bluuebunny/crossref_metadata_2025 huggingface dataset:
ctDNA detection by personalised assays in early-stage NSCLC
Authors: Heider Katrin , Wan Jonathan C. M. , Gale Davina , Ruiz-Valdepenas Andrea , Mouliere Florent , Morris James , Qureshi Nagmi R. , Qian Wendi , Knock Helena , Wulff Jerome , Howarth Karen , Green Emma , Castedo Jenny , Rundell Viona , Cooper Wendy N. , Eisen Tim , Smith Christopher G. , Massie Charles , Gilligan David , Harden Susan V. , Rassl Doris M. , Rintoul Robert C. , Rosenfeld Nitzan
Published: June 2021

Blood-based assays have shown increasing ability to detect circulating tumour DNA (ctDNA) in patients with early-stage cancer. However, detection of ctDNA in patients with non-small cell lung cancer (NSCLC) has continued to prove challenging. We performed retrospective analysis to quantify ctDNA levels in a cohort of 100 patients with early-stage NSCLC prior to treatment with curative intent enrolled in the LUCID study (NCT04153526). Where tumour tissue was available for whole exome sequencing, mutations identified were used to define patient-specific sequencing assays. For those 90 patients, plasma cell-free DNA was sequenced to high depth across capture panels targeting a median of 328 mutations specific to each patient. Data was analysed using Integration of Variant Reads (INVAR), detecting ctDNA in 66.7% of patients, including 52.7% (29 of 55) patients with stage I disease and >88% detection for patients with stage II and III disease (16/18 and 15/17). ctDNA was detected in plasma at fractional concentrations as low as 9.1×10−6, and in patients with tumour volumes as low as 0.23 cm3. A 36-gene sequencing panel (InVisionFirst-Lung™) was used to analyse plasma DNA in 27 samples including the 10 cases without tumour exome data, and detected ctDNA in 59% of samples tested (16 of 27). Across the entire cohort, detection rates were higher in squamous cell carcinoma patients compared to adenocarcinoma patients (81% vs. 59%). Detection of ctDNA prior to treatment was associated with significantly shorter time free from relapse, across all patients and in patient subgroups, with Hazard Ratios >11 for selected patient subsets. Our analysis indicates that for patients with stage I NSCLC, the median ctDNA fraction in plasma is approx. 12 parts per million (0.0012%). This indicates the limits of detection that would be required for ctDNA-based liquid biopsies to detect ctDNA in the majority of patients with early-stage NSCLC.
Causal and Candidate Gene Variants in a Large Cohort of Women with Primary Ovarian Insufficiency
Authors: Gorsi B , Hernandez EJ , Moore B , Moriwaki M , Chow CY , Coelho E , Taylor E , Lu C , Walker A , Touraine P , Nelson LM , Cooper AR , Mardis ER , Rajkovic A , Yandell M , Welt CK
Published: June 2021

A genetic etiology accounts for unexplained primary ovarian insufficiency (POI; amenorrhea with an elevated FSH level). Subjects with POI (n=291) and controls recruited for health in old age or 1000 Genomes (n=233) underwent whole exome or whole genome sequencing. Data were analyzed using a rare variant scoring method and a Bayes factor-based framework for identifying genes harboring pathogenic variants. Candidate heterozygous variants were identified in known genes and genes with functional evidence. Gene sets with increased burden of deleterious alleles included the categories transcription and translation, DNA damage and repair, meiosis and cell division. Variants were found in novel genes from the enhanced categories. Functional evidence supported 7 new risk genes for POI (USP36, VCP, WDR33, PIWIL3, NPM2, LLGL1 and BOD1L1). Aggregating clinical data and genetic risk with a categorical approach may expand the genetic architecture of heterozygous rare gene variants causing risk for POI.
Relation of vaccination with severity, oxygen requirement and outcome of COVID-19 infection in Chattogram, Bangladesh
Authors: Das Shuva , Tumpa Nadia Islam , Khan Ayesha Ahmed , Hoque Md. Minhazul , Hoque Md. Ehsanul , Safatujjahan  , Ahmed Kazi Farhad , Biswas Rajat Sanker Roy
Published: June 2021

Introduction

Peoples all around the world are waiting for vaccination against COVID -19 infection. In Bangladesh, Astra-Zeneca (AZ) vaccine was provided, but patients had infections of SARS-COV-2 even after vaccination. We focused on observing the severity, oxygen requirement and outcome of the COVID-19 infected patients who took the first dose or completed the immunization regimen.

Methods

This is an observational study done among 174 COVID-19 patients from three COVID-19 dedicated hospitals of Chattogram, Bangladesh, who took AZ vaccines 1st dose or completed the schedule. All patients were Real-Time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) positive for COVID-19. Patients were enrolled after receiving written informed consent. Suspected cases or unwilling patients were excluded from the study. Ethical approval was granted by the CMOSH–ERB. SPSS-20 was used to analyze the information gathered.

