Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.

Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of loop formation can be quantified from fixed cell images alone, while the lifetime of loops and the speed of extrusion can be estimated from dynamic live-cell data. Our delineation of appropriate imaging conditions and the proposed analytical methods lay the groundwork for a systematic quantitative characterization of loop extrusion in fixed or living cells.

Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75.

The stable insertion of the retroviral genome into the host chromosomes requires the association between integration complexes and cellular chromatin via the interaction between retroviral integrase and the nucleosomal target DNA. This final association may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To investigate this and better understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase, we used a combination of biochemical and chromosome-binding assays. Our study revealed that retroviral integrase has an intrinsic ability to bind and recognize specific chromatin regions in metaphase even in the absence of its cofactor. Furthermore, this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromosome regions. We also better determined the chromatin features recognized by each partner alone or within the functional intasome, as well as the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. Our data support a new chromatin-binding function of integrase acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate. This work also provides additional information about the behavior of retroviral integration complexes in metaphase chromatin and the mechanism of action of LEDGF/p75 in this specific context.

Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures.

BACKGROUND: The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller "topologically associated" domains. These domains are often associated with chromatin loops, which largely disappear upon removal of cohesin. Because most Hi-C implementations average contact frequencies over millions of cells and do not provide direct spatial information, it remains unclear whether and how frequently chromatin domains and loops exist in single cells. RESULTS: We combine 3D single-molecule localization microscopy with a low-cost fluorescence labeling strategy that does not denature the DNA, to visualize large portions of single human chromosomes in situ at high resolution. In parallel, we develop multi-scale, whole nucleus polymer simulations, that predict chromatin structures at scales ranging from 5 kb up to entire chromosomes. We image chromosomes in G1 and M phase and examine the effect of cohesin on interphase chromatin structure. Depletion of cohesin leads to increased prevalence of loose chromatin stretches, increased gyration radii, and reduced smoothness of imaged chromatin regions. By comparison to model predictions, we estimate that 6-25 or more purely cohesin-dependent chromatin loops coexist per megabase of DNA in single cells, suggesting that the vast majority of the genome is enclosed in loops. CONCLUSION: Our results provide new constraints on chromatin structure and showcase an affordable non-invasive approach to study genome organization in single cells.

Time-lapse imaging of molecular evolution by high-throughput sequencing.

High-throughput sequencing of in vitro selection could artificially provide large quantities of relic sequences from known times of molecular evolution. Here, we demonstrate how it can be used to reconstruct an empirical genealogical evolutionary (EGE) tree of an aptamer family. In contrast to classical phylogenetic trees, this tree-diagram represents proliferation and extinction of sequences within a population during rounds of selection. Such information, which corresponds to their evolutionary fitness, is used to infer which sequences may have been mutated through the selection process that led to the appearance and spreading of new sequences. This approach was validated by the re-analysis of an in vitro selection that had previously identified an aptamer against Annexin A2. It revealed that this aptamer might be the descendant of a sequence that was more highly amplified in early rounds. It also succeeded in predicting improved variants of this aptamer and providing a means to understand the influence of selection pressure on evolution. This is the first demonstration that HTS can provide time-lapse imaging of the evolutionary pathway that is taken by a macromolecule during in vitro selection to evolve by successive mutations through better fitness.

ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range.

Single molecule localization microscopy can generate 3D super-resolution images without scanning by leveraging the axial variations of normal or engineered point spread functions (PSF). Successful implementation of these approaches for extended axial ranges remains, however, challenging. We present Zernike Optimized Localization Approach in 3D (ZOLA-3D), an easy-to-use computational and optical solution that achieves optimal resolution over a tunable axial range. We use ZOLA-3D to demonstrate 3D super-resolution imaging of mitochondria, nuclear pores and microtubules in entire nuclei or cells up to ~5 µm deep.

Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast.

DNA double-strand breaks (DSBs) induce a cellular response that involves histone modifications and chromatin remodeling at the damaged site and increases chromosome dynamics both locally at the damaged site and globally in the nucleus. In parallel, it has become clear that the spatial organization and dynamics of chromosomes can be largely explained by the statistical properties of tethered, but randomly moving, polymer chains, characterized mainly by their rigidity and compaction. How these properties of chromatin are affected during DNA damage remains, however, unclear. Here, we use live cell microscopy to track chromatin loci and measure distances between loci on yeast chromosome IV in thousands of cells, in the presence or absence of genotoxic stress. We confirm that DSBs result in enhanced chromatin subdiffusion and show that intrachromosomal distances increase with DNA damage all along the chromosome. Our data can be explained by an increase in chromatin rigidity, but not by chromatin decondensation or centromeric untethering only. We provide evidence that chromatin stiffening is mediated in part by histone H2A phosphorylation. Our results support a genome-wide stiffening of the chromatin fiber as a consequence of DNA damage and as a novel mechanism underlying increased chromatin mobility.

18F-FDG-PET partial volume effect correction using a modified recovery coefficient approach based on functional volume and local contrast: physical validation and clinical feasibility in oncology.

