative capacity and contribute equally to the maintenance of the basal cell lineage. Similarly, CD133(+) and CD133(-) luminal cells are functionally equivalent in maintaining the luminal cell lineage. Collectively, our study demonstrates that CD133 does not enrich for the stem cell activity in vivo in adult murine prostate. This study does not contradict previous reports showing CD133(+) cells as prostate stem cells in vitro. Instead, it highlights a substantial impact of biological contexts on cellular behaviors.

Abstract A2-44: Stellaris® RNA fluorescence in situ hybridization (RNA FISH) for the detection of long non coding RNA biomarkers

Long non-coding RNAs (lncRNAs) play important roles in all the central aspects of the gene expression cascade with wide ranging effects on cell proliferation and differentiation. As such, lncRNAs are highly promising additions to many cancer biomarkers portfolios and enable more precise diagnostic staging. This, in turn, provides a clearer prognosis and treatment options of different cancers. Direct visualization and quantification of lncRNAs in single cells and in tissue are thus emerging as essential tools for both basic and clinical research. Interestingly, studies have demonstrated that transcript levels are more strongly correlated to clinical traits than the corresponding protein levels. Because RNA biomarkers have the potential to contribute to the development of targeted cancer therapies, there is also an obvious need for a robust and dependable methodology to discover and validate these RNAs.

RNA fluorescence in situ hybridization (RNA FISH) provides a powerful means to detect RNA biomarkers in single cells, while still maintaining tissue morphology. Significant advances in RNA FISH technology, such as the hybridization of pools of singly labeled fluorescent 20-mer oligonucleotides to the RNA target, now afford specific and sensitive multiplex detection of RNA to yield information on the RNA's distinct spatial distribution within cells and tissue.

Data is presented on the design of probe sets against multiple disease relevant pre-lncRNAs and against the introns of their precursors, as well as on the simultaneous dual-channel imaging of the pre-lncRNAs and mature lncRNAs. Because the absolute majority of post-transcriptional processing, including splicing of mRNAs and lncRNAs, occurs co-transcriptionally, the location of introns can be used as a proxy nuclear location for the encoding gene. We find mature lncRNAs to locate at or close to the site of transcription, but also well away from it. Next, we present data on emerging non-coding RNA biomarkers in breast and prostate cancer tissue and in cell lines utilizing RNA FISH.

In summary, the results and tools presented here will contribute to advancing the current capabilities of the detection and treatment of specific cancers, as well as in the continued discovery and development of cancer drug candidates.

Citation Format: Arturo V. Orjalo, Jr., Hans E. Johansson. Stellaris® RNA fluorescence in situ hybridization (RNA FISH) for the detection of long non coding RNA biomarkers. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-44.

Female Bias in Systemic Lupus Erythematosus is Associated with the Differential Expression of X-Linked Toll-Like Receptor 8

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of anti-nuclear antibodies. SLE is one of many autoimmune disorders that have a strong gender bias, with 70–90% of SLE patients being female. Several explanations have been postulated to account for the severity of autoimmune diseases in females, including hormonal, microbiota, and gene dosage differences. X-linked toll-like receptors (TLRs) have recently been implicated in disease progression in females. Our previous studies using the 564Igi mouse model of SLE on a Tlr7 and Tlr9 double knockout background showed that the presence of Tlr8 on both X chromosomes was required for the production of IgG autoantibodies, Ifn-I expression and granulopoiesis in females. Here, we show the results of our investigation into the role of Tlr8 expression in SLE pathogenesis in 564Igi females. Female mice have an increase in serum pathogenic anti-RNA IgG2a and IgG2b autoantibodies. 564Igi mice have also been shown to have an increase in neutrophils in vivo, which are major contributors to Ifn-α expression. Here, we show that neutrophils from C57BL/6 mice express Ifn-α in response to 564 immune complexes and TLR8 activation. Bone marrow-derived macrophages from 564Igi females have a significant increase in Tlr8 expression compared to male-derived cells, and RNA fluorescence in situ hybridization data suggest that Tlr8 may escape X-inactivation in female-derived macrophages. These results propose a model by which females may be more susceptible to SLE pathogenesis due to inefficient inactivation of Tlr8.