Results

Among 174 vaccinated patients, 55(31.61%) completed the vaccination schedule, and 119(68.39%) took their 1st dose of the COVID-19 vaccine. Gender distributions revealed 67(38.5%) female and 107(61.5%) male got the vaccine, and 55 patients completed the full two doses, and 119 patients took the 1st dose. Most of the patients were 40 years and above. In the completed vaccination group, 33(60.0%) out of 55 in and in the first dose vaccinated group, 75(63.0%) out of 119 had a mild COVID-19, and severe and critical cases were found very minimum. Among the patients who have completed the vaccination, 32(58.2%) needed no oxygen, and who was given the first dose, 78(65%) needed no oxygen. No death occurred who completed the vaccine, and 3(2.5%) patients died who took 1st dose of the vaccine.

Conclusion

Vaccine provided in Bangladesh to the people so far seems safe and effective. Severe and critical COVID-19 is low, and the need for oxygen to admitted patients is less, and the death rate is minimal.
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection
Authors: Karim F , Moosa MYS , Gosnell BI , Cele S , Giandhari J , Pillay S , Tegally H , Wilkinson E , San JE , Msomi N , Mlisana K , Khan K , Bernstein M , Manickchund N , Singh L , Ramphal U ,   COMMIT-KZN Team, Hanekom W , Lessells RJ , Sigal A , de Oliveira T
Published: June 2021

While most people effectively clear SARS-CoV-2, there are several reports of prolonged infection in immunosuppressed individuals. Here we present a case of prolonged infection of greater than 6 months with shedding of high titter SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. Through whole genome sequencing at multiple time-points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern. This provides support to the hypothesis of intra-host evolution as one mechanism for the emergence of SARS-CoV-2 variants with immune evasion properties.
Comparative Household Secondary Attack Rates associated with B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants
Authors: Brown Kevin A. , Tibebu Semra , Daneman Nick , Schwartz Kevin , Whelan Michael , Buchan Sarah
Published: June 2021

Background

The emergence of SARS-CoV-2 variants associated with increased transmissibility are driving a 3rd global surge in COVID-19 incidence. There are currently few reliable estimates for the P.1 and B.1.351 lineages. We sought to compare the secondary attack rates of SARS-COV-2 mutations and variants in Canada’s largest province of Ontario, using a previously validated household-based approach.

Methods

We identified individuals with confirmed SARS-CoV-2 infection in Ontario’s provincial reportable disease surveillance system. Cases were grouped into households based on reported residential address. Index cases had the earliest of symptom onset in the household. Household secondary attack rate was defined as the percentage of household contacts identified as secondary cases within 1-14 days after the index case.

Results

We identified 26,888 index household cases during the study period. Among these, 7,555 (28%) were wild-type, 17,058 (63%) were B.1.1.7, 1674 (6%) were B.1.351 or P.1, and 601 (2%) were non-VOC mutants (Table 1). The secondary attack rates, according to index case variant were as follows: 20.2% (wild-type), 25.1% (B.1.1.7), 27.2% (B.1.351 or P.1), and 23.3% (non-VOC mutants). In adjusted analyses, we found that B.1.1.7, B.1.351, and P.1 index cases had the highest transmissibility (presumptive B.1.1.7 ORadjusted=1.49, 95%CI 1.36, 1.64; presumptive B.1.351 or P.1 ORadjusted=1.60, 95%CI 1.37, 1.87).

Discussion

Substantially higher transmissibility associated with variants will make control of SARS-CoV-2 more difficult, reinforcing the urgent need to increase vaccination rates globally.
The timing of differentiation and potency of CD8 effector function is set by RNA binding proteins
Authors: Petkau Georg , Mitchell Twm J. , Chakraborty Krishnendu , Bell Sarah E. , D’Angeli Vanessa , Matheson Louise , Turner David J. , Saveliev Alexander , Gizlenci Ozge , Salerno Fiamma , Katsikis Peter D. , Turner Martin
Published: June 2021

CD8+ T cell differentiation into effector cells is initiated early after antigen encounter by signals from the T cell antigen receptor and costimulatory molecules. The molecular mechanisms that determine the timing and rate of differentiation however are not defined. Here we show that the RNA binding proteins (RBP) ZFP36 and ZFP36L1 limit the rate of differentiation of activated naïve CD8+ T cells and the potency of the resulting cytotoxic lymphocytes. The RBP act in an early and short temporal window to enforce dependency on costimulation via CD28 for full T cell activation and effector differentiation by directly binding mRNA of NF-ĸB, IRF8 and NOTCH1 transcription factors and cytokines, including IL2. Their absence in T cells, or the adoptive transfer of a small numbers of CD8+ T cells lacking the RBP, promotes resilience to influenza A virus infection without immunopathology. These findings highlight ZFP36 and ZFP36L1 as nodes for the integration of the early T cell activation signals determining the speed and quality of the CD8 response.
A representative reference for MRI-based human axon radius assessment using light microscopy
Authors: Mordhorst Laurin , Morozova Maria , Papazoglou Sebastian , Fricke Björn , Oeschger Jan Malte , Tabarin Thibault , Rusch Henriette , Jäger Carsten , Geyer Stefan , Weiskopf Nikolaus , Morawski Markus , Mohammadi Siawoosh
Published: June 2021

