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Cross-ancestry genetic correlation is an important parameter to understand the genetic relationship between two ancestry groups. However, existing methods cannot properly account for ancestry-specific genetic architecture, which is diverse across ancestries, producing biased estimates of cross-ancestry genetic correlation. Here, we present a method to construct a genomic relationship matrix (GRM) that can correctly account for the relationship between ancestry-specific allele frequencies and ancestry-specific allelic effects. Through comprehensive simulations, we show that the proposed method outperforms existing methods in the estimations of SNP-based heritability and cross-ancestry genetic correlation. The proposed method is further applied to anthropometric and other complex traits from the UK Biobank data across ancestry groups. For obesity, the estimated genetic correlation between African and European ancestry cohorts is significantly different from unity, suggesting that obesity is genetically heterogenous between these two ancestries. Cross-ancestry genetic correlation can reveal differences in the genetic basis of traits between populations, but methods can be biased by ancestry-specific genetic architecture. Here, the authors present a method to for estimating cross-ancestry genetic correlations, accounting for ancestry-specific genetic architecture. [ABSTRACT FROM AUTHOR]

Three-dimensional (3D) nanoframe structures are very appealing because their inner voids and ridges interact efficiently with light and analytes, allowing for effective optical-based sensing. However, the realization of complex nanoframe architecture with high yield is challenging because the systematic design of such a complicated nanostructure lacks an appropriate synthesis protocol. Here, we show the synthesis method for complex 3D nanoframes wherein two-dimensional (2D) dual-rim nanostructures are engraved on each facet of octahedral nanoframes. The synthetic scheme proceeds through multiple executable on-demand steps. With Au octahedral nanoparticles as a sacrificial template, sequential processes of edge-selective Pt deposition and inner Au etching lead to Pt octahedral mono-rim nanoframes. Then, adlayers of Au are grown on Pt skeletons via the Frank-van der Merwe mode, forming sharp and well-developed edges. Next, Pt selective deposition on both the inner and outer boundaries leads to tunable geometric patterning on Au. Finally, after the selective etching of Au, Pt octahedral dual-rim nanoframes with highly homogeneous size and shape are achieved. In order to endow plasmonic features, Au is coated around Pt frames while retaining their geometric shape. The resultant plasmonic dual-rim engraved nanoframes possess strong light entrapping capability verified by single-particle surface-enhanced Raman scattering (SERS) and show the potential of nanoprobes for biosensing through SERS-based immunoassay. Most SERS-active nanostructures suffer from low robustness against misalignment to field polarization. Here, the authors demonstrate three-dimensional nanoframes of octahedral geometry, with two rims engraved on each facet, as polarization-independent SERS nanoprobes. [ABSTRACT FROM AUTHOR]

Rotational-translational decoupling, in which translational motion is apparently enhanced over rotational motion in violation of Stokes-Einstein (SE) and Debye-Stokes-Einstein (DSE) predictions, has been observed in materials near their glass transition temperatures (Tg). This has been posited to result from ensemble averaging in the context of dynamic heterogeneity. In this work, ensemble and single molecule experiments are performed in parallel on a fluorescent probe in high molecular weight polystyrene near its Tg. Ensemble results show decoupling onset at approximately 1.15Tg, increasing to over three orders of magnitude at Tg. Single molecule measurements also show a high degree of decoupling, with typical molecules at Tg showing translational diffusion coefficients nearly 400 times higher than expected from SE/DSE predictions. At the single molecule level, higher degree of breakdown is associated with particularly mobile molecules and anisotropic trajectories, providing support for anomalous diffusion as a critical driver of rotational-translational decoupling and SE/DSE breakdown. Experiments with high-molecular-weight polystyrene provide insights into the mechanisms behind rotational-translational decoupling in glassy systems. Specifically, particularly mobile molecules exhibiting anisotropic trajectories are found to play a key role in Debye-Stokes-Einstein breakdown. [ABSTRACT FROM AUTHOR]

The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://data.4dnucleome.org/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community. This paper describes the '4DN Data Portal' that hosts data generated by the 4D Nucleome network, including Hi-C and other chromatin conformation capture assays, as well as various sequencing-based and imaging-based assays. Raw data have been uniformly processed to increase comparability and the portal is implemented with visualization tools to browse the data without download. [ABSTRACT FROM AUTHOR]

