Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells.

MOTIVATION: Essential genes are required for the reproductive success at either cellular or organismal level. The identification of essential genes is important for understanding the core biological processes and identifying effective therapeutic drug targets. However, experimental identification of essential genes is costly, time consuming and labor intensive. Although several machine learning models have been developed to predict essential genes, these models are not readily applicable to lncRNAs. Moreover, the currently available models cannot be used to predict essential genes in a specific cancer type. RESULTS: In this study, we have developed a new machine learning approach, XGEP (eXpression-based Gene Essentiality Prediction), to predict essential genes and candidate lncRNAs in cancer cells. The novelty of XGEP lies in the utilization of relevant features derived from the TCGA transcriptome dataset through collaborative embedding. When evaluated on the pan-cancer dataset, XGEP was able to accurately predict human essential genes and achieve significantly higher performance than previous models. Notably, several candidate lncRNAs selected by XGEP are reported to promote cell proliferation and inhibit cell apoptosis. Moreover, XGEP also demonstrated superior performance on cancer-type-specific datasets to identify essential genes. The comprehensive lists of candidate essential genes in specific cancer types may be used to guide experimental characterization and facilitate the discovery of drug targets for cancer therapy. AVAILABILITY AND IMPLEMENTATION: The source code and datasets used in this study are freely available at https://github.com/BioDataLearning/XGEP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Rapid isolation of lentivirus particles from cell culture media via a hydrophobic interaction chromatography method on a polyester, capillary-channeled polymer fiber stationary phase.

Lentiviruses are increasingly used as gene delivery vehicles for vaccines and immunotherapies. However, the purification of clinical-grade lentivirus vectors for therapeutic use is still troublesome and limits preclinical and clinical experiments. Current purification methods such as ultracentrifugation and ultrafiltration are time consuming and do not remove all of the impurities such as cellular debris, membrane fragments, and denatured proteins from the lentiviruses. The same challenges exist in terms of their analytical characterization. Presented here is the novel demonstration of the chromatographic isolation of virus particles from culture media based on the hydrophobicity characteristics of the vesicles. A method was developed to isolate lentivirus from media using a hydrophobic interaction chromatography (HIC) method performed on a polyester, capillary-channeled polymer (PET C-CP) stationary phase and a standard liquid chromatography apparatus. The method is an extension of the approach developed in this laboratory for the isolation of extracellular vesicles (EVs). Quantitative polymerase chain reaction (qPCR) was used to verify and quantify lentiviruses in elution fractions. Load and elution mobile phase compositions were optimized to affect high efficiency and throughput. The process has been visualized via scanning electron microscopy (SEM) of the fiber surfaces following media injection, the elution of proteinaceous material, and the elution of lentiviruses. This effort has yielded a rapid (<10 min), low-cost (< $15 per column, providing multiple separations), and efficient method for the isolation/purification of lentivirus particles from cell culture media at the analytical scale.

Bioactive Sesquiterpene Lactones Isolated from the Whole Plants of Vernonia cinerea.

Twelve sesquiterpene lactones were isolated from the whole plants of Vernonia cinerea. These included eight new compounds, vercinolides A-H (1-8), along with four known substances (9-12). The structures of the new compounds were determined by 1D and 2D NMR experiments and mass spectrometric methods. The absolute configurations of compounds 1-8 were determined by Mosher experiments and ECD data. Compounds 1-8 are the first examples of a new class of sesquiterpene lactones possessing a rare 4α,10α-ether ring and a 2,14-ether ring. Compounds 1-4, 6, 8, 10, and 12 were evaluated for their cytotoxic and anti-inflammatory activities. Compounds 10 and 12 exhibited inhibitory effects against nitric oxide production in lipopolysaccharide-activated RAW 264.7 mouse macrophage cells with IC50 values of 21 and 23 µM, respectively. Both compounds were inactive for HeLa cells (IC50 > 10 µM).

Fusion Proteins of NKG2D/NKG2DL in Cancer Immunotherapy.