Non-invasive assessment of axon radii via MRI bears great potential for clinical and neuroscience research as it is a main determinant of the neuronal conduction velocity. However, there is a lack of representative histological reference data on the scale of the cross-section of MRI voxels for validating the MRI-visible, effective radius (reff). Because the current gold standard stems from neuroanatomical studies designed to estimate the frequency-weighted arithmetic mean radius (rarith) on small ensembles of axons, it is unsuited to estimate the tail-weighted reff. We propose CNN-based segmentation on high-resolution, large-scale light microscopy (lsLM) data to generate a representative reference for reff. In a human corpus callosum, we assessed estimation accuracy and bias of rarith and reff. Furthermore, we investigated whether mapping anatomy-related variation of rarith and reff is confounded by low-frequency variation of the image intensity, e.g., due to staining heterogeneity. Finally, we analyzed the potential error due to outstandingly large axons in reff. Compared to rarith, reff was estimated with higher accuracy (normalized-root-mean-square-error of reff: 7.2 %; rarith: 21.5 %) and lower bias (normalized-mean-bias-error of reff: −1.7 %; rarith: 16 %). While rarith was confounded by variation of the image intensity, variation of reff seemed anatomy-related. The largest axons contributed between 0.9 % and 3 % to reff. In conclusion, the proposed method accurately estimates reff at MRI voxel resolution across a human corpus callosum sample. Further investigations are required to assess generalization to brain areas with different axon radii ensembles.
Indexable signal amplification for multiparametric imaging
Authors: Simonson Paul D. , Valencia Itzel , Patel Sanjay S.
Published: June 2021

Multiparametric imaging allows researchers to measure the expression of many biomarkers simultaneously, allowing detailed characterization of cell microenvironments. One such technique, CODEX, allows fluorescence imaging of >30 proteins in a single tissue section. In the commercial CODEX system, primary antibodies are conjugated to DNA barcodes. This modification can result in antibody dysfunction, and development of a custom antibody panel can be very costly and time consuming as trial and error of modified antibodies proceeds. To address these challenges, we developed novel tyramide-conjugated DNA barcodes that can be used with primary antibodies via peroxidase-conjugated secondary antibodies. This approach results in signal amplification and imaging without the need to conjugate primary antibodies. When combined with commercially available barcode-conjugated primary antibodies, we can very quickly develop working antibody panels. We also present methods to perform antibody staining using a commercially available automated tissue stainer and in situ hybridization imaging on a CODEX platform.
Opportunity or catastrophe? Effect of sea salt on host-parasite survival and reproduction
Authors: Yu Ao , Vannatta J. Trevor , Gutierrez Stephanie O. , Minchella Dennis J.
Published: June 2021

Seawater intrusion caused by anthropogenic climate change may affect freshwater species and their parasites. While brackish water certainly impacts freshwater systems globally, its impact on disease transmission is largely unknown. This study examined the effect of artificial seawater on host-parasite interactions using a freshwater snail host, Biomphalaria alexandrina, and the human trematode parasite Schistosoma mansoni. Four components were analyzed to evaluate the impact of increasing salinity on disease transmission: snail survival, snail reproduction, infection prevalence, and the survival of the parasite infective stage (cercariae). We found a decrease in snail survival, snail egg mass production, and snail infection prevalence as salinity increases. However, cercarial survival peaked at an intermediate salinity value. Our results suggest that seawater intrusion into freshwaters has the potential to decrease schistosome transmission to humans.

Author Summary

Climate change will have numerous impacts on many systems, including host-parasite systems. One mechanism by which climate change with impact host-parasite interactions is by rising sea levels flooding coastal regions, increasing salinity in many freshwaters. Host-parasite interactions are a key component of freshwater ecosystems, but the effects of sea water intrusion on host-parasite dynamics are largely unknown. In this study, we quantify the effects of sea salt concentration on the model host-parasite system, Biomphalaria alexandrina and Schistosoma mansoni. We demonstrate a significant, negative relationship between sea salt concentration and host-parasite survival and reproduction. The increase in freshwater salinity associated with sea level rise has the potential to decrease parasite transmission and disease burden in humans and wildlife.

Abstract Figure
PHARP: A pig haplotype reference panel for genotype imputation
Authors: Wang Zhen , Zhang Zhenyang , Chen Zitao , Sun Jiabao , Cao Caiyun , Wu Fen , Xu Zhong , Zhao Wei , Sun Hao , Guo Longyu , Zhang Zhe , Wang Qishan , Pan Yuchun
Published: June 2021