To date, four rituximab biosimilars have received regulatory approval from the European Medicines Agency and/or US Food and Drug Administration. CT-P10 was the first rituximab biosimilar to be approved by each agency, in 2017 and 2018, respectively. Regulatory approval of CT-P10 followed demonstration of pharmacokinetic equivalence to the reference product in a phase I study in patients with rheumatoid arthritis. Phase III pivotal studies of CT-P10 subsequently demonstrated equivalence or non-inferiority of pharmacokinetics and efficacy between CT-P10 and reference rituximab in patients with rheumatoid arthritis, advanced-stage follicular lymphoma, and low-tumour-burden follicular lymphoma. Almost 5 years after its initial regulatory approval, significant real-world experience has accumulated with CT-P10 use, particularly in diffuse large B-cell lymphoma, one of the indications approved by extrapolation. This article summarises the pivotal data underlying regulatory approval for the four licensed rituximab biosimilars, before focusing on real-world data gathered with CT-P10. These data provide further support for the safety and effectiveness of CT-P10 and should boost healthcare professional and patient confidence in its use. Pharmacoeconomic analyses support the potential healthcare system cost savings offered by rituximab biosimilar uptake, which could lead to improved patient access to biologic treatments. Opportunities arising from biosimilar uptake extend further, potentially enabling innovative investigator-led research and therapeutic advances. [ABSTRACT FROM AUTHOR]

Biosimilar regulatory evaluation considers the totality of evidence gathered through analytical, non-clinical and clinical studies. CT-P17 is the first high-concentration (100 mg/mL), citrate-free adalimumab biosimilar to receive regulatory approval in Europe for all indications held by reference adalimumab, following comprehensive non-clinical and clinical development programmes. State-of-the art physicochemical and biological methods demonstrated quality, analytical and functional comparability between CT-P17 and reference adalimumab; non-clinical in vivo studies supported biosimilarity. Three phase I and two phase III studies were conducted, with pharmacokinetic equivalence of CT-P17 and reference adalimumab shown in healthy volunteers, and equivalent efficacy demonstrated in patients with rheumatoid arthritis. Safety and immunogenicity profiles were comparable between CT-P17 and reference adalimumab across studies. CT-P17 is available for administration by autoinjector/prefilled pen (AI/PFP), prefilled syringe (PFS) and PFS with needle guard, providing diverse self-injection options for patients. Equivalent pharmacokinetics and comparable overall safety and usability were demonstrated between AI/PFP and PFS devices during the clinical development programme. All CT-P17 devices include fine, 29-gauge needles; combined with the citrate-free, high-concentration formulation, these characteristics reflect the newer reference adalimumab formulation (100 mg/mL) and are associated with reduced injection-site pain. The high-concentration formulation also facilitates treatment delivery via fewer injections. Compared with reference adalimumab, CT-P17 remains stable for longer at room temperature, enhancing ease of storage for patients and healthcare providers. In summary, the totality of evidence supports the biosimilarity of CT-P17 to high-concentration reference adalimumab, and several distinctive features differentiate it from existing adalimumab biosimilars. [ABSTRACT FROM AUTHOR]

The objective of this study was to develop an accessible and accurate analysis method for microplastics that have been unintentionally added to cream cosmetic products. An experiment was performed on three cleansing creams in rich and viscous formulations. A spiked sample was prepared by adding polyethylene (PE) microspheres to the cleansing creams. After removing cosmetic ingredients from the creams using chemical digestion, damage to the PE microspheres was identified using Fourier transform infrared (FT-IR) spectroscopy. Field emission scanning electron microscopy (FE-SEM) images were obtained before and after digestion and used to characterize the morphology of the PE microspheres. The highest digestion efficiency was obtained using a chemical digestion method consisting of heating and stirring a sample in a 10 wt% KOH solution at 55 °C and 300 rpm for 5 days and did not damage the PE microspheres. The Nile red (9-diethylamino-5H-benzo[α]phenoxazine-5-one) staining method was effective in identifying small microplastics (< 106 μm). The optimal staining conditions are 5 μg/ml Nile red in n-hexane for green wavelengths. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea. Identification of transposable element (TE) insertions from whole genome sequencing data remains challenging. Here the authors developed a comprehensive TE insertion detection algorithm xTea that can be applied to both short-read and long-read sequencing data. [ABSTRACT FROM AUTHOR]

