Combination antibody therapy with epratuzumab and rituximab in relapsed or refractory non-Hodgkin's lymphoma.

PURPOSE: To explore the safety and therapeutic activity of combination anti-B-cell monoclonal antibody therapy in non-Hodgkin's lymphoma (NHL). PATIENTS AND METHODS: Twenty-three patients with recurrent B-cell lymphoma received anti-CD22 epratuzumab 360 mg/m(2) and anti-CD20 rituximab 375 mg/m(2) monoclonal antibodies weekly for four doses each. Sixteen patients had indolent histologies (15 with follicular lymphoma) and seven had aggressive NHL (all diffuse large B-cell lymphoma [DLBCL]). Indolent patients had received a median of one (range, one to six) prior treatment, with 31% refractory to their last therapy and 81% with high-risk Follicular Lymphoma International Prognostic Index scores. Patients with DLBCL had a median of three (range, one to eight) prior regimens (14% resistant to last treatment) and 71% had high intermediate-risk or high-risk International Prognostic Index scores. All patients were rituximab na?ve. RESULTS: Treatment was well tolerated, with toxicities principally infusion-related and predominantly grade 1 or 2. Ten (67%) patients with follicular NHL achieved an objective response (OR), including nine of 15 (60%) with complete responses (CRs and unconfirmed CRs). Four of six assessable patients (67%) with DLBCL achieved an OR, including three (50%) CRs. Median time to progression for all indolent NHL patients was 17.8 months. CONCLUSION: The full-dose combination of epratuzumab with rituximab was well tolerated and had significant clinical activity in NHL, suggesting that this combination should be tested in comparison with single-agent treatment.     

The Isolation and Characterization of a Broad Host Range Bcep22-like Podovirus JC1

Bacteriophage JC1 is a Podoviridae phage with a C1 morphotype, isolated on host strain Burkholderia cenocepacia Van1. Phage JC1 is capable of infecting an expansive range of Burkholderia cepacia complex (Bcc) species. The JC1 genome exhibits significant similarity and synteny to Bcep22-like phages and to many Ralstonia phages. The genome of JC1 was determined to be 61,182 bp in length with a 65.4% G + C content and is predicted to encode 76 proteins and 1 tRNA gene. Unlike the other Lessieviruses, JC1 encodes a putative helicase gene in its replication module, and it is in a unique organization not found in previously analyzed phages. The JC1 genome also harbours 3 interesting moron genes, that encode a carbon storage regulator (CsrA), an N-acetyltransferase, and a phosphoadenosine phosphosulfate (PAPS) reductase. JC1 can stably lysogenize its host Van1 and integrates into the 5′ end of the gene rimO. This is the first account of stable integration identified for Bcep22-like phages. JC1 has a higher global virulence index at 37 °C than at 30 °C (0.8 and 0.21, respectively); however, infection efficiency and lysogen stability are not affected by a change in temperature, and no observable temperature-sensitive switch between lytic and lysogenic lifestyle appears to exist. Although JC1 can stably lysogenize its host, it possesses some desirable characteristics for use in phage therapy. Phage JC1 has a broad host range and requires the inner core of the bacterial LPS for infection. Bacteria that mutate to evade infection by JC1 may develop a fitness disadvantage as seen in previously characterized LPS mutants lacking inner core.     

Mutations in the NDP gene: contribution to Norrie disease, familial exudative vitreoretinopathy and retinopathy of prematurity

Background: To examine the contribution of mutations within the Norrie disease (NDP) gene to the clinically similar retinal diseases Norrie disease, X‐linked familial exudative vitreoretinopathy (FEVR), Coat’s disease and retinopathy of prematurity (ROP). Methods: A dataset comprising 13 Norrie‐FEVR, one Coat’s disease, 31 ROP patients and 90 ex‐premature babies of <32 weeks’ gestation underwent an ophthalmologic examination and were screened for mutations within the NDP gene by direct DNA sequencing, denaturing high‐performance liquid chromatography or gel electrophoresis. Controls were only screened using denaturing high‐performance liquid chromatography and gel electrophoresis. Confirmation of mutations identified was obtained by DNA sequencing. Results: Evidence for two novel mutations in the NDP gene was presented: Leu103Val in one FEVR patient and His43Arg in monozygotic twin Norrie disease patients. Furthermore, a previously described 14‐bp deletion located in the 5′ unstranslated region of the NDP gene was detected in three cases of regressed ROP. A second heterozygotic 14‐bp deletion was detected in an unaffected ex‐premature girl. Only two of the 13 Norrie‐FEVR index cases had the full features of Norrie disease with deafness and mental retardation. Conclusion: Two novel mutations within the coding region of the NDP gene were found, one associated with a severe disease phenotypes of Norrie disease and the other with FEVR. A deletion within the non‐coding region was associated with only mild‐regressed ROP, despite the presence of low birthweight, prematurity and exposure to oxygen. In full‐term children with retinal detachment only 15% appear to have the full features of Norrie disease and this is important for counselling parents on the possible long‐term outcome.     