Pigs not only function as a major meat source worldwide but also are commonly used as an animal model for studying human complex traits. A large haplotype reference panel has been used to facilitate efficient phasing and imputation of relatively sparse genome-wide microarray chips and low-coverage sequencing data. Using the imputed genotypes in the downstream analysis, such as GWASs, TWASs, eQTL mapping and genomic prediction (GS), is beneficial for obtaining novel findings. However, currently, there is still a lack of publicly available and high-quality pig reference panels with large sample sizes and high diversity, which greatly limits the application of genotype imputation in pigs. In response, we built the pig Haplotype Reference Panel (PHARP) database. PHARP provides a reference panel of 2,012 pig haplotypes at 34 million SNPs constructed using whole-genome sequence data from more than 49 studies of 71 pig breeds. It also provides Web-based analytical tools that allow researchers to carry out phasing and imputation consistently and efficiently. PHARP is freely accessible at http://alphaindex.zju.edu.cn/PHARP/index.php. We demonstrate its applicability for pig commercial 50K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~ 17× sequencing coverage). We also applied our reference panel to impute the low-density SNP chip into the high-density data for three GWASs and found novel significantly associated SNPs that might be casual variants.
Investigating the concept of accessibility for predicting novel RNA-RNA interactions
Authors: Reißer Sabine , Meyer Irmtraud M
Published: June 2021

State-of-the-art methods for predicting novel trans RNA-RNA interactions use the so-called accessibility as key concept. It estimates whether a region in a given RNA sequence is accessible for forming trans interactions, using a thermodynamic model which quantifies its secondary structure features. RNA-RNA interactions are then predicted by finding the minimum free energy base-pairing between the two transcripts, taking into account the accessibility as energy penalty.

We investigated the underlying assumptions of this approach using the two methods RNAplex and IntaRNA on two datasets, containing sRNA-mRNA and snoRNA-rRNA interactions, respectively.

We find that (1) known trans RNA-RNA interactions frequently overlap regions containing RNA structure features, (2) the estimated accessibility reflects sRNA structures fairly well, but often disagrees with structure annotations of longer transcripts, (3) the prediction performance of RNA-RNA interaction prediction methods is independent of the quality of the estimated accessibility profiles, and (4) one important overall effect of accessibility profiles is to prevent the thermodynamic model from predicting too long interactions.

Based on our findings, we conclude that the accessibility concept to the minimum free energy approach to predicting novel RNA-RNA interactions has conceptual limitations and discuss potential ways of improving the field in the future.
A large chromosomal inversion shapes gene expression in seaweed flies (Coelopa frigida)
Authors: Berdan Emma L. , Mérot Claire , Pavia Henrik , Johannesson Kerstin , Wellenreuther Maren , Butlin Roger K.
Published: June 2021

Inversions often underlie complex adaptive traits, but the genic targets inside them are largely unknown. Gene expression profiling provides a powerful way to link inversions with their phenotypic consequences. We examined the effects of the Cf-Inv(1) inversion in the seaweed fly Coelopa frigida on gene expression variation across sexes and life stages. Our analyses revealed that Cf-Inv(1) shapes global expression patterns but the extent of this effect is variable with much stronger effects in adults than larvae. Furthermore, within adults, both common as well as sex specific patterns were found. The vast majority of these differentially expressed genes mapped to Cf-Inv(1). However, genes that were differentially expressed in a single context (i.e. in males, females or larvae) were more likely to be located outside of Cf-Inv(1). By combining our findings with genomic scans for environmentally associated SNPs, we were able to pinpoint candidate variants in the inversion that may underlie mechanistic pathways that determine phenotypes. Together the results in this study, combined with previous findings, support the notion that the polymorphic Cf-Inv(1) inversion in this species is a major factor shaping both coding and regulatory variation resulting in highly complex adaptive effects.
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner
Authors: Hamelin David J. , Fournelle Dominique , Grenier Jean-Christophe , Schockaert Jana , Kovalchik Kevin , Kubiniok Peter , Mostefai Fatima , Duquette Jérôme D. , Saab Frederic , Sirois Isabelle , Smith Martin A. , Pattijn Sofie , Soudeyns Hugo , Decaluwe Hélène , Hussin Julie , Caron Etienne
Published: June 2021

The rapid, global dispersion of SARS-CoV-2 since its initial identification in December 2019 has led to the emergence of a diverse range of variants. The initial concerns regarding the virus were quickly compounded with concerns relating to the impact of its mutated forms on viral infectivity, pathogenicity and immunogenicity. To address the latter, we seek to understand how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic, before mass vaccination. We analyzed a total of 330,246 high quality SARS-CoV-2 genome assemblies sampled across 143 countries and all major continents. Strikingly, we found that specific mutational patterns in SARS-CoV-2 diversify T cell epitopes in an HLA supertype-dependent manner. In fact, we observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family. In addition, we show that this predicted global loss of epitopes is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7 supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic. Together, our study lays the foundation to help understand how SARS-CoV-2 mutants shape the repertoire of T cell targets and T cell immunity across human populations. The proposed theoretical framework has implications in viral evolution, disease severity, vaccine resistance and herd immunity.
Lack of p62 impairs glycogen aggregation and exacerbates pathology in a mouse model of myoclonic epilepsy of Lafora
Authors: Pellegrini Pasquale , Hervera Arnau , Varea Olga , Brewer M. Kathryn , López-Soldado Iliana , Guitart Anna , Aguilera Mònica , Prat Neus , del Río José Antonio , Guinovart Joan J. , Duran Jordi
Published: June 2021

Background

Lafora disease (LD) is a fatal childhood-onset dementia characterized by the extensive accumulation of glycogen aggregates—the so-called Lafora Bodies (LBs)—in several organs. The accumulation of LBs in the brain underlies the neurological phenotype of the disease. LBs are composed of abnormal glycogen and various associated proteins, including p62, an autophagy adaptor that participates in the aggregation and clearance of misfolded proteins.

