Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.

MOTIVATION: In recent years, many algorithms for inferring gene regulatory networks from single-cell transcriptomic data have been published. Several studies have evaluated their accuracy in estimating the presence of an interaction between pairs of genes. However, these benchmarking analyses do not quantify the algorithms' ability to capture structural properties of networks, which are fundamental, e.g., for studying the robustness of a gene network to external perturbations. Here, we devise a three-step benchmarking pipeline called STREAMLINE that quantifies the ability of algorithms to capture topological properties of networks and identify hubs. RESULTS: To this aim, we use data simulated from different types of networks as well as experimental data from three different organisms. We apply our benchmarking pipeline to four inference algorithms and provide guidance on which algorithm should be used depending on the global network property of interest. AVAILABILITY AND IMPLEMENTATION: STREAMLINE is available at https://github.com/ScialdoneLab/STREAMLINE. The data generated in this study are available at https://doi.org/10.5281/zenodo.10710444.

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.

Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data.

A powerful feature of single-cell genomics is the possibility of identifying cell types from their molecular profiles. In particular, identifying novel rare cell types and their marker genes is a key potential of single-cell RNA sequencing. Standard clustering approaches perform well in identifying relatively abundant cell types, but tend to miss rarer cell types. Here, we have developed CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types), a cluster-independent computational tool designed to select genes that are likely to be markers of rare cell types. Genes selected by CIARA are subsequently integrated with common clustering algorithms to single out groups of rare cell types. CIARA outperforms existing methods for rare cell type detection, and we use it to find previously uncharacterized rare populations of cells in a human gastrula and among mouse embryonic stem cells treated with retinoic acid. Moreover, CIARA can be applied more generally to any type of single-cell omic data, thus allowing the identification of rare cells across multiple data modalities. We provide implementations of CIARA in user-friendly packages available in R and Python.

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.

Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve 'active' regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain 'inactive' regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.

Emergent statistical laws in single-cell transcriptomic data.

Large-scale data on single-cell gene expression have the potential to unravel the specific transcriptional programs of different cell types. The structure of these expression datasets suggests a similarity with several other complex systems that can be analogously described through the statistics of their basic building blocks. Transcriptomes of single cells are collections of messenger RNA abundances transcribed from a common set of genes just as books are different collections of words from a shared vocabulary, genomes of different species are specific compositions of genes belonging to evolutionary families, and ecological niches can be described by their species abundances. Following this analogy, we identify several emergent statistical laws in single-cell transcriptomic data closely similar to regularities found in linguistics, ecology, or genomics. A simple mathematical framework can be used to analyze the relations between different laws and the possible mechanisms behind their ubiquity. Importantly, treatable statistical models can be useful tools in transcriptomics to disentangle the actual biological variability from general statistical effects present in most component systems and from the consequences of the sampling process inherent to the experimental technique.

Adaptive Optics of Kyrieleis Plaques in Varicella Zoster Virus-Associated Posterior Uveitis: A Multimodal Imaging Analysis.

Kyrieleis plaques (KP) represent a peculiar type of vasculitis affecting retinal arterial branches in a beaded segmental pattern that can be found in several posterior inflammatory ocular conditions. The nature and precise location of KP is unclear. Adaptive Optics (AO) provides an in vivo visualization of retinal vasculature on a microscopic level, thus permitting a more detailed characterization of KP as compared to traditional imaging techniques. This study aims to report AO imaging of KP in Varicella Zoster virus (VZV)-associated posterior uveitis and to correlate the findings with traditional imaging techniques. Three patients diagnosed with VZV posterior uveitis underwent adaptive optics (AO) imaging and traditional multimodal imaging techniques, including fundus photography, fluorescein angiography, indocyanine green angiography and optical coherence tomography. In all subjects, AO imaging revealed segmental hyporeflectivity confined to the vessel wall, with no evidence of arterial wall disruption or extravascular involvement. In our series, AO findings support the view that KP are localized within the inner arterial wall, possibly at the endothelial level.

Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control.