The metabolism of 2,3,4-trimethylpentane in male Fischer-344 rats

The urinary metabolites of the potent nephrotoxic hydrocarbon 2,3,4-trimethylpentane (2,3,4-TMP) given Fischer-344 male rats by gavage included 1-hydroxy-2,3,4-trimethylpentane, 2,3,4-trimethyl-1-pentanoic acid and 2,3,4-trimethyl-5-hydroxy-1-pentanoic acid. Analyses were performed by gas-liquid chromatography (GC) and gas-liquid chromatography/mass spectrometry (GC/MS). A comparison of the urinary metabolites of 2,3,4-TMP with those of 2,2,4-trimethylpentane (2,2,4-TMP) showed that more monocarboxylic acid was produced with 2,3,4-TMP.     

Direct-to-Biology Accelerates PROTAC Synthesis and the Evaluation of Linker Effects on Permeability and Degradation

A platform to accelerate optimization of proteolysis targeting chimeras (PROTACs) has been developed using a direct-to-biology (D2B) approach with a focus on linker effects. A large number of linker analogs—with varying length, polarity, and rigidity—were rapidly prepared and characterized in four cell-based assays by streamlining time-consuming steps in synthesis and purification. The expansive dataset informs on linker structure–activity relationships (SAR) for in-cell E3 ligase target engagement, degradation, permeability, and cell toxicity. Unexpected aspects of linker SAR was discovered, consistent with literature reports on “linkerology”, and the method dramatically speeds up empirical optimization. Physicochemical property trends emerged, and the platform has the potential to rapidly expand training sets for more complex prediction models. In-depth validation studies were carried out and confirm the D2B platform is a valuable tool to accelerate PROTAC design–make–test cycles.     

Home Parenteral and Enteral Nutrition

While the history of nutrition support dates to the ancient world, modern home parenteral and enteral nutrition (HPEN) has been available since the 1960s. Home enteral nutrition is primarily for patients in whom there is a reduction in oral intake below the amount needed to maintain nutrition or hydration (i.e., oral failure), whereas home parenteral nutrition is used for patients when oral-enteral nutrition is temporarily or permanently impossible or absorption insufficient to maintain nutrition or hydration (i.e., intestinal failure). The development of home delivery of these therapies has revolutionized the field of clinical nutrition. The use of HPEN appears to be increasing on a global scale, and because of this, it is important for healthcare providers to understand all that HPEN entails to provide safe, efficacious, and cost-effective support to the HPEN patient. In this article, we provide a comprehensive review of the indications, patient requirements, monitoring, complications, and overall process of managing these therapies at home. Whereas some of the information in this article may be applicable to the pediatric patient, the focus is on the adult population.     

The NHS England 100,000 Genomes Project: feasibility and utility of centralised genome sequencing for children with cancer

Background Whole-genome sequencing (WGS) of cancers is becoming an accepted component of oncological care, and NHS England is currently rolling out WGS for all children with cancer. This approach was piloted during the 100,000 genomes (100 K) project. Here we share the experience of the East of England Genomic Medicine Centre (East-GMC), reporting the feasibility and clinical utility of centralised WGS for individual children locally.Methods Non-consecutive children with solid tumours were recruited into the pilot 100 K project at our Genomic Medicine Centre. Variant catalogues were returned for local scrutiny and appraisal at dedicated genomic tumour advisory boards with an emphasis on a detailed exploration of potential clinical value.Results Thirty-six children, representing one-sixth of the national 100 K cohort, were recruited through our Genomic Medicine Centre. The diagnoses encompassed 23 different solid tumour types and WGS provided clinical utility, beyond standard-of-care assays, by refining (2/36) or changing (4/36) diagnoses, providing prognostic information (8/36), defining pathogenic germline mutations (1/36) or revealing novel therapeutic opportunities (8/36).Conclusion Our findings demonstrate the feasibility and clinical value of centralised WGS for children with cancer. WGS offered additional clinical value, especially in diagnostic terms. However, our experience highlights the need for local expertise in scrutinising and clinically interpreting centrally derived variant calls for individual children.Subject terms: Cancer genomics, Cancer genomics     

Generalizing Bayesian phylogenetics to infer shared evolutionary events

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.