Methods

To study the role of p62 in the formation of LBs and its participation in the pathology of LD, we generated a mouse model of the disease (malinKO) lacking p62.

Results

Deletion of p62 prevented LB accumulation in skeletal muscle and cardiac tissue. In the brain, the absence of p62 altered LB morphology and increased susceptibility to epilepsy.

Conclusions

These results demonstrate that p62 participates in the formation of LBs and suggest that the sequestration of abnormal glycogen into LBs is a protective mechanism through which to reduce the deleterious consequences of its accumulation in the brain.
ProFuMCell and ProModb: web services for analyzing interaction-based functionally localized protein modules in a cell
Authors: Das Barnali , Mitra Pralay
Published: June 2021

The modular organization of a cell which can be determined by its interaction network allows us to understand a mesh of cooperation among the functional modules. Therefore, cellular level identification of functional modules aids in understanding the functional and structural characteristics of the biological network of a cell and also assists in determining or comprehending the evolutionary signal. We develop ProFuM-Cell that performs real-time web scraping for generating clusters of the cellular level functional units of an organism. ProFuMCell constructs the Protein Locality Graphs and clusters the cellular level functional units of an organism by utilizing experimentally verified data from various online sources. Also, we develop ProModb, a database service that houses precomputed whole-cell protein-protein interaction network-based functional modules of an organism using ProFuMCell. Our web service is entirely synchronized with the KEGG pathway database and allows users to generate spatially localized protein modules for any organism belonging to the KEGG genome using its real-time web scraping characteristics. Hence, the server will host as many organisms as is maintained by the KEGG database. Our web services provide the users a comprehensive and integrated tool for an efficient browsing and extraction of the spatial locality-based protein locality graph and the functional modules constructed by gathering experimental data from several interaction databases and pathway maps. We believe that our web services will be beneficial in pharmacological research, where a novel research domain called modular pharmacology has initiated the study on the diagnosis, prevention, and treatment of deadly diseases using functional modules.

Graphical TOC Entry
Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation
Authors: Elorbany Reem , Popp Joshua M , Rhodes Katherine , Strober Benjamin J , Barr Kenneth , Qi Guanghao , Gilad Yoav , Battle Alexis
Published: June 2021

Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.
Deciphering biological evolution exploiting the topology of Protein Locality Graph
Authors: Das Barnali , Mitra Pralay
Published: June 2021

The conventional sequence comparison-based evolutionary studies ignore other evolutionary constraints like interaction among proteins, functions of proteins and genes etc. A lot of speculations exist in literature regarding the presence of species divergence at the level of the Protein Interaction Networks. Additionally, it has been conjectured that the intra-module connections stay conserved whereas the inter-module connections change during evolution. The most important components of the biological networks are the functional modules which are more conserved among the evolutionary closer species. Here, we demonstrate an alternative method to decipher biological evolution by exploiting the topology of a spatially localized Protein Interaction Network called Protein Locality Graph (PLG). Our lossless graph compression from PLG to a power graph called Protein Cluster Interaction Network (PCIN) results in a 90% size reduction and aids in improving computational time. Further, we exploit the topology of PCIN and demonstrate our capability of deriving the correct species tree by focusing on the cross-talk between the protein modules exclusively. Our results provide new evidence that traces of evolution are not only present at the level of the Protein-Protein Interactions, but are also very much present at the level of the inter-module interactions.
CNS antigen-specific control of early B-lineage development in the meninges
Authors: Wang Yan , Chen Dianyu , Xu Di , Huang Chao , He Danyang , Xu Heping
Published: June 2021

