Cytomegalovirus post kidney transplantation: prophylaxis versus pre‐emptive therapy?

Cytomegalovirus is the most important pathogen causing opportunistic infections in kidney allograft recipients. The occurrence of CMV disease is associated with higher morbidity, higher incidence of other opportunistic infections, allograft loss and death. Therefore, an efficient strategy to prevent CMV disease after kidney transplantation is required. Two options are currently available: pre‐emptive therapy based on regular CMV PCR monitoring and generalized antiviral prophylaxis during a defined period. In this review, we describe those two approaches, highlight the distinct advantages and risks of each strategy and summarize the four randomized controlled trials performed in this field so far. Taken this evidence together, pre‐emptive therapy and anti‐CMV prophylaxis are both equally potent in preventing CMV‐associated complications; however, the pre‐emptive approach may have distinct advantages in allowing for development of long‐term anti‐CMV immunity. We propose a risk‐adapted use of these approaches based on serostatus, immunosuppressive therapy and availability of resources at a particular transplant centre.     

Results after the surgical treatment of anterior cervical hyperostosis causing dysphagia

Purpose

The objective of this study was to investigate the outcome of a case series of patients with dysphagia resulting from diffuse idiopathic skeletal hyperostosis (DISH) of the cervical spine who were treated surgically with resection and fusion.

Methods

A retrospective study was performed on all patients who presented (2005?2013) with complaints of dysphagia or respiratory compromise and who underwent anterior cervical osteophyte resection with fusion (polyether ether ketone cage and/or plate system) using an anterior approach. All patients were diagnosed with DISH and underwent preoperative esophageal and laryngoscopic examinations and a fluoroscopic swallowing study. Initial non-operative strategies were performed, including diet, change in head position during swallowing, non-steroidal anti-inflammatory drugs and pantoprazole.

Results

A total of six patients with DISH were included. The mean age was 67 ± 5 years. All patients were male and had symptoms of dysphagia and neck pain, one had simultaneous airway complaints, and another had regurgitation with a sleep disorder. All patients had significant improvements in dysphagia, respiratory complaints and regurgitation 6 weeks after surgery. The postoperative radiographs showed complete removal of the compressive structures. There were no postoperative complications. At the final follow-up (23 ± 8 months), the radiographic examinations showed no pathological regrowth, and the patients reported no recurrence of dysphagia.

Conclusion

Diffuse idiopathic skeletal hyperostosis may lead to osteophyte-associated pathologies of the aerodigestive tract. Preoperative investigations with esophageal and laryngoscopic examinations combined with fluoroscopic swallowing tests are essential. Surgical decompression through osteophytectomy and fusion is an effective management strategy in selected patients and should be considered when non-operative strategies have failed.

     

Phylogenomics with paralogs

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer.Molecular phylogenetics is primarily concerned with the reconstruction of evolutionary relationships between species based on sequence information. To this end, alignments of protein or DNA sequences are used, whose evolutionary history is believed to be congruent to that of the respective species. This property can be ensured most easily in the absence of gene duplications and horizontal gene transfer (HGT). Phylogenetic studies judiciously select families of genes that rarely exhibit duplications (such as rRNAs, most ribosomal proteins, and many of the housekeeping enzymes). In phylogenomics, elaborate automatic pipelines such as HaMStR (1), are used to filter genome-wide data sets to at least deplete sequences with detectable paralogs (homologs in the same species).In the presence of gene duplications, however, it becomes necessary to distinguish between the evolutionary history of genes (gene trees) and the evolutionary history of the species (species trees) in which these genes reside. Leaves of a gene tree represent genes. Their inner nodes represent two kinds of evolutionary events, namely the duplication of genes within a genome—giving rise to paralogs—and speciations, in which the ancestral gene complement is transmitted to two daughter lineages. Two genes are (co)orthologous if their last common ancestor in the gene tree represents a speciation event, whereas they are paralogous if their last common ancestor is a duplication event; see refs. 2 and 3 for a more recent discussion on orthology and paralogy relationships. Speciation events, in turn, define the inner vertices of a species tree. However, they depend on both the gene and the species phylogeny, as well as the reconciliation between the two. The latter identifies speciation vertices in the gene tree with a particular speciation event in the species tree and places the gene duplication events on the edges of the species tree. Intriguingly, it is nevertheless possible in practice to distinguish orthologs with acceptable accuracy without constructing either gene or species trees (4). Many tools of this type have become available over the last decade; see refs. 5 and 6 for a recent review. The output of such methods is an estimate Θ of the true orthology relation Θ^?, which can be interpreted as a graph G_Θ whose vertices are genes and whose edges connect estimated (co)orthologs.Recent advances in mathematical phylogenetics suggest that the estimated orthology relation Θ contains information on the structure of the species tree. To make this connection, we combine here three abstract mathematical results that are made precise in Materials and Methods below.