NKG2D (natural killer group 2, member D) is an important activating receptor in natural killer (NK) cells and some T cells. NKG2D ligands (NKG2DLs) are specifically expressed on most tumor cells. The engagement of these ligands on tumor cells to NKG2D on NK cells will induce cell-mediated cytotoxicity and have target cells destroyed. This gives NKG2D/NKG2DLs great potential in cancer therapeutic application. The creation of NKG2D/NKG2DL-based multi-functional fusion proteins is becoming one of the most promising strategies in immunotherapy for cancer. Antibodies, cytokines, and death receptors have been fused with NKG2D or its ligands to produce many powerful fusion proteins, including NKG2D-based chimeric antigen receptors (CARs). In this article, we review the recent developments of the fusion proteins with NKG2D/NKG2DL ligands in cancer immunotherapy.

Anti-inflammatory and Quinone Reductase Inducing Compounds from Fermented Noni (Morinda citrifolia) Juice Exudates.

A new fatty acid ester disaccharide, 2-O-(ß-d-glucopyranosyl)-1-O-(2E,4Z,7Z)-deca-2,4,7-trienoyl-ß-d-glucopyranose (1), a new ascorbic acid derivative, 2-caffeoyl-3-ketohexulofuranosonic acid γ-lactone (2), and a new iridoid glycoside, 10-dimethoxyfermiloside (3), were isolated along with 13 known compounds (4-16) from fermented noni fruit juice (Morinda citrifolia). The structures of the new compounds, together with 4 and 5, were determined by 1D and 2D NMR experiments, as well as comparison with published values. Compounds 2 and 7 showed moderate inhibitory activities in a TNF-α-induced NF-κB assay, and compounds 4 and 6 exhibited considerable quinone reductase-1 (QR1) inducing effects.

Single-cell-level microplasma cancer therapy.

A flexible microplasma endoscope based on a 15 µm hollow-core glass optical fiber is fabricated, and tumor cell apoptotic analysis supports its potential use in targeted cancer therapies. The optical-fiber microplasma jet reveals antitumor activity at a certain plasma dose in animal studies.

Expression of CD226 antagonizes apoptotic cell death in murine thymocytes.

CD226 is known to be expressed on many types of peripheral lymphoid cells and involved in T cell differentiation, activation, and cytotoxicity. In this study, we report that CD226 is also expressed on mouse thymocytes at varying developmental stages, and its expression is associated with resistance of thymocytes to apoptosis. The levels of CD226 expression appeared to be closely coupled with thymocyte development, in that it was preferentially expressed on CD4(+)CD8(-) and CD4(-)CD8(+) thymocytes at all stages during mouse development, and was markedly increased on the cells in neonatal mice. Of the CD4(+)CD8(+) population, CD226 was predominantly expressed by the cells also positive for CD69, suggesting that CD226 expression may be induced in thymocyte-positive selection. Inhibition of CD226 by short hairpin RNA in a fetal thymus organ culture model led to reduced thymus cellularity, which was associated with enhanced apoptotic cell death. In contrast, CD226-transgenic mice displayed enlarged thymus lobes resulting from increased thymus cellularity. CD226 on thymocytes seemed to play a role in regulating the expression of survivin, as inhibition of CD226 down-regulated survivin, but overexpression of CD226 rescued thymocytes from apoptosis through up-regulation of survivin. In addition, overexpression of CD226 reduced sensitivity of EL-4 thymoma cells to apoptosis by up-regulating the expression of survivin. Taken together, these results indicate that CD226 is an antiapoptotic molecule and may play an important role in murine thymocyte development.

MICA-G129R: A bifunctional fusion protein increases PRLR-positive breast cancer cell death in co-culture with natural killer cells.