BACKGROUND: 2-deoxy-2-[18F]fluoro-D-glucose 18F-FDG uptake within tumors reflects the glucose consumption of malignant tumors, i.e., the tumor activity. Thus, 18F-FDG uptake measurements enable improved therapeutic monitoring of patients in chemo- or radiotherapy treatment through the detection of changes in tumor uptake via quantitative measurements of the lesion standard uptake values (SUVs) or activity concentrations. A major bias that affects positron emission tomography (PET) image quantitation is the partial volume effect (PVE), which most strongly affects the smallest structures due to the poor spatial resolution of PET. Thus, PVE corrections are important when 18F-FDG-PET images are used as a quantitative tool for monitoring responses to therapy. The aim of this paper was to propose a PVE correction based on a modified recovery coefficient method (termed FARCAS) that considers the functional volumes and local contrasts of lesions that are automatically determined using a semi-automatic iterative segmentation algorithm. METHODS: The FARCAS method consists of establishing a set of calibration curves based on the mathematical fitting of the RC values as a function of the automatically determined functional lesion volume and local lesion contrast. We set up our method using data from a cylindrical phantom that included spheres of different volumes (range: 0.43 to 97.8 mL) and contrasts (range: 1.7 to 22.9), and we assessed the method using both cylindrical and anthropomorphic phantom data that also included spheres of different volumes and contrasts. FARCAS was also compared with conventional RC methods that only considered the lesion functional volume, either automatically determined (RCVa) or using the ground truth volume (RCVgt). Finally, the clinical feasibility of FARCAS and its evaluation on tumor classification were also assessed on 24 NSCLC lesions. RESULTS: Whatever the phantom considered, for the spheres with contrast <5, FARCAS obtained comparable results to RCVgt and better than RCVa. For the spheres with contrast >5, FARCAS and RCVa were not statistically different, neither for the cylindrical and nor the anthropomorphic phantom. For the cylindrical phantom FARCAS yielded corrections that were not statistically different to those of RCVa for the smallest spheres (V<2 mL), but statistically superior for the larger spheres (V≥2 mL). RCVgt maintained a non-statistically superior accuracy. Regarding the anthropomorphic data, FARCAS was statistically more accurate than RCVa but not RCVgt. As main findings regarding the clinical data, FARCAS modified the classifications of five of 24 NSCLC lesions based on quantitative PERCIST criteria. CONCLUSIONS: The PVE correction proposed in this paper allows the accurate quantification of the PVE-corrected SUV, allowing also an automatic definition of the Metabolic Target Volume (MTV). Our results revealed that the PVE correction based on FARCAS is a better approach than conventional RC to significantly reduce the impact of PVE on lesion quantification, thus improving the evaluation of tumor response to treatment based on PET-CT images.

In Vitro and In Vivo Imaging of Fluorescent Aptamers.

Fluorescence imaging techniques could be used in different ways to study the interaction of aptamers with biological systems from cell culture to animal models. Here, we present the methods developed in our laboratory for fluorescently labeled aptamers, study their internalization inside living cells using time-lapse microscopy, and monitor their biodistribution in mice bearing subcutaneous xenograft tumors using planar fluorescence imaging and fluorescence diffuse optical tomography (fDOT).

Stable and compact zwitterionic polydiacetylene micelles with tumor-targeting properties.

Compact polymerized polydiacetylene-micelles with "stealth" zwitterionic surface coating were assembled and tested in a murine xenograft model of breast cancer. In vivo fluorescence imaging indicated accumulation in the tumor area and histological studies revealed predominant uptake of the micelles at the margins of the tumor, thereby allowing the delineation of its volume.

Fusion of multi-tracer PET images for dose painting.

PET imaging with FluoroDesoxyGlucose (FDG) tracer is clinically used for the definition of Biological Target Volumes (BTVs) for radiotherapy. Recently, new tracers, such as FLuoroThymidine (FLT) or FluoroMisonidazol (FMiso), have been proposed. They provide complementary information for the definition of BTVs. Our work is to fuse multi-tracer PET images to obtain a good BTV definition and to help the radiation oncologist in dose painting. Due to the noise and the partial volume effect leading, respectively, to the presence of uncertainty and imprecision in PET images, the segmentation and the fusion of PET images is difficult. In this paper, a framework based on Belief Function Theory (BFT) is proposed for the segmentation of BTV from multi-tracer PET images. The first step is based on an extension of the Evidential C-Means (ECM) algorithm, taking advantage of neighboring voxels for dealing with uncertainty and imprecision in each mono-tracer PET image. Then, imprecision and uncertainty are, respectively, reduced using prior knowledge related to defects in the acquisition system and neighborhood information. Finally, a multi-tracer PET image fusion is performed. The results are represented by a set of parametric maps that provide important information for dose painting. The performances are evaluated on PET phantoms and patient data with lung cancer. Quantitative results show good performance of our method compared with other methods.

Segmentation of biological target volumes on multi-tracer PET images based on information fusion for achieving dose painting in radiotherapy.

Medical imaging plays an important role in radiotherapy. Dose painting consists in the application of a nonuniform dose prescription on a tumoral region, and is based on an efficient segmentation of biological target volumes (BTV). It is derived from PET images, that highlight tumoral regions of enhanced glucose metabolism (FDG), cell proliferation (FLT) and hypoxia (FMiso). In this paper, a framework based on Belief Function Theory is proposed for BTV segmentation and for creating 3D parametric images for dose painting. We propose to take advantage of neighboring voxels for BTV segmentation, and also multi-tracer PET images using information fusion to create parametric images. The performances of BTV segmentation was evaluated on an anthropomorphic phantom and compared with two other methods. Quantitative results show the good performances of our method. It has been applied to data of five patients suffering from lung cancer. Parametric images show promising results by highlighting areas where a high frequency or dose escalation could be planned.