A functional assay for microRNA target identification and validation

MicroRNAs (miRNA) are a class of small RNA molecules that regulate numerous critical cellular processes and bind to partially complementary sequences resulting in down-regulation of their target genes. Due to the incomplete homology of the miRNA to its target site identification of miRNA target genes is difficult and currently based on computational algorithms predicting large numbers of potential targets for a given miRNA. To enable the identification of biologically relevant miRNA targets, we describe a novel functional assay based on a 3′-UTR-enriched library and a positive/negative selection strategy. As proof of principle we have used mir-130a and its validated target MAFB to test this strategy. Identification of MAFB and five additional targets and their subsequent confirmation as mir-130a targets by western blot analysis and knockdown experiments validates this strategy for the functional identification of miRNA targets

Novel costimulators in the immune gene therapy of cancer.

One of the major goals of cancer immunotherapy is the induction of tumour-specific T-lymphocyte responses that will be effective in the rejection of established tumours. The prospects for such therapy rely on the identification of tumour antigens, and although there is persuasive evidence for the presence of such antigens,1,2 the occurrence of the disease does illustrate that the immune system is at least, on some occasions, unable to recognise and destroy these targets. Tumour antigens may be novel proteins (from genetic lesions or viral infections), modified existing antigens (eg, abnormally glycosylated cell surface proteins), or inappropriately expressed normal gene products (eg, CA125, carcinoembryonic antigen, and alpha-fetoprotein).1 Involvement of the immune system in the normal surveillance and suppression of cancer is further suggested by the increased incidence of tumours in immunocompromised patients.3 However, recent evidence has shown that, at least in model systems, cancer cells can be modulated in such a way that they stimulate cells of the immune system to recognise and destroy these malignant cells. This review summarizes the costimulatory molecules involved in the activation of such cells, the principles and mechanisms underlying their activation, and how such knowledge can be used to persuade the immune system to challenge cancer

Novel costimulators in the immune gene therapy of cancer.

One of the major goals of cancer immunotherapy is the induction of tumour-specific T-lymphocyte responses that will be effective in the rejection of established tumours. The prospects for such therapy rely on the identification of tumour antigens, and although there is persuasive evidence for the presence of such antigens,1,2 the occurrence of the disease does illustrate that the immune system is at least, on some occasions, unable to recognise and destroy these targets. Tumour antigens may be novel proteins (from genetic lesions or viral infections), modified existing antigens (eg, abnormally glycosylated cell surface proteins), or inappropriately expressed normal gene products (eg, CA125, carcinoembryonic antigen, and alpha-fetoprotein).1 Involvement of the immune system in the normal surveillance and suppression of cancer is further suggested by the increased incidence of tumours in immunocompromised patients.3 However, recent evidence has shown that, at least in model systems, cancer cells can be modulated in such a way that they stimulate cells of the immune system to recognise and destroy these malignant cells. This review summarizes the costimulatory molecules involved in the activation of such cells, the principles and mechanisms underlying their activation, and how such knowledge can be used to persuade the immune system to challenge cancer

Low-speed centrifugation of retroviral vectors absorbed to a particulate substrate: a highly effective means of enhancing retroviral titre.

For many gene therapy applications the effective titre of retroviral vectors is a limiting factor both in vitro and in vivo. Purification and concentration of retrovirus from packaging cell supernatant can overcome this problem. To this end we have investigated a novel procedure which involves complexing retrovirus to a dense and particulate substrate followed by a short low-speed centrifugation. The study reported here uses heat-killed, formaldehyde fixed Staphylococcus aureus (Pansorbin) absorbed to PG13 derived retrovirus. This complex was then used to harvest retrovirus from packaging cell supernatant: centrifugation and washing of this complex allows the retrovirus to be both purified and concentrated. This procedure increases the effective titre of retrovirus by up to 7500-fold after an only 200-fold reduction in volume. The affinity of Pansorbin for retrovirus allows concentration regardless of its encoded genes and makes this protocol applicable to other popular packaging cells and envelope proteins. Possible explanations for the marked increase in titre of concentrated virus and the mechanism governing the complexing of retrovirus to Pansorbin are discussed

Expression of a variant of CD28 on a subpopulation of human NK cells: implications for B7-mediated stimulation of NK cells.

The ability of NK cells to kill tumor cells is controlled by a balance between activating and inhibitory signals transduced by distinct receptors. In murine tumor models, the costimulatory molecule B7.1 not only acts as a positive trigger for NK-mediated cytotoxicity but can also overcome negative signaling transduced by MHC class I molecules. In this study, we have evaluated the potential of human B7.1-CD28 interaction as an activating trigger for human blood NK cells. Using multiparameter flow cytometric analysis and a panel of different CD28 mAbs, we show that human peripheral blood NK cells (defined by CD56+, CD16+, and CD3- surface expression) express the CD28 costimulatory receptor, with its detection totally dependent on the mAb used. In addition, the level of CD28 varies among individuals and on different NK cell lines, irrespective of CD28 steady-state mRNA levels. By performing Ab binding studies on T cells, our data strongly suggest that binding of two of the anti-CD28 Abs (clones 9.3 and CD28.2) is to a different epitope to that recognized by clones L293 and YTH913.12, which is perhaps modified in the CD28 molecule expressed by the NK cells. We also show that B7.1 enhances the NK-mediated lysis of NK-sensitive but not of NK-resistant tumor cells and that this increased lysis is dependent on CD28-B7 interactions as shown by the ability of Abs to block this lysis. Coculture of the B7.1-positive NK-sensitive cells also led to the activation of the NK cells, as determined by the expression of CD69, CD25, and HLA class II

Expression of a variant of CD28 on a subpopulation of human NK cells: implications for B7-mediated stimulation of NK cells.