There are many processes of biological diversification that affect multiple evolutionary lineages, generating patterns of temporally clustered divergences across the tree of life. Understanding such processes of diversification has important implications across many fields and scales of biology. At the scale of genome evolution, the duplication of a chromosome segment harboring multiple members of a gene family causes multiple, simultaneous (or “shared”) divergences across the phylogenetic history of the gene family (1–4). In epidemiology, when a pathogen is spread by multiple infected individuals at a social gathering, this will create shared divergences across the pathogen’s “transmission tree” (5–7). If one of these individuals infects two or more others, this will create a multifurcation (a lineage diverging into three or more descendants) in the transmission tree. At regional or global scales, when biogeographic processes fragment communities, this can cause shared divergences across multiple affected species (8–13). If the landscape is fragmented into three or more regions, this can also cause multifurcations (14). For example, the repeated fragmentation of the Philippines by interglacial rises in sea level since the late Pliocene (15–19) has been an important model to help explain remarkably high levels of microendemism and biodiversity across the archipelago (20–30). This model predicts that recently diverged taxa across the islands should have (potentially multifurcating) divergence times clustered around the beginning of interglacial periods. We are limited in our ability to infer patterns of divergences predicted by such processes because phylogenetic methods assume that lineages diverge independently.To formalize this assumption of independent divergences and develop ways to relax it, it is instructive to view phylogenetic inference as an exercise of statistical model selection, where each topology is a separate model (31–33). Current methods for estimating rooted phylogenies with N tips only consider tree models with N−1 bifurcating divergences and assume that these divergences are independent, conditional on the topology (see ref. 34 for multifurcations in unrooted trees). If, in the history leading to the tips we are studying, diversification processes affected multiple lineages simultaneously or caused them to diverge into more than two descendants, the true tree could have shared or multifurcating divergences. This would make current phylogenetic models with N−1 independent divergence times overparameterized, introducing unnecessary error (Fig. 1). Even worse, with current methods, we lack an obvious way of using our data to test for patterns of shared or multifurcating divergences predicted by such processes.Open in a separate windowFig. 1.A hypothetical evolutionary history with shared divergences (Left) and the benefits of the generalizing tree space under such conditions (Right). Current methods are restricted to one class of tree models, where the tree is fully bifurcating and independent divergence-time parameters are estimated for all internal nodes (Center). Figure was made by using Gram [v4.0.0 (35)] and the P4 phylogenetic toolkit [v1.4 5742542 (36)]. Image credit for top and bottom lizard silhouettes: Phylopic/Steven Traver. Image credit for middle lizard silhouettes: Pixabay/No-longer-here.We relax the assumption of independent, bifurcating divergences by introducing a Bayesian approach to generalizing the space of tree models to allow for shared and multifurcating divergences. In our approach, we view trees with N−1 bifurcating divergences as only one class of tree models in a greater space of trees with anywhere from 1 to N−1 potentially shared and/or multifurcating divergences (SI Appendix, Fig. S1). We introduce reversible-jump Markov chain Monte Carlo (MCMC) algorithms (37–39) to sample this generalized space of trees, allowing us to jointly infer evolutionary relationships, shared and multifurcating divergences, and divergence times. We couple these algorithms with a likelihood model for directly calculating the probability of biallelic characters, given a population (or species) phylogeny, while analytically integrating over all possible gene trees under a coalescent model and all possible mutational histories under a finite-sites model of character evolution (40, 41). Using simulations, we find that the generalized tree model accurately infers shared and multifurcating divergences, while maintaining a low rate of falsely inferring such divergences. To test for patterns of shared and multifurcating divergences predicted by repeated fragmentation of the Philippines by interglacial rises in sea level (42–44), we apply the generalized tree model to genomic data from two genera of geckos codistributed across the islands.