Background: Rituximab is a biologic medicine widely used for the treatment of autoimmune diseases and lymphoma. Several biosimilars of rituximab have been developed and marketed with the expiration of the originator rituximab's patent; thus, systematic combination and analysis of the latest data on the efficacy and safety of biosimilars and the demonstration of the interchangeability of biosimilar agents are required. Objective: The objective of this study was to collate available data from head-to-head randomized controlled trials (RCTs) and evaluate the efficacy and safety of biosimilar rituximab compared with the reference drug in patients with rheumatoid arthritis (RA) and non-Hodgkin's lymphoma (NHL). Methods: The PubMed, EMBASE, Cochrane Library, and Google Scholar databases were searched to identify head-to-head RCTs that directly compare the efficacy and safety of biosimilar rituximab and its originator. The efficacy outcome for RA was the American College of Rheumatology (ACR) response rates and the outcome for NHL was the response rate. The occurrence of adverse events (AEs) and anti-drug antibodies (ADAs) were evaluated for the safety outcome. Data on the pharmacokinetic profile were also included as a secondary outcome. Results: Eleven head-to-head RCTs with 3163 patients were included (1744 patients with RA and 1419 patients with NHL). Biosimilars of rituximab showed similar efficacy in the clinical response in both RA and NHL. The pooled risk ratio (RR) of the ACR 20% response rate (ACR20) response in patients with RA at weeks 24 and 48 was 0.99 (p = 0.70, 95% confidence interval [CI] 0.92–1.06) and 1.04 (p = 0.73, 95% CI 0.83–1.31), respectively. The pooled RR of the overall response at week 24 in NHL patients was 1.02 (p = 0.31, 95% CI 0.98–1.07). No significant differences were found in the formation of ADAs (RR 0.86, p = 0.20, 95% CI 0.68–1.08) or AEs (RR 1.04, p = 0.30, 95% CI 0.97–1.12). Conclusion: This systematic review and conventional meta-analysis demonstrated the overall similarity of the long-term efficacy and safety of biosimilar rituximab to those of originator rituximab in RA and NHL patients by combining direct evidence from head-to-head trials. PROSPERO registration No. CRD42019125138. [ABSTRACT FROM AUTHOR]

Correction to: I Nature Communications i https://doi.org/10.1038/s41467-022-29697-4, published online 02 May 2022 The original version of this Article omitted from the author list the 6th author, Luisa Mercado, who is from the Department of Biomedical Informatics, Harvard Medical School. This author was already included in the Author Contributions as L.M. and therefore no further corrections to this statement were made. [Extracted from the article]

The equivalence of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) remains controversial. Here we use genetically matched hESC and hiPSC lines to assess the contribution of cellular origin (hESC vs. hiPSC), the Sendai virus (SeV) reprogramming method and genetic background to transcriptional and DNA methylation patterns while controlling for cell line clonality and sex. We find that transcriptional and epigenetic variation originating from genetic background dominates over variation due to cellular origin or SeV infection. Moreover, the 49 differentially expressed genes we detect between genetically matched hESCs and hiPSCs neither predict functional outcome nor distinguish an independently derived, larger set of unmatched hESC and hiPSC lines. We conclude that hESCs and hiPSCs are molecularly and functionally equivalent and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional and epigenetic comparisons of pluripotent cell lines, explaining some of the previously observed differences between genetically unmatched hESCs and hiPSCs. [ABSTRACT FROM AUTHOR]

The article reports on efforts by seven scientific laboratories to replicate the findings of a study of stimulus-triggered acquisition of pluripotency (STAP) cells, which was published in “Nature” in 2014 and later retracted. The article reports that the STAP stem-cell line discussed in the 2014 article was contaminated by embryonic stem (ES) cells. The authors call for validation of the properties and the origin of pluripotent stem cells using different scientific methods in future STAP research.