The random V(D)J recombination of immunoglobulins (Ig) loci often creates autoreactive B cell progenitors expressing self-recognized B-cell receptors (BCRs)1, which are eliminated or inactivated through an autoantigen-dependent central tolerance checkpoint to prevent autoimmune reactions2,3, a process thought to be restricted to the bone marrow (BM) in the adult mammals4. Here we report that early developing B cells are also present in the meninges of mice at all ages. Single cell RNA-sequencing (scRNA-seq) analysis revealed a consecutive trajectory of meningeal developing B cells in mice and non-human primates (NHPs). Parabiosis together with lineage tracing of hematopoietic stem cells (HSCs) showed that meningeal developing B cells are continuously replenished from the HSC-derived progenitors via a circulationindependent route. Importantly, autoreactive immature B cells which recognize myelin oligodendrocyte glycoprotein (MOG)5, a central nervous system (CNS)-specific antigen, are eliminated from the meninges but not BM. Furthermore, genetic deletion of MOG restored the self-reactive B cells in the meninges. Thus, we propose that meninges function as a unique reservoir for B cell development, allowing in situ negative selection of CNS-antigen-autoreactive B cells to ensure a local non-self-reactive immune repertoire.
The impact of mutational processes on structural genomic plasticity in cancer cells
Authors: Funnell Tyler , O’Flanagan Ciara H , Williams Marc J , McPherson Andrew , McKinney Steven , Kabeer Farhia , Lee Hakwoo , Masud Tehmina , Eirew Peter , Yap Damian , Zhang Allen W , Lim Jamie L P , Wang Beixi , Brimhall Jazmine , Biele Justina , Ting Jerome , Liu Yi Fei , Beatty Sean , Lai Daniel , Pham Jenifer , Grewal Diljot , Abrams Douglas , Havasov Eliyahu , Leung Samantha , Bojilova Viktoria , Moore Richard A , Rusk Nicole , Uhlitz Florian , Ceglia Nicholas , Weiner Adam C , Douglas J Maxwell , Zamarin Dmitriy , Weigelt Britta , Kim Sarah H , Da Cruz Paula Arnaud , Reis-Filho Jorge S. , Li Yangguang , Xu Hong , de Algara Teresa Ruiz , Lee So Ra , Llanos Viviana Cerda ,   IMAXT consortium, Shah Sohrab P. , Aparicio Samuel
Published: June 2021

Structural genome alterations are determinants of cancer ontogeny and therapeutic response. While bulk genome sequencing has enabled delineation of structural variation (SV) mutational processes which generate patterns of DNA damage, we have little understanding of how these processes lead to cell-to-cell variations which underlie selection and rates of accrual of different genomic lesions. We analysed 309 high grade serous ovarian and triple negative breast cancer genomes to determine their mutational processes, selecting 22 from which we sequenced >22,000 single cell whole genomes across a spectrum of mutational processes. We show that distinct patterns of cell-to-cell variation in aneuploidy, copy number alteration (CNA) and segment length occur in homologous recombination deficiency (HRD) and fold-back inversion (FBI) phenotypes. Widespread aneuploidy through induction of HRD throughBRCA1andBRCA2inactivation was mirrored by continuous whole genome duplication in HRD tumours, contrasted with early ploidy fixation in FBI. FBI tumours exhibited copy number distributions skewed towards gains, widespread clone-specific variation in amplitude of high-level amplifications, often impacting oncogenes, and break-point variability consistent with progressive genomic diversification, which we termed serriform structural variation (SSV). SSVs were consistent with a CNA-based molecular clock reflecting a continual and distributed process across clones within tumours. These observations reveal previously obscured genome plasticity and evolutionary properties with implications for cancer evolution, therapeutic targeting and response.
Efficacy of heat-killed and formalin-killed vaccines againstTilapia tilapinevirusin juvenile Nile tilapia (Oreochromis niloticus)
Authors: Mai Thao Thu , Kayansamruaj Pattanapon , Taengphu Suwimon , Senapin Saengchan , Costa Janina Z. , del-Pozo Jorge , Thompson Kim D. , Rodkhum Channarong , Dong Ha Thanh
Published: June 2021

Tilapia tilapinevirus(also known as tilapia lake virus, TiLV) is considered to be a new threat to the global tilapia industry. The objective of this study was to develop simple cell culture-based heat-killed (HKV) and formalin-killed (FKV) vaccines for the prevention of disease caused by TiLV. The fish were immunized with 100 µL of either HKV or FKV by intraperitoneal injection with each vaccine containing 1.8 × 106TCID50inactivated virus. A booster vaccination was carried out at 21-day post vaccination (dpv) using the same protocol. The fish were then challenged with a lethal dose of TiLV at 28 dpv. The expression of five immune genes (IgM, IgD, IgT, CD4andCD8) in the head kidney and spleen of experimental fish was assessed at 14 and 21 dpv and again after the booster vaccination at 28 dpv. TiLV-specific IgM responses were measured by ELISA at the same time points. The results showed that both vaccines conferred significant protection, with relative percentage survival (RPS) of 71.3% and 79.6% for HKV and FKV, respectively. Significant up-regulation ofIgMandIgTwas observed in the head kidney of fish vaccinated with HKV at 21 dpv, whileIgM, IgDandCD4expression increased in the head kidney of fish receiving FKV at the same time point. After booster vaccination,IgTand CD8transcripts were significantly increased in the spleen of fish vaccinated with the HKV, but not with FKV. Both vaccines induced a specific IgM response in both serum and mucus. In summary, this study showed that both HKV and FKV are promising injectable vaccines for the prevention of disease caused by TiLV in Nile tilapia.
TRPC3 and NALCN channels drive pacemaking in substantia nigra dopaminergic neurons
Authors: Um Ki Bum , Hahn Suyun , Kim So Woon , Lee Yoon Je , Birnbaumer Lutz , Kim Hyun Jin , Park Myoung Kyu
Published: June 2021