Simultaneous detection of nuclear and cytoplasmic RNA variants utilizing Stellaris® RNA fluorescence in situ hybridization in adherent cells

RNA fluorescence in situ hybridization (FISH) has long been an indispensable tool for the detection and localization of RNA and is increasingly becoming an important complement to other gene expression analysis methods. We detail a streamlined RNA FISH protocol for the simultaneous imaging of multiple RNA gene products and RNA variants in fixed mammalian cells. The technique utilizes fluorescently pre-labeled, short DNA oligonucleotides (20 nucleotides in length), pooled into sets of up to 48 individual probes. The overall binding of multiple oligonucleotides to the same RNA target results in punctate fluorescent signals representing individual RNA molecules without the need for enzymatic signal amplification. Visualization of these punctate signals, through the use of wide-field fluorescence microscopy, enables the quantification of single RNA transcripts. Additionally, by utilizing probe sets with spectrally distinct fluorophores, multiplex analysis of specific RNAs, or RNA variants, can be achieved. We focus on the detection of a cytoplasmic mRNA and a nuclear long noncoding RNA to illustrate the benefits of this method for cell-specific detection and subcellular localization. Post-processing of images and spot counting is briefly discussed to demonstrate the capabilities of this method for the statistical analysis of RNA molecule number per cell, which is information that can be utilized to determine overall gene expression levels and cell-to-cell gene expression variation.

Abstract 3399: Detection and validation of novel RNA cancer biomarkers by single molecule RNA fluorescence in situ hybridization (smRNA FISH)

RNA biomarkers are discovered and validated through advanced transcriptome analysis at a fast pace. These markers that allow the interrogation of the active genes hold promise for more precise staging, prognosis, and treatment of cancer. Long RNA markers comprise pre-mRNAs found in the cell nucleus, long non-coding RNAs (lncRNAs) that may be found in both the nucleus and the cytoplasm, as well as mature and mostly cytoplasmic mRNAs. Importantly, comparative studies in mouse have demonstrated that transcript levels are more strongly correlated with clinical traits than the corresponding protein levels. Because lncRNA and mRNA biomarkers have the potential to contribute to the development of targeted cancer therapies, there is an obvious need for a robust and dependable methodology to reliably detect and validate these RNA targets. RNA fluorescence in situ hybridization (RNA FISH) provides a powerful means to detect specific RNAs in single cells, while still maintaining tissue morphology. Significant advances in RNA FISH technology, such as the hybridization of multiple, fluorescently labeled 20-mer oligonucleotides to the RNA target, allow for the detection of single RNAs and yields information on the RNA's distinct spatial distribution within tissues and even within cells. In this study, we investigate emerging RNA biomarkers in prostate cancer cell lines and tissue utilizing RNA FISH. We also examine established breast cancer biomarkers such as human epidermal growth factor receptor 2 (HER2 / ERBB2), estrogen receptor α (ER α / ESR1), and progesterone receptor (PR / PGR) in breast cancer tumors and cell lines. The results and tools presented here will contribute to advancing the current capabilities of the detection and treatment of specific cancers, as well as in the continued discovery and development of cancer drug candidates.

Citation Format: Hans E. Johansson, Arturo V. Orjalo, Sally R. Coassin, Raymund Yin. Detection and validation of novel RNA cancer biomarkers by single molecule RNA fluorescence in situ hybridization (smRNA FISH). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3399. doi:10.1158/1538-7445.AM2014-3399

Abstract 1940: High-throughput imaging and high content analysis of disease relevant lncRNAs examined by RNA fluorescence in situ hybridization (RNA FISH)

The genome is extensively transcribed, yet more than 50 % of RNA transcripts lack protein coding potential. In recent years, long noncoding RNAs (lncRNAs) have been shown to play extensive roles in all the central aspects of gene function including imprinting, epigenetic regulation, transcription, splicing and nuclear/cytoplasmic trafficking, translation and RNA stability, with wide ranging effects on cell cycle and differentiation. Due to the increasingly central role of lncRNAs in gene transcription and disease states, it is important to develop tools to allow direct visualization and quantification of lncRNAs that could be useful both in the basic science arena and in the clinical setting with possible uses both in diagnostics and prognostics.

