Functional unknomics: Systematic screening of conserved genes of unknown function.

The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable "Unknome database" that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.

Multicentre study of physical abuse and limb fractures in young children in the East Anglia Region, UK.

OBJECTIVE: To determine if the detection of physical abuse in young children with fractures is of uniform high standard in the East Anglia Region of the UK, and whether we can identify areas for improvement in our detection of high-risk groups. DESIGN: Multicentre retrospective 4-year study. SETTING: 7 hospitals across the East Anglia Region of Britain (East Anglia Paediatric Physical Abuse and Fractures study). PARTICIPANTS: Age groups and fractures indicated as being at higher risk for physical abuse (all children under 12 months of age, and fractures of humerus and femur in children under 36 months of age). OUTCOME MEASURES: Our criterion for physical abuse was the decision of a multiagency child protection case conference (CPCC). RESULTS: Probability of CPCC decision of physical abuse was highest in infants, ranging from 50% of fractures sustained in the first month of life (excluding obstetric injuries) to 10% at 12 months of age. Only 46%-86% of infants (under 12 months) with a fracture were assessed by a paediatrician for physical abuse after their fracture. Significant variation in the use of skeletal surveys and in CPCC decision of physical abuse was noted in children attending different hospitals. CONCLUSIONS: It is a concern that significant variation between hospitals was found in the investigation and detection of physical abuse as confirmed by CPCC decisions. To minimise failure to detect true cases of physical abuse, we recommend that all high-risk children should be assessed by a paediatrician prior to discharge from the emergency department. Our proposed criteria for assessment (where we found probability of CPCC decision of physical abuse was at least 10%) are any child under the age of 12 months with any fracture, under 18 months of age with femur fracture and under 24 months with humeral shaft fracture (not supracondylar).

Diffuse large B-cell lymphoma classification system that associates normal B-cell subset phenotypes with prognosis.

PURPOSE: Current diagnostic tests for diffuse large B-cell lymphoma use the updated WHO criteria based on biologic, morphologic, and clinical heterogeneity. We propose a refined classification system based on subset-specific B-cell-associated gene signatures (BAGS) in the normal B-cell hierarchy, hypothesizing that it can provide new biologic insight and diagnostic and prognostic value. PATIENTS AND METHODS: We combined fluorescence-activated cell sorting, gene expression profiling, and statistical modeling to generate BAGS for naive, centrocyte, centroblast, memory, and plasmablast B cells from normal human tonsils. The impact of BAGS-assigned subtyping was analyzed using five clinical cohorts (treated with cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP], n = 270; treated with rituximab plus CHOP [R-CHOP], n = 869) gathered across geographic regions, time eras, and sampling methods. The analysis estimated subtype frequencies and drug-specific resistance and included a prognostic meta-analysis of patients treated with first-line R-CHOP therapy. RESULTS: Similar BAGS subtype frequencies were assigned across 1,139 samples from five different cohorts. Among R-CHOP-treated patients, BAGS assignment was significantly associated with overall survival and progression-free survival within the germinal center B-cell-like subclass; the centrocyte subtype had a superior prognosis compared with the centroblast subtype. In agreement with the observed therapeutic outcome, centrocyte subtypes were estimated as being less resistant than the centroblast subtype to doxorubicin and vincristine. The centroblast subtype had a complex genotype, whereas the centrocyte subtype had high TP53 mutation and insertion/deletion frequencies and expressed LMO2, CD58, and stromal-1-signature and major histocompatibility complex class II-signature genes, which are known to have a positive impact on prognosis. CONCLUSION: Further development of a diagnostic platform using BAGS-assigned subtypes may allow pathogenetic studies to improve disease management.