Breast cancer cells were reported to up-regulate human prolactin receptor (PRLR) to assist their growth through the utilization of prolactin (PRL) as the growth factor, which makes PRLR a potential therapeutic target for breast cancer. On the other hand, advanced cancer cells tend to down-regulate or shed off stress signal proteins to evade immune surveillance and elimination. In this report, we created a fusion protein consisting of the extracellular domain of MHC class I chain-related protein (MICA), a stress signal protein and ligand of the activating receptor NKG2D of natural killer (NK) cells, and G129R, an antagonistic variant of PRL. We hypothesize that the MICA portion of the fusion protein binds to NKG2D to activate NK cells and the G129R portion binds to PRLR on breast cancer cells, so that the activated NK cells will kill the PRLR-positive breast cancer cells. We demonstrated that the MICA-G129R fusion protein not only binds to human natural killer NK-92 cells and PRLR-positive human breast cancer T-47D cells, but also promotes NK cells to release granzyme B and IFN-γ and enhances the cytotoxicity of NK cells specifically on PRLR-positive cells. The fusion protein, therefore, represents a new approach for the development of breast cancer specific immunotherapy.

Fermented Noni Exudate-treated dendritic cells directly stimulate B lymphocyte proliferation and differentiation.

Noni juice as a folk medicine has been used for over two thousand years. Recently, some active ingredients of Noni juice have been successfully isolated and intensively studied. Because dendritic cells (DCs) are central regulators both in priming innate and adaptive immune responses and in maintaining self tolerance, in the current study we treated DCs with fermented Noni Exudate (fNE) in order to explore their function in regulating other immune cells. It was shown that fNE-treated DCs stimulate proliferation of splenocytes, among which, B cells are the major responsive cell group. The proliferative response of B cells to fNE-treated DCs is cell contact-dependent, CD40L-independent; and the adhesion feature of DCs was enhanced to form large DC-B conjugation cluster. Moreover, it was demonstrated that fNE-treated DCs promote B cell differentiation and Ig class switching. These results lay a foundation for the further exploration of fNE as a biological response modifier in the immune system.

Fermented Noni exudate (fNE): a mediator between immune system and anti-tumor activity.

The anti-tumor activity of Morinda citrifolia fruit juice (Noni) has been previously reported. However, the mechanism behind this activity remains unknown. In the present study, we studied the anti-tumor activity of fermented Noni exudate (fNE) and demonstrated that intraperitoneal injection of this material significantly increased the percentages of granulocytes and NK cells in the peripheral blood, peritoneum, and spleen. Furthermore, in preventive and treatment settings, fNE injection induced complete tumor rejection in normal C57BL/6J mice, partial tumor rejection in C57 nude mice lacking functional lymphocytes, and no tumor rejection in NK cell deficient beige mice. Over 85% of the C57BL/6J mice that received fNE survived the first tumor injection and rejected up to 5 x 10(6) tumor cells when re-challenged. The anti-tumor activity remains in the heat-inactivated and filtrated supernatant of fNE. These data demonstrate that fNE appears to be able to stimulate the innate immune system and the adaptive immune system to reject tumor cells. NK cells respond quickly and appear to be among the major players of the innate immune system, while the adaptive immune system reacts later with a retained memory.

Lentiviral delivery of novel fusion protein IL12/FasTI for cancer immune/gene therapy.

Many of the cytokine-based cancer immunotherapies are hindered by the devastating side effects of systemic delivery of the cytokines. To address this problem, we previously described a novel approach to locally achieve high doses of interleukin-12 (IL-12) in tumors and demonstrated that bi-functional fusion protein mIL-12/FasTI expressed by stable clones of TC-1 cells efficiently suppressed tumor proliferation by activating natural killer (NK) cells and other cytolytic killer cells and sending apoptotic signals into tumor cells. In the present study, we employed a lentiviral vector-based gene delivery system to deliver this fusion construct directly into tumor cells. We show that lentiviral vector efficiently delivers the fusion constructs into Hela cells in vitro as assayed by RT-PCR and immunohistochemistry (IHC). We also confirm that fusion protein mIL-12/FasTI delivered by the viral vector significantly enhanced killer cell activation, increased caspase-3 activity and decreased tumor growth in vitro. This study offers a further step for fusion protein cancer therapy for cancer patients.

