Single Cell Micro RNA Sequencing Library Preparation.

Micro RNAs represent important post-transcriptional regulators in health and are involved in the onset of many diseases. Therefore, the further characterization of physiological miRNA functions is an important basic research question, and miRNAs even have high potential as biomarkers both for prognosis and diagnosis. In order to exploit this potential, it is mandatory to accurately quantify the miRNA expression not only in bulk but also on the single-cell level. Here, we describe a protocol, which facilitates miRNA sequencing library preparation of very low input samples, single cells, and even clinical samples such as circulating tumor cells. The protocol can be combined with different single-cell isolation methods (e.g., micromanipulation and FACS sorting). After cell lysis, sequencing adapters are ligated to the miRNAs, other ncRNA species, and adapter dimers are reduced by exonuclease digest, the miRNA library is reverse transcribed, amplified, and purified. Furthermore, quality controls are described to select only high-quality samples for sequencing.

Synthesis and evaluation of radioiodinated estrogens for diagnosis and therapy of male urogenital tumours.

The preparation of 24 estrogens, their estrogen receptor (ER) affinity and studies of radioiodinated estrogen binding to ER-positive male bladder tumor cells (HTB9) are described. The estrogens with the highest affinity were selected using fluorescence anisotropy assays. A 2,2,2-trifluoroethyl group at the 11ß-position caused particularly promising affinity. (Radio)iodination was performed on the 17α-vinyl group. Binding studies on HTB9 cells revealed picomolar affinities of radioconjugates 19 and 31, indicating promising ability for targeting of urogenital tumors.

Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells.

Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing.

Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during clinical latency.

Although thousands of breast cancer cells disseminate and home to bone marrow until primary surgery, usually less than a handful will succeed in establishing manifest metastases months to years later. To identify signals that support survival or outgrowth in patients, we profile rare bone marrow-derived disseminated cancer cells (DCCs) long before manifestation of metastasis and identify IL6/PI3K-signaling as candidate pathway for DCC activation. Surprisingly, and similar to mammary epithelial cells, DCCs lack membranous IL6 receptor expression and mechanistic dissection reveals IL6 trans-signaling to regulate a stem-like state of mammary epithelial cells via gp130. Responsiveness to IL6 trans-signals is found to be niche-dependent as bone marrow stromal and endosteal cells down-regulate gp130 in premalignant mammary epithelial cells as opposed to vascular niche cells. PIK3CA activation renders cells independent from IL6 trans-signaling. Consistent with a bottleneck function of microenvironmental DCC control, we find PIK3CA mutations highly associated with late-stage metastatic cells while being extremely rare in early DCCs. Our data suggest that the initial steps of metastasis formation are often not cancer cell-autonomous, but also depend on microenvironmental signals.

Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia.

Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche.

Interleukin-29 induces epithelial production of CXCR3A ligands and T-cell infiltration.

UNLABELLED: Psoriasis is considered as a model for chronic immune-mediated disorders. Th17-cells are pivotal players in those diseases. Recently, we demonstrated that Th17-cells produce interleukin (IL)-29 and that IL-29 is highly present in psoriatic lesions. Whether IL-29, with its action on epithelial cells and melanocytes, contributes to psoriasis pathogenesis, was unknown so far. Analysis of IL-29-treated human keratinocytes revealed induction of the chemokines CXCL10, CXCL11, and, to a much lesser extent, CXCL9. Unlike these CXCR3A ligands, known to attract Th1-, CD8(+), NK-, and Th1/Th17 transient cells, no influence was found on chemokines attracting other immune cell populations or on molecules modulating the CXCR3A/CXCR3A ligand interaction. CXCR3A ligand expression was also induced by IL-29 in melanocytes and in epidermis models and explanted skin. Regarding other psoriasis-relevant cytokines, interferon-γ and, less potently, tumor necrosis factor-α and IL-1ß shared and strengthened IL-29's capacity. Murine IL-29 counterpart injected into mouse skin provoked local CXCL10 and CXCL11 expression, T-cell infiltration, and, in consequence, skin swelling. The elevated IL-29 expression in psoriatic lesions was associated with upregulation of CXCR3A ligands compared to non-lesional skin of these patients and to the skin of healthy donors and atopic dermatitis patients, which lack IL-29 production. Importantly, neutralization of IL-29 reduced CXCR3A ligand levels in explant cultures of psoriatic lesions. Finally, elevated blood CXCL11 levels were found in psoriasis that might be useful for monitoring lesional activity of the IL-29 axis. In summary, the Th17-cytokine IL-29 induces specific chemokines and, in consequence, provokes skin infiltration of potentially pathogenic T-cells. KEY MESSAGES: IL-29 selectively induces CXCR3A-binding chemokines (CXCL9, CXCL10, CXCL11) in skin cells. Murine IL-29 counterpart induces skin T-cell infiltration and inflammation in mice. CXCR3A ligands are IL-29-dependently increased in lesional skin of psoriasis patients. CXCR3A ligand levels in psoriatic skin correlate with epidermal T-cell numbers. Increased blood CXCL11 levels in psoriasis may be a biomarker for local IL-29 action.