We recently streamlined both the design and synthesis of fluorescently labeled probe sets containing multiple tiled 20-mer GC-balanced oligonucleotides for use in RNA fluorescence in situ hybridization (RNA FISH). In contrast to traditional cell-disruptive RNA analyses (e.g. northern blotting and qPCR) that report relative population averages of RNA content, single molecule RNA FISH affords specific and sensitive detection of RNAs and quantitatively establishes the intracellular localization of the target lncRNAs.

We have validated an imaging based platform to perform RNA FISH in both manual (coverslip) and automated (384 well) formats that allows tremendous multiplexing and throughput using high throughput microscopy. Moreover, we developed high content analysis routines that permit quantification of RNA particles at the single cell level and determine their localization and pattern (texture). As specific lncRNAs (e.g. MALAT1) are known to target specific intranuclear domains (e.g. splicing speckles) we developed classification methods based upon sets of intensity and texture features to compare intracellular patterns of novel/less characterized ncRNAs. Moreover, this framework will also permit to address changes in lncRNA expression and patterns during the cell cycle since large number of cells can be analyzed simultaneously. We are now expanding our analysis to primary tumor tissues where lncRNAs patterns will be correlated with known FISH-compatible biomarkers, thus providing a picture simultaneously for intra- and inter-cell variation.

In summary, the results and tools presented here will enable the study of disease related lncRNAs in a high content, high throughput mode. These efforts will enable gaining better understanding of how expression and localization of lncRNAs may contribute to the diseased phenotype, and add a large selection of novel biomarkers that can be interrogated for improved diagnosis, prognosis, and therapeutic choice.

Citation Format: Hans E. Johansson, Arturo V. Orjalo, Sally R. Coassin, Jerry. L. Ruth, Fabio Stossi, Michael A. Mancini. High-throughput imaging and high content analysis of disease relevant lncRNAs examined by RNA fluorescence in situ hybridization (RNA FISH). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1940. doi:10.1158/1538-7445.AM2013-1940

MicroRNAs miR-146a/b negatively modulate the senescence-associated inflammatory mediators IL-6 and IL-8

Senescence is a cellular program that irreversibly arrests the proliferation of damaged cells and induces the secretion of the inflammatory mediators IL- 6 and IL-8 which are part of a larger senescence associated secretory phenotype (SASP). We screened quiescent and senescent human fibroblasts for differentially expressed microRNAS (miRNAs) and found that miRNAs 146a and 146b (miR-146a/b) were significantly elevated during senescence. We suggest that delayed miR-146a/b induction might be a compensatory response to restrain inflammation. Indeed, ectopic expression of miR-146a/b in primary human fibroblasts suppressed IL-6 and IL-8 secretion and downregulated IRAK1, a crucial component of the IL-1 receptor signal transduction pathway. Cells undergoing senescence without induction of a robust SASP did not express miR-146a/b. Further, IL-1α neutralizing antibodies abolished both miR-146a/b expression and IL-6 secretion. Our findings expand the biological contexts in which miRNA-146a/b modulates inflammatory responses. They suggest that IL-1 receptor signaling initiates both miR-146a/b upregulation and cytokine secretion, and that miR-146a/b is expressed in response to rising inflammatory cytokine levels as part of a negative feedback loop that restrains excessive SASP activity.

ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division

Nuclear pores span the nuclear envelope and act as gated aqueous channels to regulate the transport of macromolecules between the nucleus and cytoplasm, from individual proteins and RNAs to entire viral genomes. By far the largest subunit of the nuclear pore is the Nup107-160 complex, which consists of nine proteins and is critical for nuclear pore assembly. At mitosis, the Nup107-160 complex localizes to kinetochores, suggesting that it may also function in chromosome segregation. To investigate the dual roles of the Nup107-160 complex at the pore and during mitosis, we set out to identify binding partners by immunoprecipitation from both interphase and mitotic Xenopus egg extracts and mass spectrometry. ELYS, a putative transcription factor, was discovered to copurify with the Nup107-160 complex in Xenopus interphase extracts, Xenopus mitotic extracts, and human cell extracts. Indeed, a large fraction of ELYS localizes to the nuclear pore complexes of HeLa cells. Importantly, depletion of ELYS by RNAi leads to severe disruption of nuclear pores in the nuclear envelope, whereas lamin, Ran, and tubulin staining appear normal. At mitosis, ELYS targets to kinetochores, and RNAi depletion from HeLa cells leads to an increase in cytokinesis defects. Thus, we have identified an unexpected member of the nuclear pore and kinetochore that functions in both pore assembly at the nucleus and faithful cell division.