Midbrain dopamine (DA) neurons are slow pacemakers that maintain extracellular DA levels. During the interspike intervals, subthreshold slow depolarization underlies autonomous pacemaking and determines its rate. However, the ion channels that determine slow depolarization are unknown. Here we show that TRPC3 and NALCN channels together form sustained inward currents responsible for the slow depolarization of nigral DA neurons. Specific TRPC3 channel blockade completely blocked DA neuron pacemaking, but the pacemaking activity in TRPC3 knock-out (KO) mice was perfectly normal, suggesting the presence of compensating ion channels. Blocking NALCN channels abolished pacemaking in both TRPC3 KO and wild-type mice. The NALCN current and mRNA and protein expression are increased in TRPC3 KO mice, indicating that NALCN compensates for TRPC3 currents. In normal conditions, TRPC3 and NALCN contribute equally to slow depolarization. Therefore, we conclude that TRPC3 and NALCN are two major leak channels that drive robust pacemaking in nigral DA neurons.
Immunological profiling of COVID-19 patients with pulmonary sequelae
Authors: Wu Jianghua , Tang Lu , Ma Yanling , Li Yu , Zhang Dongmei , Li Qian , Mei Heng , Hu Yu
Published: June 2021

Cellular immunity may be involved in organ damage and rehabilitation in patients with coronavirus disease 2019 (COVID-19). We aimed to delineate immunological features of COVID-19 patients with pulmonary sequelae (PS) one year after discharge. 50 COVID-19 survivors were recruited and classified according to radiological characteristics: 24 patients with PS and 26 patients without PS. Phenotypic and functional characteristics of immune cells were evaluated by multiparametric flow cytometry. Patients with PS had an increased proportion of natural killer (NK) cells and lower percentage of B cells compared to patients without PS. Phenotypic and functional features of T cells in patients with PS were predominated by the accumulation of CD4+ T cells secreting IL-17A, short-lived effector-like CD8+ T cells (CD27-CD62L-) and senescent T cells with excessive secretion of granzyme-B/perforin/IFN-γ. NK cells were characterized by the excessive secretion of granzyme-B and perforin and the downregulation of NKP30 and NKP46; highly activated NKT and γδ T cells exhibited NKP30 and TIM-3 upregulation and NKB1 downregulation in patients with PS. However, immunosuppressive cells were comparable between the two groups. The interrelation of immune cells in COVID-19 was intrinsically identified, whereby T cells secreting IL-2, IL-4 and IL-17A were enriched among CD28+ and CD57-cells and cells secreting perforin/granzyme-B/IFN-γ/TNF-α expressed markers of terminal differentiation. CD57+NK cells, CD4+perforin+ T cells and CD8+CD27+CD62L+ T cells were identified as the independent predictors for residual lesions. Overall, our findings unveil the profound imbalance of immune landscape that may correlate with organ damage and rehabilitation in COVID-19.

IMPORTANCE

A considerable proportion of COVID-19 survivors have residual lung lesions, such as ground glass opacity and fiber streak shadow. To determine the relationship between host immunity and residual lung lesions, we performed an extensive analysis of immune responses in convalescent patients with COVID-19 one year after discharge. We found significant differences in immunological characteristics between patients with pulmonary sequelae and patients without pulmonary sequelae one year after discharge. Our study highlights the profound imbalance of immune landscape in the COVID-19 patients with pulmonary sequelae, characterized by the robust activation of cytotoxic T cells, NK cells and γδ T cells as well as the deficiencies of immunosuppressive cells. Importantly, CD57+NK cells, CD4+perforin+ T cells and CD8+CD27+CD62L+ T cells were identified as the independent predictors for residual lesions.
Structural mapping of GABRB3 variants reveals genotype-phenotype correlations
Authors: Johannesen Katrine M , Iqbal Sumaiya , Guazzi Milena , Mohammadi Nazanin A , Pérez-Palma Eduardo , Schaefer Elise , De Saint Martin Anne , Abiwarde Marie Therese , McTague Amy , Pons Roser , Piton Amelie , Kurian Manju A , Ambegaonkar Gautam , Firth Helen , Sanchis-Juan Alba , Deprez Marie , Jansen Katrien , De Waele Liesbeth , Briltra Eva H , Verbeek Nienke E , van Kempen Marjan , Fazeli Walid , Striano Pasquale , Zara Federico , Visser Gerhard , Braakman Hilde M H , Haeusler Martin , Elbracht Miriam , Sternman David , Vaher Ulvi , Smol Thomas , Lemke Johannes R , Platzer Konrad , Kennedy Joanna , Klein Karl Martin , Billie Au Ping Yee , Smyth Kimberly , Kaplan Julie , Thomas Morgan , Dewenter Malin K , Dinopoulos Argirios , Campbell Arthur J , Lal Dennis , Lederer Damien , Liao Vivian W Y , Ahring Philip K , Møller Rikke S. , Gardella Elena
Published: June 2021

Purpose

Pathogenic variants in GABRB3 have been associated with a spectrum of phenotypes from severe developmental disorders and epileptic encephalopathies to milder epilepsy syndromes and mild intellectual disability. In the present study, we analyzed a large cohort of individuals with GABRB3 variants to deepen the phenotypic understanding and investigate genotype-phenotype correlations.