• i)Building upon the theory of symbolic ultrametrics (7), we showed that in the absence of horizontal gene transfer, the orthology relation of each gene family is a cograph (8). Cographs can be generated from the single-vertex graph K₁ by complementation and disjoint union (9). This special structure of cographs imposes very strong constraints that can be used to reduce the noise and inaccuracies of empirical estimates of orthology from pairwise sequence comparison. To this end, the initial estimate of G_Θ is modified to the closest correct orthology relation G_Θ^? in such a way that a minimal number of edges (i.e., orthology assignments) are introduced or removed. This amounts to solving the cograph-editing problem (10, 11).
• ii)It is well known that each cograph is equivalently represented by its cotree (9). The cotree is easily computed for a given cograph. In our context, the cotree of G_Θ^? is an incompletely resolved event-labeled gene tree. That is, in addition to the tree topology, we know for each internal branch point whether it corresponds to a speciation or a duplication event. Even though adjacent speciations or adjacent duplications cannot be resolved, the tree faithfully encodes the relative order of any pair of duplication and speciation (8). In the presence of horizontal gene transfer, G_Θ may deviate from the structural requirements of a cograph. Still, the situation can be described in terms of edge-colored graphs whose subgraphs are cographs (7, 8), so that the cograph structure remains an acceptable approximation.
• iii)Every triple (rooted binary tree on three leaves) in the cotree that has leaves from three species and is rooted in a speciation event also appears in the underlying species tree (12). Thus, the estimated orthology relation, after editing to a cograph and conversion to the equivalent event-labeled gene tree, provides much information on the species tree. This result allows us to collect, from the cotrees for each gene family, partial information on the underlying species tree. Interestingly, only gene families that harbor duplications, and thus have a nontrivial cotree, are informative. If no paralogs exist, then the orthology relation G_Θ is a clique (i.e., every family member is orthologous to every other family member) and the corresponding cotree is completely unresolved, and hence contains no triple. On the other hand, full resolution of the species tree is guaranteed if at least one duplication event between any two adjacent speciations is observable. The achievable resolution therefore depends on the frequency of gene duplications and the number of gene families.

Despite the variance reduction due to cograph editing, noise in the data, as well as the occasional introduction of contradictory triples as a consequence of horizontal gene transfer, is unavoidable. The species triples collected from the individual gene families thus will not always be congruent. A conceptually elegant way to deal with such potentially conflicting information is provided by the theory of supertrees in the form of the largest set of consistent triples (13, 14). The data will not always contain a sufficient set of duplication events to achieve full resolution. To this end, we consider trees with the property that the contraction of any edge leads to the loss of an input triple. There may be exponentially many alternative trees of this type. They can be listed efficiently using Semple’s algorithms (15). To reduce the solution space further, we search for a least resolved tree in the sense of ref. 16, i.e., a tree that has the minimum number of inner vertices. It constitutes one of the best estimates of the phylogeny without pretending a higher resolution than actually supported by the data. In SI Appendix, we discuss alternative choices.The mathematical reasoning summarized above, outlined in Materials and Methods, and presented in full detail in SI Appendix, directly translates into a computational workflow, Fig. 1. It entails three NP-hard combinatorial optimization problems: cograph editing (11), maximal consistent triple set (17–19), and least resolved supertree (16). We show here that they are nevertheless tractable in practice by formulating them as Integer Linear Programs (ILP) that can be solved for both artificial benchmark data sets and real-life data sets, comprising genome-scale protein sets for dozens of species, even in the presence of horizontal gene transfer.Open in a separate windowFig. 1.Outline of the computational framework. Starting from an estimated orthology relation Θ, its graph representation G_Θ is edited to obtain the closest cograph G_Θ^*, which, in turn, is equivalent to a (not necessarily fully resolved) gene tree T and an event labeling t. From (T, t), we extract the set ?? of all relevant species triples. As the triple set ?? need not be consistent, we compute the maximal consistent subset ??^? of ??. Finally, we construct a least resolved species tree from ??^?.     