The chromatin environment at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how and which chromatin features control the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we use site-specific recombination and single-locus chromatin isolation to purify EE and LI replication origins in Saccharomyces cerevisiae. Using mass spectrometry, we define the protein composition of native chromatin regions surrounding the EE and LI replication start sites. In addition to known origin interactors, we find the microtubule-binding Ask1/DASH complex as an origin-regulating factor. Strikingly, tethering of Ask1 to individual origin sites advances replication timing (RT) of the targeted chromosomal domain. Targeted degradation of Ask1 globally changes RT of a subset of origins, which can be reproduced by inhibiting microtubule dynamics. Thus, our findings mechanistically connect RT and chromosomal organization via Ask1/DASH with the microtubule cytoskeleton.

Reduced Posology of an Ophthalmic Hydrogel Containing Dexamethasone/Netilmicin to Prevent and Treat Ocular Inflammation After Cataract Surgery: Efficacy and Tolerability.

INTRODUCTION: To demonstrate efficacy and safety of an ophthalmic hydrogel formulation of netilmicin/dexamethasone, containing xanthan gum twice a day (b.i.d.) versus netilmicin/dexamethasone eye drops four times a day (q.i.d) to treat inflammation and prevention of infection after cataract surgery. METHODS: Patients undergoing phacoemulsification with intraocular lens implantation (IOL) were randomised in two groups: group 1, twice daily (b.i.d.) dexamethasone 0.1%/netilmicin 0.3% (Netildex) ophthalmic gel; group 2, four times daily (q.i.d.) dexamethasone 0.1%/netilmicin 0.3% (Netildex) eye drops. Both treatments were administered for 14 days after surgery. Patients were evaluated before surgery, on the day of surgery and at 1, 7, 15 and 60 postoperative days. The primary efficacy endpoint was evaluation of cellularity and flare in the anterior chamber through slit-lamp biomicroscopy 7 days after surgery. Secondary endpoints included: presence of signs/symptoms of postoperative ocular inflammation and incidence of infection. RESULTS: One hundred seventy-three patients were randomised and 168 were evaluable. Flare and cellularity were resolved at day 7 in 92.5% of patients and almost completely by day 15. In both intent to treat (ITT) and per-protocol (PP) populations, the efficacy analysis demonstrated that the gel formulation administered twice a day was non-inferior to the eye drops administered four times a day. For ITT analysis, the lower limit of the 97.5% confidence interval (- 0.0535) was greater than the non-inferiority limit of -0.10. For the PP analysis, the lower limit of the 97.5% confidence interval (- 0.0526) was greater than the non-inferiority limit of - 0.10. The patient's global tolerability and reported symptoms were similar between treatment groups. No microbial load and no safety events were observed. CONCLUSIONS: Efficacy of the gel reduced posology (twice a day) is not inferior to four times a day eye drops. Both treatments were well tolerated and efficacious. The new reduced posology hydrogel formulation may improve patient compliance and quality of life. TRIAL REGISTRATION: Eudract: 2016-0021138-63; ClinicalTrial.gov: NCT029738880.

EBNA2-EBF1 complexes promote MYC expression and metabolic processes driving S-phase progression of Epstein-Barr virus-infected B cells.

Epstein-Barr virus (EBV) is a human tumor virus which preferentially infects resting human B cells. Upon infection in vitro, EBV activates and immortalizes these cells. The viral latent protein EBV nuclear antigen 2 (EBNA2) is essential for B cell activation and immortalization; it targets and binds the cellular and ubiquitously expressed DNA-binding protein CBF1, thereby transactivating a plethora of viral and cellular genes. In addition, EBNA2 uses its N-terminal dimerization (END) domain to bind early B cell factor 1 (EBF1), a pioneer transcription factor specifying the B cell lineage. We found that EBNA2 exploits EBF1 to support key metabolic processes and to foster cell cycle progression of infected B cells in their first cell cycles upon activation. The α1-helix within the END domain was found to promote EBF1 binding. EBV mutants lacking the α1-helix in EBNA2 can infect and activate B cells efficiently, but activated cells fail to complete the early S phase of their initial cell cycle. Expression of MYC, target genes of MYC and E2F, as well as multiple metabolic processes linked to cell cycle progression are impaired in EBVΔα1-infected B cells. Our findings indicate that EBF1 controls B cell activation via EBNA2 and, thus, has a critical role in regulating the cell cycle of EBV-infected B cells. This is a function of EBF1 going beyond its well-known contribution to B cell lineage specification.

The role of cell geometry and cell-cell communication in gradient sensing.