Principles of Whole-Genome Amplification.

Modern molecular biology relies on large amounts of high-quality genomic DNA. However, in a number of clinical or biological applications this requirement cannot be met, as starting material is either limited (e.g., preimplantation genetic diagnosis (PGD) or analysis of minimal residual cancer) or of insufficient quality (e.g., formalin-fixed paraffin-embedded tissue samples or forensics). As a consequence, in order to obtain sufficient amounts of material to analyze these demanding samples by state-of-the-art modern molecular assays, genomic DNA has to be amplified. This chapter summarizes available technologies for whole-genome amplification (WGA), bridging the last 25 years from the first developments to currently applied methods. We will especially elaborate on research application, as well as inherent advantages and limitations of various WGA technologies.

Biology of interleukin-10.

Interleukin (IL)-10 is the most important cytokine with anti-inflammatory properties besides TGF-ß and IL-35. It is produced by activated immune cells, in particular monocytes/macrophages and T cell subsets including Tr1, Treg, and Th1 cells. IL-10 acts through a transmembrane receptor complex, which is composed of IL-10R1 and IL-10R2, and regulates the functions of many different immune cells. In monocytes/macrophages, IL-10 diminishes the production of inflammatory mediators and inhibits antigen presentation, although it enhances their uptake of antigens. Additionally, IL-10 plays an important role in the biology of B cells and T cells. The special physiological relevance of this cytokine lies in the prevention and limitation of over-whelming specific and unspecific immune reactions and, in consequence, of tissue damage. At the same time, IL-10 strengthens the "scavenger"-function and contributes to induced tolerance. This review provides an overview about the cellular sources, molecular mechanisms, effects, and biological role of IL-10.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

BACKGROUND: Segmental duplications (SDs) are euchromatic portions of genomic DNA (> or = 1 kb) that occur at more than one site within the genome, and typically share a high level of sequence identity (>90%). Approximately 5% of the human genome is composed of such duplicated sequences. Here we report the detailed investigation of CHEK2 duplications. CHEK2 is a multiorgan cancer susceptibility gene encoding a cell cycle checkpoint kinase acting in the DNA-damage response signalling pathway. The continuous presence of the CHEK2 gene in all eukaryotes and its important role in maintaining genome stability prompted us to investigate the duplicative evolution and phylogeny of CHEK2 and its paralogs during anthropoid evolution. RESULTS: To study CHEK2 duplicon evolution in anthropoids we applied a combination of comparative FISH and in silico analyses. Our comparative FISH results with a CHEK2 fosmid probe revealed the single-copy status of CHEK2 in New World monkeys, Old World monkeys and gibbons. Whereas a single CHEK2 duplication was detected in orangutan, a multi-site signal pattern indicated a burst of duplication in African great apes and human. Phylogenetic analysis of paralogous and ancestral CHEK2 sequences in human, chimpanzee and rhesus macaque confirmed this burst of duplication, which occurred after the radiation of orangutan and African great apes. In addition, we used inter-species quantitative PCR to determine CHEK2 copy numbers. An amplification of CHEK2 was detected in African great apes and the highest CHEK2 copy number of all analysed species was observed in the human genome. Furthermore, we detected variation in CHEK2 copy numbers within the analysed set of human samples. CONCLUSION: Our detailed analysis revealed the highly dynamic nature of CHEK2 duplication during anthropoid evolution. We determined a burst of CHEK2 duplication after the radiation of orangutan and African great apes and identified the highest CHEK2 copy number in human. In conclusion, our analysis of CHEK2 duplicon evolution revealed that SDs contribute to inter-species variation. Furthermore, our qPCR analysis led us to presume CHEK2 copy number variation in human, and molecular diagnostics of the cancer susceptibility gene CHEK2 inside the duplicated region might be hampered by the individual-specific set of duplicons.

Quantitative time- and frequency-domain analysis of the two-pulse COSY revamped by asymmetric Z-gradient echo detection NMR experiment: Theoretical and experimental aspects, time-zero data truncation artifacts, and radiation damping.