The Nup107-160 nucleoporin complex is required for correct bipolar spindle assembly

The Nup107-160 complex is a critical subunit of the nuclear pore. This complex localizes to kinetochores in mitotic mammalian cells, where its function is unknown. To examine Nup107-160 complex recruitment to kinetochores, we stained human cells with antisera to four complex components. Each antibody stained not only kinetochores but also prometaphase spindle poles and proximal spindle fibers, mirroring the dual prometaphase localization of the spindle checkpoint proteins Mad1, Mad2, Bub3, and Cdc20. Indeed, expanded crescents of the Nup107-160 complex encircled unattached kinetochores, similar to the hyperaccumulation observed of dynamic outer kinetochore checkpoint proteins and motors at unattached kinetochores. In mitotic Xenopus egg extracts, the Nup107-160 complex localized throughout reconstituted spindles. When the Nup107-160 complex was depleted from extracts, the spindle checkpoint remained intact, but spindle assembly was rendered strikingly defective. Microtubule nucleation around sperm centrosomes seemed normal, but the microtubules quickly disassembled, leaving largely unattached sperm chromatin. Notably, Ran-GTP caused normal assembly of microtubule asters in depleted extracts, indicating that this defect was upstream of Ran or independent of it. We conclude that the Nup107-160 complex is dynamic in mitosis and that it promotes spindle assembly in a manner that is distinct from its functions at interphase nuclear pores.

Removal of a single pore subcomplex results in vertebrate nuclei devoid of nuclear pores

The vertebrate nuclear pore complex, 30 times the size of a ribosome, assembles from a library of soluble subunits and two membrane proteins. Using immunodepletion of Xenopus nuclear reconstitution extracts, it has previously been possible to assemble nuclei lacking pore subunits tied to protein import, export, or mRNA export. However, these altered pores all still possessed the bulk of pore structure. Here, we immunodeplete a single subunit, the Nup107-160 complex, using antibodies to Nup85 and Nup133, two of its components. The resulting reconstituted nuclei are severely defective for NLS import and DNA replication. Strikingly, they show a profound defect for every tested nucleoporin. Even the integral membrane proteins POM121 and gp210 are absent or unorganized. Scanning electron microscopy reveals pore-free nuclei, while addback of the Nup107-160 complex restores functional pores. We conclude that the Nup107-160 complex is a pivotal determinant for vertebrate nuclear pore complex assembly.

Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon

The Escherichia coli cydAB operon, encoding the subunits of the high-affinity cytochrome d oxidase, is maximally transcribed in microaerobiosis as a result of the combined action of the oxygen-responsive regulators Fnr and ArcA. Here, we report that the histone-like protein H-NS is an aerobic repressor of cydAB expression. ArcA is shown to antagonize H-NS action to render cydAB expression insensitive to H-NS repression in anaerobiosis. The targets for H-NS-mediated aerobic repression are the four oxygen-regulated promoters, designated P1, P2, P3 and P4. H-NS control is the result of H-NS binding to an extended region within the cydAB promoter element, including sequences upstream from and overlapping the four regulated promoters. We propose a regulatory model in which oxygen control of cydAB transcription is mediated by three alternative protein-DNA complexes that are assembled sequentially on the promoter region as the cells are shifted from aerobic to microaerobic and to anaerobic conditions. According to this model, ArcA-P plays a central role in cydAB regulation by antagonizing H-NS repression of cydAB transcription when oxygen becomes limiting. This allows peak gene expression and subsequent repression by Fnr under fully anaerobic conditions.