Cells can measure shallow gradients of external signals to initiate and accomplish a migration or a morphogenetic process. Recently, starting from mathematical models like the local-excitation global-inhibition (LEGI) model and with the support of empirical evidence, it has been proposed that cellular communication improves the measurement of an external gradient. However, the mathematical models that have been used have over-simplified geometries (e.g., they are uni-dimensional) or assumptions about cellular communication, which limit the possibility to analyze the gradient sensing ability of more complex cellular systems. Here, we generalize the existing models to study the effects on gradient sensing of cell number, geometry and of long- versus short-range cellular communication in 2D systems representing epithelial tissues. We find that increasing the cell number can be detrimental for gradient sensing when the communication is weak and limited to nearest neighbour cells, while it is beneficial when there is long-range communication. We also find that, with long-range communication, the gradient sensing ability improves for tissues with more disordered geometries; on the other hand, an ordered structure with mostly hexagonal cells is advantageous with nearest neighbour communication. Our results considerably extend the current models of gradient sensing by epithelial tissues, making a step further toward predicting the mechanism of communication and its putative mediator in many biological processes.

A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell.

The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain understudied. The spatial location of odorant receptor genes (Olfrs) in the nose is thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we create a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that both Olfrs and non-Olfrs are distributed in a continuous and overlapping fashion over at least five broad zones in the OM. The spatial locations of Olfrs correlate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolves the molecular architecture of the mouse OM and will inform future studies on mechanisms underlying Olfr gene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.

DNA replication fork speed underlies cell fate changes and promotes reprogramming.

Totipotency emerges in early embryogenesis, but its molecular underpinnings remain poorly characterized. In the present study, we employed DNA fiber analysis to investigate how pluripotent stem cells are reprogrammed into totipotent-like 2-cell-like cells (2CLCs). We show that totipotent cells of the early mouse embryo have slow DNA replication fork speed and that 2CLCs recapitulate this feature, suggesting that fork speed underlies the transition to a totipotent-like state. 2CLCs emerge concomitant with DNA replication and display changes in replication timing (RT), particularly during the early S-phase. RT changes occur prior to 2CLC emergence, suggesting that RT may predispose to gene expression changes and consequent reprogramming of cell fate. Slowing down replication fork speed experimentally induces 2CLCs. In vivo, slowing fork speed improves the reprogramming efficiency of somatic cell nuclear transfer. Our data suggest that fork speed regulates cellular plasticity and that remodeling of replication features leads to changes in cell fate and reprogramming.

"HIDE AND SEEK" NEUROSENSORY RETINAL DETACHMENTS IN PERIPAPILLARY PACHYCHOROID SYNDROME ASSOCIATED WITH PULMONARY ARTERIAL HYPERTENSION.

PURPOSE: To report the case of a patient with peripapillary pachychoroid syndrome and recurrent and spontaneous resolving peripapillary neurosensory retinal detachments associated with pulmonary arterial hypertension. METHODS: Case report imaged with spectral-domain optical coherence tomography, swept-source optical coherence tomography angiography, fundus autofluorescence, and fluorescein and indocyanine green angiography. RESULTS: A 47-year-old woman presented with unilateral blurred vision and metamorphopsia in her left eye and was diagnosed with peripapillary serous retinal detachments associated with peripapillary pachychoroid syndrome. Cardiologic examination was remarkable for heart failure secondary to severe pulmonary arterial hypertension. Neurosensory detachments spontaneously resolved after 1 day but recurred again three days from baseline. Fluorescein and indocyanine green angiography illustrated choroidal hyperpermeability associated with pachyvessels, whereas optical coherence tomography angiography displayed numerous areas of choriocapillaris nonperfusion, more severe in the left eye of the patient. CONCLUSION: In pulmonary arterial hypertension, hemodynamic changes caused by increased central venous pressure and endothelin-1 may explain the development of exudative retinal detachment and choroidal ischemia. The pathophysiological mechanisms explaining the peripapilary location of the fluid and the thick choroid, as with the peripapillary pachychoroid syndrome, are explored and discussed.

Effectiveness and safety of intravenous dexmedetomidine sedation for ophthalmic surgery under regional anesthesia.