MHC class I chain-related A: Polymorphism, regulation and therapeutic value in cancer.

MICA and MICB are stress-induced molecules recognized by NKG2D, one of major activation receptors of natural killer (NK) cells. Upon binding to NKG2D, NKG2D-mediated cytolytic immune response of immune effector cells will be activated against virally infected and tumor cells expressing MICA. In the early oncogenic development, membrane-bound MICA serves as a key signal to recruit anti-tumor immune effectors. Nevertheless, both MICA polymorphic features and its dysregulated expression in evolving tumors have resulted in tumor evasion in various cancer types. Therefore, in order to reconstitute tumor immunosurveilance, it is of great significance that we understand MICA genetics, polymorphisms, mechanisms of MICA-associated tumor escape and molecular/cellular modulation of MICA. In this review, the MICA-associated co-expression networks involving microRNAs (miRNAs) and novel candidate long non-coding RNAs (lncRNAs) were also discussed. Given the current importance in the study of MICA gene, this review paper focuses on the role of MICA in different cancer types, and strategies that we manipulate MICA regulation against tumor proliferation.

Investigation of composition, structure and bioactivity of extracellular polymeric substances from original and stress-induced strains of Thraustochytrium striatum.

This paper was the first to study extracellular polymeric substances (EPSs) of Thraustochytrium striatum on composition, structure and bioactivities. Two strains of T. striatum including original (ori) and high-biomass (mut) strains (induced by high-nitrogen stress) were compared. The EPSs from both strains mainly contained polysaccharide (41-64%, w/w, dry basis) and protein (25-40%, w/w, dry basis), which was shown by the morphology study with an AFM. The monosaccharide profile of the EPS polysaccharide was consisted of glucose, galactose, arabinose, and trace amount of xylose. Glucose and arabinose took up to 82-90% (w/w, dry basis) of the total polysaccharide. The structure and functional groups of EPSs were determined by FTIR and NMR. The NMR results revealed that the major structural linkages of the polysaccharides of both ori and mut EPSs were 1 → 6-ß-glucan and 1 → 4-α-galactan branched with l-α-arabinose. The EPSs were found to have anti-tumor activities against mouse melanoma B16-F0, human prostate carcinoma DU145, human cervical carcinoma HeLa, and human lung carcinoma A549. The EPSs also showed antioxidant and anti-inflammatory activities and antibacterial activity against Pseudomonas aeruginosa.

Transfer of in vitro expanded T lymphocytes after activation with dendritomas prolonged survival of mice challenged with EL4 tumor cells.

Adoptive T cell transfer after in vitro expansion represents an attractive cancer immunotherapy. The majority of studies so far have been focusing on the expansion of tumor infiltrated lymphocytes (TIL) and some have shown very encouraging results. Recently, we have developed a unique tumor immune response activator, dendritomas, by fusion of dendritic cells and tumor cells. Animal studies and early clinical trials have shown that dendritomas are able to activate tumor specific immune responses. In this study, we hypothesized that naïve T cells can be primed with dendritomas and expanded in vitro to develop an adoptive transfer therapy for patients who do not have solid tumors, such as leukemia. T cells were isolated and purified from lymph nodes of mice. The cells were then incubated with dendritomas made from syngeneic DCs and tumor cells and expanded in vitro using Dynabeads mouse CD3/CD28 T cell expander for approximately three weeks. The in vitro primed and expanded T cells showed tumor cell specific CTL activity and increased secretion of IFN-gamma. Tumor bearing mice receiving the in vitro expanded T cells survived significantly longer than control mice. Furthermore, the depletion of regulator T cells enhanced the survival of the mice that received the adoptive transfer therapy.

Combined treatment of dendritoma vaccine and low-dose interleukin-2 in stage IV renal cell carcinoma patients induced clinical response: A pilot study.

