Molecular pixelation: spatial proteomics of single cells by sequencing.

The spatial distribution of cell surface proteins governs vital processes of the immune system such as intercellular communication and mobility. However, fluorescence microscopy has limited scalability in the multiplexing and throughput needed to drive spatial proteomics discoveries at subcellular level. We present Molecular Pixelation (MPX), an optics-free, DNA sequence-based method for spatial proteomics of single cells using antibody-oligonucleotide conjugates (AOCs) and DNA-based, nanometer-sized molecular pixels. The relative locations of AOCs are inferred by sequentially associating them into local neighborhoods using the sequence-unique DNA pixels, forming >1,000 spatially connected zones per cell in 3D. For each single cell, DNA-sequencing reads are computationally arranged into spatial proteomics networks for 76 proteins. By studying immune cell dynamics using spatial statistics on graph representations of the data, we identify known and new patterns of spatial organization of proteins on chemokine-stimulated T cells, highlighting the potential of MPX in defining cell states by the spatial arrangement of proteins.

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture.

DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.

[Capsaicin Cutaneous Patch: a Cost-consequences Study in a French University Hospital]. / Étude coût-conséquences sur la capsaïcine en patch cutané dans un CHU français.

INTRODUCTION: The capsaïcine 8% cutaneous patch (Qutenza®) was recently approved for the management of patients with peripheral neuropathic pain (PNP). Considering its limited clinical efficacy data, its improvement of medical benefit was determined to be 5 which was insufficient to support its reimbursement in addition to diagnosis related groups'tarifs. Nevertheless its commercialization was associated with a marked interest considering the unmet therapeutic needs for patients with PNP. OBJECTIVES: Our objectives were to assess the effectiveness, the safety, and the economic impact of Qutenza® in real-life conditions. METHODS: An observational cost-consequences study was launched under the aegis of the Drug Committee of our hospital. Medical charts and prescriptions of all patients who received at least one patch application were analyzed. Effectiveness and safety were assessed after 12-week and 24-week of follow-up. The economic impact was measured within the Hospital and Health Insurance perspective and with limitation to direct costs. RESULTS: From March 2012 to October 2013, 91 patients (54.3 ± 14.1 years; 52.7% of male) received at least one application. The average follow- up duration was 188.3 ± 86.4 days. The PNP etiologies were mainly post-surgery (42.9%) and post-traumatology (20.8%). A therapeutic response (decrease of ENS score of least 30%) after 12 weeks and 24 weeks was observed in 27.9% and 37.1% of patients respectively. The SF-36 mental score was significantly improved. The safety profile was good. The application of the patch resulted in incremental costs of 154 euros per hospital stay without impact on outpatient-prescription drug expenditures. CONCLUSION: This study confirms the interest of Qutenza® for heavily pretreated, refractory patients with PNP. The clinical profile of responders has to be further investigated in large observational studies.