PURPOSE: To assess the effectiveness and safety of intravenous (IV) dexmedetomidine for sedation in ophthalmic surgery. METHODS: Prospective, observational, uncontrolled, single-center study. Patients were sedated with a continuous dexmedetomidine IV infusion started 15 min before regional anesthesia administration and maintained up to the end of surgery. Effectiveness of dexmedetomidine was assessed by the Modified Observer's Assessment of Alertness and Sedation (MOAA/S) targeted at 5. Safety was assessed by the incidence of patients' movements/snoring and by the incidence of respiratory and haemodynamic complications. An eleven-point numerical rating scale (NRS) was used to assess the level of satisfaction of both the surgeon and the patient. RESULTS: 123 patients (73 males, mean age: 63 ± 13) were included; 81 (81/123; 65.8%) patients reached the requested MOAA/S score of 5. Any intraoperative movement - mostly voluntary - occurred in 34 (34/123; 27.6%) cases with no need for a switch to general anaesthesia; no ocular complications related to the intraoperative movements occurred. Intraoperative snoring occurred in 30 (30/123; 24.4%) patients and it did not affect the surgical manoeuvres. Respiratory drive depression requiring manual or mechanical ventilation never occurred. Bradycardia occurred in 14 (14/123; 11.3%), cases but only 4 (4/123; 3.2%) patients required atropine administration, which was always effective. Intraoperative analgesia was consistently obtained and both the surgeons and the patients reported a high NRS satisfaction score. CONCLUSION: Dexmedetomidine provided adequate sedation in patients undergoing ocular surgery under local anaesthesia and showed a good effectiveness and safety profile. Upper airway obstruction, apnoea and snoring can occur.

Placoid lesions of the retina: progress in multimodal imaging and clinical perspective.

Placoid lesions of the retina may be secondary to a wide spectrum of acquired inflammatory conditions that have been reported as single entities with different presentation and clinical course. These conditions include acute posterior multifocal placoid pigment epitheliopathy, persistent placoid maculopathy, serpiginous choroiditis, serpiginous-like choroiditis, relentless placoid chorioretinitis and acute syphilitic posterior placoid chorioretinitis. In this article, we will group these conditions under the name of 'placoids'. The recognition of the specific condition may be challenging in clinical practice, often resulting in diagnostic and therapeutic delay. Given the complex nature of placoids and their similarities, a systematic approach including differentiating between infectious and non-infectious aetiologies increases the chance of reaching the correct diagnosis. Detailed history and comprehensive clinical examination are the first steps to formulate a diagnostic hypothesis that should be corroborated by multimodal imaging and appropriate investigations. The advent of multimodal imaging has made it possible to extensively study placoids and revealed a constellation of specific findings that may help clinicians in the diagnostic process. The treatment of the conditions other than syphilis is complex and sometimes challenging. Our article is aimed at giving an overview of the individual entities associated with placoids and discussing the differential diagnosis. A practical and systematic approach is then proposed.

Single-cell transcriptomic characterization of a gastrulating human embryo.

Gastrulation is the fundamental process in all multicellular animals through which the basic body plan is first laid down1-4. It is pivotal in generating cellular diversity coordinated with spatial patterning. In humans, gastrulation occurs in the third week after fertilization. Our understanding of this process in humans is relatively limited and based primarily on historical specimens5-8, experimental models9-12 or, more recently, in vitro cultured samples13-16. Here we characterize in a spatially resolved manner the single-cell transcriptional profile of an entire gastrulating human embryo, staged to be between 16 and 19 days after fertilization. We use these data to analyse the cell types present and to make comparisons with other model systems. In addition to pluripotent epiblast, we identified primordial germ cells, red blood cells and various mesodermal and endodermal cell types. This dataset offers a unique glimpse into a central but inaccessible stage of our development. This characterization provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development.

Cell competition is emerging as a quality-control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mice, 35% of epiblast cells are eliminated before gastrulation. Here we show that cells with mitochondrial defects are eliminated by cell competition during early mouse development. Using single-cell transcriptional profiling of eliminated mouse epiblast cells, we identify hallmarks of cell competition and mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function triggers cell competition. Moreover, we show that in the mouse embryo, cell competition eliminates cells with sequence changes in mt-Rnr1 and mt-Rnr2, and that even non-pathological changes in mitochondrial DNA sequences can induce cell competition. Our results suggest that cell competition is a purifying selection that optimizes mitochondrial performance before gastrulation.