Vaccination using dendritic/tumor cell hybrids represents a novel and promising cancer immunotherapy. We have developed a technology that can instantly purify the hybrids (dendritomas) from the fusion mixture of dendritic cells (DCs) and tumor cells. Our animal studies and a phase I study of stage IV melanoma patients demonstrated that dendritoma vaccination could be conducted without major toxicity and induced tumor cell-specific immunological and clinical responses. In this pilot study, ten stage IV renal cell carcinoma patients were studied. Dendritomas were made from autologous DCs and tumor cells and administered by subcutaneous injection. After initial vaccination, three escalating doses of IL-2 (3, 6, and 9 million units each) were followed within five days. This treatment regimen was tolerated well without severe adverse events directly related to the dendritoma vaccine. Most adverse events were related to IL-2 administration or pre-existing disease. Patient-specific immune responses were evaluated by flow cytometric measurement of interferon-gamma-producing T-cells before and after vaccination in response to stimulation with tumor antigens. Nine out of nine patients eligible for the analysis showed an increase of IFN-gamma-expressing CD4+ T cells after vaccination(s); while five out of eight patients eligible for the analysis showed an increase of IFN-gamma-expressing CD8+ T cells. Clinical responses were documented in 40% of the patients, three with stabilization of disease and one with a partial response documented by a reduction in tumor size. This pilot study demonstrated that dendritoma vaccines could be administered safely to patients with metastatic renal cell carcinoma, while producing both clinical and immunologic evidence of response.

MICA/IL-12: A novel bifunctional protein for killer cell activation.

Natural killer (NK) cells have the potential to be effective killers of tumor cells. They are governed by inhibitory and activating receptors such as NKG2D, whose ligands are normally upregulated in cells that are stressed, like cancer cells. Advanced cancer cells, however, have ways to reduce the expression of these ligands, leaving them less detectable by NK cells. Along with these receptors, NK cells also require activating cytokines, such as IL-12. A previous study in our laboratory showed that a fusion protein of the extracellular domain of mouse UL-16 binding protein-like transcript 1 (MULT1E) and mouse interleukin 12 (IL-12) can effectively activate mouse NK cells by in vitro assays and in vivo in animal tumor models. The aim of the present study was to expand the concept of developing a novel bifunctional fusion protein for enhanced NK cell activation to human killer cells. The proposed protein combines the extracellular domain of a human NKG2D ligand, MHC class I polypeptide-related sequence A (MICA) and IL-12. It is hypothesized that when expressed by tumor cells, the protein will activate human NK and other killer cells using the NKG2D receptor, and deliver IL-12 to the NK cells where it can interact with the IL-12R and enhance cytotoxicity. The fusion protein, when expressed by engineered tumor cells, indeed activated NK92 cells as measured by an increase in interferon-γ (IFN-γ) production and an increase in cytotoxicity of tumor cells. The fusion protein was also able to increase the proliferation of human peripheral blood mononuclear cells (PBMCs) and augment their production of IFN-γ. This study along with the data from the previous mouse studies suggest that the MICA/IL-12 bifunctional fusion protein represents an effective activator of killer cells for cancer treatment.

Dendritoma vaccination combined with low dose interleukin-2 in metastatic melanoma patients induced immunological and clinical responses.