The ability of NK cells to kill tumor cells is controlled by a balance between activating and inhibitory signals transduced by distinct receptors. In murine tumor models, the costimulatory molecule B7.1 not only acts as a positive trigger for NK-mediated cytotoxicity but can also overcome negative signaling transduced by MHC class I molecules. In this study, we have evaluated the potential of human B7.1-CD28 interaction as an activating trigger for human blood NK cells. Using multiparameter flow cytometric analysis and a panel of different CD28 mAbs, we show that human peripheral blood NK cells (defined by CD56+, CD16+, and CD3- surface expression) express the CD28 costimulatory receptor, with its detection totally dependent on the mAb used. In addition, the level of CD28 varies among individuals and on different NK cell lines, irrespective of CD28 steady-state mRNA levels. By performing Ab binding studies on T cells, our data strongly suggest that binding of two of the anti-CD28 Abs (clones 9.3 and CD28.2) is to a different epitope to that recognized by clones L293 and YTH913.12, which is perhaps modified in the CD28 molecule expressed by the NK cells. We also show that B7.1 enhances the NK-mediated lysis of NK-sensitive but not of NK-resistant tumor cells and that this increased lysis is dependent on CD28-B7 interactions as shown by the ability of Abs to block this lysis. Coculture of the B7.1-positive NK-sensitive cells also led to the activation of the NK cells, as determined by the expression of CD69, CD25, and HLA class II

Blood First Edition paper

Key Points • There is 100% concordance in the cytogenetic and mutation profile between PB and BM in myelodysplastic syndrome. Recent studies have shown that more than 80% of bone marrow (BM) samples from patients with myelodysplastic syndrome (MDS) harbor somatic mutations and/or genomic aberrations, which are of diagnostic and prognostic importance. We investigated the potential use of peripheral blood (PB) and serum to identify and monitor BM-derived genetic markers using high-resolution single nucleotide polymorphism array (SNP-A) karyotyping and parallel sequencing of 22 genes frequently mutated in MDS. This pilot study showed a 100% SNP-A karyotype concordance and a 97% mutation concordance between the BM and PB. In contrast, mutation analysis using Sanger sequencing of PB and serum-derived DNA showed only 65% and 42% concordance to BM, respectively. Our results show the potential utility of PB as a surrogate for BM for MDS patients, thus avoiding the need for repeated BM aspirates particularly in elderly patients and those with fibrotic or hypocellular marrows. (Blood. 2013;122(4):567-570) Introduction The myelodysplastic syndromes (MDSs) are clonal disorders of hematopoiesis that occur predominantly in the elderly (median age 72 years) and are characterized by morphologic dysplasia, ineffective hematopoiesis, peripheral blood (PB) cytopenias, chromosomal aberrations, and propensity to myeloid leukemic transformation. The advent of high-throughput and high-resolution techniques for genetic analysis has shown that more than 80% of MDS patients harbor somatic mutations and/or genomic aberrations in their bone marrow (BM), which provide pathogenetic as well as diagnostic and prognostic insights into this disease. 1-4 Frequent BM aspirates may be required for morphological Study design Genomic DNA from PB and BM was extracted (Qiagen) from frozen cell pellets and 100 ng was whole genome amplified (WGA; Qiagen), both per manufacturer's protocols. Serum DNA was purified from 200 mL of serum using a modified sodium iodide/Triton-based lysis followed by isopropanol precipitation as described. 12 Affymetrix SNP 6.0 array (SNP-A) karyotyping and 454-PS of all exons of DNMT3a, RUNX1, CEBPa, TP53, EZH2, and ZRSR2 and mutation "hot spots" for NPM1, FLT3, ASXL1, IDH1, IDH2, MPL, JAK2, BRAF, cCBL, NRAS, KRAS, C-KIT, SF3B1, SRSF2, and U2AF35 were performed and analyzed as previously described. 13,14 TET2 was analyzed using Sanger sequencing. Independent validation for all mutations was performed using Sanger sequencing of unamplified genomic DNA. Polymerase chain reaction (PCR) conditions for serum were identical to those for PB; however, a second 10-cycle PCR reaction using nested primers (US1-GTAGTGCGATGGCCAGT, US2-CAGTGTGCAGCGATGAC) was required to provide adequate amplicon yield for Sanger sequencing. The study was approved by the local research ethics committee under project 0033 and conducted in accordance with the Declaration of Helsinki. Results and discussion Karyotype analysis Karyotype aberrations were assessed using SNP-A on PB samples from 31 MDS patients, from whom metaphase cytogenetics (MC) and BM SNP-A karyotypes were available. These consisted of th