Drosophila E-cadherin is required for the maintenance of ring canals anchoring to mechanically withstand tissue growth

Intercellular bridges called “ring canals” (RCs) resulting from incomplete cytokinesis play an essential role in intercellular communication in somatic and germinal tissues. During Drosophila oogenesis, RCs connect the maturing oocyte to nurse cells supporting its growth. Despite numerous genetic screens aimed at identifying genes involved in RC biogenesis and maturation, how RCs anchor to the plasma membrane (PM) throughout development remains unexplained. In this study, we report that the clathrin adaptor protein 1 (AP-1) complex, although dispensable for the biogenesis of RCs, is required for the maintenance of the anchorage of RCs to the PM to withstand the increased membrane tension associated with the exponential tissue growth at the onset of vitellogenesis. Here we unravel the mechanisms by which AP-1 enables the maintenance of RCs’ anchoring to the PM during size expansion. We show that AP-1 regulates the localization of the intercellular adhesion molecule E-cadherin and that loss of AP-1 causes the disappearance of the E-cadherin–containing adhesive clusters surrounding the RCs. E-cadherin itself is shown to be required for the maintenance of the RCs’ anchorage, a function previously unrecognized because of functional compensation by N-cadherin. Scanning block-face EM combined with transmission EM analyses reveals the presence of interdigitated, actin- and Moesin-positive, microvilli-like structures wrapping the RCs. Thus, by modulating E-cadherin trafficking, we show that the sustained E-cadherin–dependent adhesion organizes the microvilli meshwork and ensures the proper attachment of RCs to the PM, thereby counteracting the increasing membrane tension induced by exponential tissue growth.E-cadherin (E-Cad) is a core component of intercellular adhesion complexes in cohesive metazoan tissues. E-Cad assembles into clusters that are stabilized by actin filaments via β- and α-catenin at the level of adherens junctions and form an adhesive belt mechanically linking cells together. A key feature of adherens junctions is their plasticity, which enables tissue remodeling, sustained by a constant endocytosis- and exocytosis-regulated E-Cad turnover (1) that is critical for various morphogenetic processes in epithelia (2–5).Drosophila oogenesis is a rich, multifaceted developmental process during which E-Cad function is not limited to epithelia, because it also regulates intercellular collective migration (6, 7) and the adhesion of stem cells to their niche (8). Cells derived from two different stem cell populations initially assemble into egg chambers composed of a follicular epithelium surrounding a 16-cell germline cyst (GC), itself composed of one oocyte and 15 nurse cells. During the next 64 h, GC cells grow to hundreds of times their initial volume. Oocyte growth is supported by cytoplasmic connections with nurse cells through ring canals (RCs) (Fig. 1 A and B), intercellular bridges that, instead of undergoing abscission, are stabilized on arrested cleavage furrows (9, 10). Recent findings revealed that RCs play a vital role in germline as well as in somatic tissues (10). RCs are composed of a noncontracting subcortical actin ring (11), the inner rim, attached to an electron-dense plasma membrane (PM) (12), the outer rim (Fig. 1A). RCs have been studied mainly in Drosophila female GCs (9) where genetic screens uncovered a variety of actin regulators controlling their establishment at the onset of oogenesis and their growth throughout the entire process (13–17). However, the molecular machinery involved in anchoring the PM to the RC remains unknown. Mutations in several membrane-traffic regulators affect the integrity of nurse cells’ PM, causing multinucleation and giving rise to remnants of detached RCs (18–24); these observations suggest that an unidentified membrane cargo is required for anchoring RCs to the PM.Open in a separate windowFig. 1.Nurse cells’ multinucleation in AP-1 mutant female GCs. (A) Schematic representation of the GC consisting of a single oocyte (Oo, nucleus) connected to 15 nurse cells (blue) via RCs (red) and a surrounding monolayer of about 650 somatic follicle cells (green). (Inset) Schematic representation of a transverse section through the RCs composed of an inner rim [red, containing the Adducin-like Hu-li tai shao (Hts) (13, 15) and the filamin Cheerio (16)] contacting an electron-dense PM (outer rim, black) that itself is connected to the rest of the nurse cell PM (gray). (B) Stereotyped organization of the female GC before and after detachment of nurse cells’ RCs. The oocyte has a gray nucleus; nurse cells have colored nuclei. (C) Stage 8 wild-type and AP-1 mutant [identified by the loss of nuclear localization signal (NLS)::GFP, blue] GCs stained for actin (green) and DAPI (red). Arrows indicate RCs connecting nurse cells in control GCs. Arrowheads indicate RCs floating in the cytoplasm of multinucleated nurse cells in AP-1 mutant GCs (at least one floating ring was observed in 29 of 34 mutant stage 8 or older GCs). (C′) Quantitation of multinucleated AP-1 mutant GCs at stage 7 to stage 9 or older. (D) Maximal projections of 5 µm of anchored and clustered floating RCs in control and AP-1 mutant GCs.Here we describe an RC detachment phenotype in mutants of the clathrin adaptor protein 1 (AP-1), a protein complex regulating polarized membrane protein sorting from the trans-Golgi network and endosomal compartments (25), and provide direct evidence that polarized membrane trafficking to RCs allows an E-Cad–mediated mechanical strengthening of RC anchoring necessary to resist the membrane tension generated by cellular growth.