A pilot clinical trial using dendritomas, purified hybrids from the fusion of dendritic/tumor cells combined with a low dose of IL-2, in metastatic melanoma patients was conducted in order to determine its safety and potential immunological and clinical responses. Ten metastatic melanoma patients were enrolled into this study. Dendritoma vaccines were created by fusing dendritic cells stained with green fluorescent dye with irradiated autologous tumor cells stained with red fluorescent dye and purifying the hybrids using immediate fluorescent-activated cell sorting. Initial vaccine was given subcutaneously and followed by IL-2 in serially elevated doses from 3-9 million units/m2 for 5 days. Repeated vaccinations were administered without IL-2, at 3-month intervals for a maximum of 5 times. Immune reactions were measured by the increase of interferon-gamma (IFN-gamma) expressing T cells. Vaccine doses ranged from 250,000 to 1,000,000 dendritomas. There was no grade 2 or higher toxicity directly attributable to the vaccine. All patients experienced toxicity due to IL-2 administration (9-grade 2, 3-grade 3, 1-grade 4). Eight of nine evaluable patients demonstrated immunologic reactions by increased IFN-gamma expressing T cells. One patient developed partial response at 12 weeks after the first vaccine. Nine months later, this patient achieved a complete response. In addition, two patients had stable disease for 9 and 4 months, respectively; one patient had a mixed response. Our findings demonstrated that dendritoma vaccines with a low dose of IL-2 can be safely administered to patients with metastatic melanoma and induce immunological and clinical responses.

Mouse interleukin-12/FasTI: A novel bi-functional fusion protein for cancer immuno/gene therapy.

Whereas cancer immunotherapy with cytokines in recent research was demonstrated effective in activating immune response against tumor cells, one major obstacle with the use of these cytokines is their severe side effects when delivered systemically at high doses. Another challenge is that advanced tumor cells often evade immunosurveillance of the immune system as well as of the Fas-mediated apoptosis by various mechanisms. We report the design and preliminary evaluation of the antitumor activity of a novel fusion protein-mIL-12/FasTI, consisting of mouse interleukin-12 and the transmembrane and intracellular domains of mouse Fas. The fusion construct (pmIL-12/FasTI) was transfected into mouse lung carcinoma cell line TC-1. Stable cell clones expressing the fusion protein were established as assayed by RT-PCR and immunohistochemistry. ELISA and cell proliferation analyses demonstrated that NK cells were effectively activated by the fusion protein with increased IFN-γ production and cytotoxicity. Enhanced caspase-3 activity of the clones when co-cultured with NK cells indicated that apoptosis was induced through Fas/FasL signaling pathway. The preliminary results suggest a synergized anticancer activity of the fusion protein. It may represent a promising therapeutic agent for cancer treatment.

Bovine serum albumin coated nanoparticles for in vitro activated fluorescence.

A fluorophore modified nanoparticle was developed that can only fluoresce when a specific environmental parameter interacts with the system. The model system consisted of an azide modified bovine serum albumin (azBSA) that had been covalently attached to an alkyne modified silicon phthalocyanine (alSiPc) derivative through a copper catalyzed azide/alkyne Huisgen cycloaddition (click reaction). The azBSA/alSiPc assembly was then clicked to a ca. 67 nm poly(propargyl acrylate) (PA) nanoparticle (PA/azBSA/alSiPc). The resulting particles did not exhibit any florescence when the alSiPc was excited. Incubating the particles at 37 °C for 30 min with a proteolytic enzyme (trypsin) degraded the linking BSA and resulted in the appearance of florescence that was attributed to a "free" silicon phthalocyanine. The PA/azBSA/alSiPc particles were incubated with human non-small cell lung cancer cells (A549) and the florescence of the initially quenched particles was achieved with cellular uptake.

Sequestering survivin to functionalized nanoparticles: a strategy to enhance apoptosis in cancer cells.

Survivin belongs to the family of inhibitor of apoptosis proteins (IAP) and is present in most cancers while being below detection limits in most terminally differentiated adult tissues, making it an attractive protein to target for diagnostic and, potentially, therapeutic roles. Sub-100 nm poly(propargyl acrylate) (PA) particles were surface modified through the copper-catalyzed azide/alkyne cycloaddition of an azide-terminated survivin ligand derivative (azTM) originally proposed by Abbott Laboratories and speculated to bind directly to survivin (protein) at its dimer interface. Using affinity pull-down studies, it was determined that the PA/azTM nanoparticles selectively bind survivin and the particles can enhance apoptotic cell death in glioblastoma cell lines and other survivin over-expressing cell lines such as A549 and MCF7 relative to cells incubated with the original Abbott-derived small molecule inhibitor.