The two-pulse COSY revamped by asymmetric Z-gradient echo detection (CRAZED) NMR experiment has the basic form 90 degrees -Gdelta-t(rec)-beta-nGdelta-t(rec)-FID, with a phase-encoding gradient pulse G of length delta applied during the evolution time tau for transverse magnetization, readout pulse beta, rephasing gradient nGdelta, and recovery time t(rec) prior to acquisition of the free-induction decay. Based on the classical treatment of the spatially modulated dipolar demagnetizing field and without invoking intermolecular multiple-quantum coherence, a new formulation of the first-order approximation for the theoretical solution of the nonlinear Bloch equations has been developed. The nth-order CRAZED signal can be expressed as a simple product of a scaling function C(n)(beta,tau) and a signal amplitude function A(n)(t), where the domain t begins immediately after the beta pulse. Using a single-quantum coherence model, a generalized rf phase shift function has also been developed, which explains all known phase behavior, including nth-order echo selection by phase cycling. Details of the derivations are provided in two appendices as supplementary material. For n>1, A(n)(t) increases from zero to a maximum value at t=t(max) before decaying and can be expressed as a series of n exponential decays with antisymmetric binomial coefficients. Fourier transform gives an antisymmetric binomial series of Lorentzians, where the composite lineshape exhibits negative wings, zero integral, and a linewidth that decreases with n. Analytical functions are presented for t(max) and A(n)(t(max)) and for estimating the maximal percent error incurred for A(n)(t(max)) when using the first-order model. The preacquisition delay Delta=delta+t(rec) results in the loss of the data points for t=0 to Delta. Conventional Fourier transformation produces time-zero truncation artifacts (reduced negative wing amplitude, nonzero integral, and reduced effective T(2) ( *)), which can be avoided by time-domain fitting after right shifting the data by Delta. A doped water sample (9.93 mM NiSO(4), 10 mm sample tube) was used to study the behavior of the CRAZED signal for n=1-4 with beta=90 degrees at 7 T (300 MHz (1)H frequency) as a function of Delta, with and without radiation damping. Pulse-acquire experiments were used to determine the relaxation times (T(1)=61.8 ms and T(2) ( *)=29.7 ms), and the radiation damping time constant T(rd)=18.5 ms. When experimental CRAZED data sets were right shifted by Delta, excellent least-squares fits to the first-order model function were obtained for all n using a minimal set of free variables. Without radiation damping the fitted T(2) ( *)values (29.7-30.2 ms) agreed with the reference value. With radiation damping the fitted effective T(2) ( *) values were 16.2 ms for a 90 degrees pulse-acquire experiment and 18.8-20.2 ms for the CRAZED experiment with n=1-4 and signal amplitudes spanning a range of 10(5).

Synthesis of 4-iodo-3-furanones utilizing electrophile-induced tandem cyclization/1,2-migration reactions.

Two protocols for the construction of 4-iodo-3-furanones through a sequence consisting of cyclization and 1,2-migration of 2-alkynyl-2-silyloxy carbonyl compounds were developed. In one, electrophilic cyclization is directly induced by N-iodosuccinimide (NIS). In the second less limited variant, AuCl3 catalyzes the tandem reaction in the presence of NIS to provide highly substituted heterocycles in moderate to excellent yields.

Impact of stroma on the growth, microcirculation, and metabolism of experimental prostate tumors.

In prostate cancers (PCa), the formation of malignant stroma may substantially influence tumor phenotype and aggressiveness. Thus, the impact of the orthotopic and subcutaneous implantations of hormone-sensitive (H), hormone-insensitive (HI), and anaplastic (AT1) Dunning PCa in rats on growth, microcirculation, and metabolism was investigated. For this purpose, dynamic contrast-enhanced magnetic resonance imaging and (1)H magnetic resonance spectroscopy ([(1)H]MRS) were applied in combination with histology. Consistent observations revealed that orthotopic H tumors grew significantly slower compared to subcutaneous ones, whereas the growth of HI and AT1 tumors was comparable at both locations. Histologic analysis indicated that glandular differentiation and a close interaction of tumor cells and smooth muscle cells (SMC) were associated with slow tumor growth. Furthermore, there was a significantly lower SMC density in subcutaneous H tumors than in orthotopic H tumors. Perfusion was observed to be significantly lower in orthotopic H tumors than in subcutaneous H tumors. Regional blood volume and permeability-surface area product showed no significant differences between tumor models and their implantation sites. Differences in growth between subcutaneous and orthotopic H tumors can be attributed to tumor-stroma interaction and perfusion. Here, SMC, may stabilize glandular structures and contribute to the maintenance of differentiated phenotype.