Stem cells self-renew and generate specialized progeny through differentiation, but vary in the range of cells and tissues they generate, a property called developmental potency. Pluripotent stem cells produce all cells of an organism, while multipotent or unipotent stem cells regenerate only specific lineages or tissues. Defining stem-cell potency relies upon functional assays and diagnostic transcriptional, epigenetic and metabolic states. Here we describe functional and molecular hallmarks of pluripotent stem cells, propose a checklist for their evaluation, and illustrate how forensic genomics can validate their provenance. [ABSTRACT FROM AUTHOR]

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function. [ABSTRACT FROM AUTHOR]

The influence of motor activity on sensory processing is crucial for perception and motor execution. However, the underlying circuits are not known. To unravel the circuit by which activity in the primary vibrissal motor cortex (vM1) modulates sensory processing in the primary somatosensory barrel cortex (S1), we used optogenetics to examine the long-range inputs from vM1 to the various neuronal elements in S1. We found that S1-projecting vM1 pyramidal neurons strongly recruited vasointestinal peptide (VIP)-expressing GABAergic interneurons, a subset of serotonin receptor-expressing interneurons. These VIP interneurons preferentially inhibited somatostatin-expressing interneurons, neurons that target the distal dendrites of pyramidal cells. Consistent with this vM1-mediated disinhibitory circuit, the activity of VIP interneurons in vivo increased and that of somatostatin interneurons decreased during whisking. These changes in firing rates during whisking depended on vM1 activity. Our results suggest previously unknown circuitry by which inputs from motor cortex influence sensory processing in sensory cortex. [ABSTRACT FROM AUTHOR]

Anticancer drug resistance is a major challenge of cancer therapy. We found that irinotecan-resistant NSCLC cells showed increased mitochondrial oxidative phosphorylation compared to the drug sensitive NSCLC cells. Previously, we found that combined inhibition of aldehyde dehydrogenase using gossypol, and mitochondrial complex I using phenformin, effectively reduced oxidative phosphorylation in NSCLC. Here, we showed that targeting oxidative phosphorylation with gossypol and phenformin abrogated irinotecan resistance in NSCLC. Furthermore, irinotecan treatment by blocking oxidative phosphorylation induced synergistic anti-cancer effect in NSCLC. The pre-clinical xenograft model of human NSCLC also demonstrated a therapeutic response to the dual targeting treatment. Therefore, this combination of gossypol and phenformin increases irinotecan sensitivity as well as preventing irinotecan resistance. [ABSTRACT FROM AUTHOR]

A key question within systems neuroscience is to understand how the brain encodes spatially and temporally distributed local features and binds these together into one perceptual representation. Previous works in animal and human have shown that changes in neural synchrony occur during the perceptual processing and these changes are distinguished by the emergence of gamma-band oscillations (GBO, 30-80 Hz, centered at 40 Hz). Here, we used the mouse electroencephalogram to investigate how different cortical areas play roles in perceptual processing by assessing their GBO patterns during the visual presentation of coherently/incoherently moving random-dot kinematogram and static dots display. Our results revealed that GBO in the visual cortex were strongly modulated by the moving dots regardless of the existence of a global dot coherence, whereas GBO in frontal cortex were modulated by coherence of the motion. Moreover, concurrent GBO across the multiple cortical area occur more frequently for coherently moving dots. Taken together, these findings of GBO in the mouse frontal and visual cortex are related to the perceptual binding of local features into a globally-coherent representation, suggesting the dynamic interplay across the local/distributed networks of GBO in the global processing of optic flow. [ABSTRACT FROM AUTHOR]

Bacteria use chemical signals to sense each other and to regulate various physiological functions. Although it is known that some airborne volatile organic compounds function as bacterial signalling molecules, their identities and effects on global gene expression and bacterial physiological processes remain largely unknown. Here we perform microarray analyses of Escherichia coli exposed to volatile organic compounds emitted from Bacillus subtilis. We find that 2,3-butanedione and glyoxylic acid mediate global changes in gene expression related to motility and antibiotic resistance. Volatile organic compound-dependent phenotypes are conserved among bacteria and are regulated by the previously uncharacterized ypdB gene product through the downstream transcription factors soxS, rpoS or yjhU. These results strongly suggest that bacteria use airborne volatile organic compounds to sense other bacteria and to change master regulatory gene activity to adapt. [ABSTRACT FROM AUTHOR]