Methods

Through an international collaboration, we analyzed electro-clinical data of unpublished individuals with variants in GABRB3 and we reviewed previously published cases. All missense variants were mapped onto the 3D structure of the GABRB3 subunit and clinical phenotypes associated with the different key structural domains were investigated.

Results

We characterize 71 individuals with GABRB3 variants, including 22 novel subjects, expressing a wide spectrum of phenotypes. Interestingly, phenotypes correlated with structural locations of the variants. Generalized epilepsy, with a median age at onset of 10.5 months, and mild-to-moderate intellectual disability were associated with variants in the extracellular domain. Focal epilepsy with early onset (median: 2.75 months of age) and severe intellectual disability were associated with variants in the pore-lining helical transmembrane domain.

Conclusion

These genotype/phenotype correlations will aid the genetic counseling and treatment of individuals affected by GABRB3-related disorders. Future studies may reveal whether functional differences underlie the phenotypic differences.

Key points

Pathogenic variants in GABRB3 cause a wide range of phenotypes

Missense variants in the ECD have generalized epilepsy with later onset and non-severe ID

Missense variants in the TMD have focal epilepsy with early onset and severe ID

Behavioral issues are common features of GABRB3 disease

Precision medicine approaches for GABRB3 disease is limited
A studyforrest extension, MEG recordings while watching the audio-visual movie “Forrest Gump”
Authors: Liu Xingyu , Dai Yuxuan , Xie Hailun , Zhen Zonglei
Published: June 2021

Naturalistic stimuli, such as movies, are being increasingly used to map brain function because of their high ecological validity. The pioneering studyforrest and other naturalistic neuroimaging projects have provided free access to multiple movie-watching functional magnetic resonance imaging (fMRI) datasets to prompt the community for naturalistic experimental paradigms. However, sluggish blood-oxygenation-level-dependent fMRI signals are incapable of resolving neuronal activity with the temporal resolution at which it unfolds. Instead, magnetoencephalography (MEG) measures changes in the magnetic field produced by neuronal activity and is able to capture rich dynamics of the brain at the millisecond level while watching naturalistic movies. Herein, we present the first public prolonged MEG dataset collected from 11 participants while watching the 2 h long audio-visual movie “Forrest Gump”. Minimally preprocessed data was also provided to facilitate the use of the dataset. As a studyforrest extension, we envision that this dataset, together with fMRI data from the studyforrest project, will serve as a foundation for exploring the neural dynamics of various cognitive functions in real-world contexts.
Evolution of genome fragility enables microbial division of labor
Authors: Colizzi E.S. , van Dijk B. , Merks R.M.H. , Rozen D.E. , Vroomans R.M.A.
Published: June 2021

Division of labor can evolve when social groups benefit from the functional specialization of its members. Recently, a novel means of coordinating division of labor was found in the antibiotic-producing bacterium Streptomyces coelicolor, where functionally specialized cells are generated through large-scale genomic re-organization. Here, we investigate how the evolution of a genome architecture enables such mutation-driven division of labor, using a multi-scale mathematical model of bacterial evolution. We let bacteria compete on the basis of their antibiotic production and growth rate in a spatially structured environment. Bacterial behavior is determined by the structure and composition of their genome, which encodes antibiotics, growth-promoting genes and fragile genomic loci that can induce chromosomal deletions. We find that a genomic organization evolves that partitions growth-promoting genes and antibiotic-coding genes to distinct parts of the genome, separated by fragile genomic loci. Mutations caused by these fragile sites mostly delete growth-promoting genes, generating antibiotic-producing mutants from non-producing (and weakly-producing) progenitors, in agreement with experimental observations. Mutants protect their colony from competitors but are themselves unable to replicate. We further show that this division of labor enhances the local competition between colonies by promoting antibiotic diversity. These results show that genomic organization can co-evolve with genomic instabilities to enable reproductive division of labor.

Motivation of current work

Division of labor can evolve if trade-offs are present between different traits. To organize a division of labor, the genome architecture must evolve to enable differentiated cellular phenotypes. Cell differentiation may be coordinated through gene regulation, as occurs during embryonic development. Alternatively, when mutation rates are high, mutations themselves can guide cell and functional differentiation; however, how this evolves and is organized at the genome level remains unclear. Here, using a model of antibiotic-producing bacteria based on multicellular Streptomyces, we show that if antibiotic production trades off with replication, genome architecture can evolve to support a mutation-driven division of labor. These results are consistent with recent experimental observations and may underlie division of labor in many bacterial groups.
The genetic diversity of honeybee colonies predicts the gut bacterial diversity of individual colony members
Authors: Bridson C , Vellaniparambil L , Antwis R E , Müller W , Gilman R T , Rowntree J K
Published: June 2021

The gut microbiota of social bees is relatively simple and dominated by a core set of taxa that have been reported consistently in individual workers from around the world. Yet, variation remains, and this has been shown to affect host health.

We characterised the individual- and regional-scale variation in the honeybee (Apis mellifera) gut microbiota in the North West of England, and asked whether the microbiota was influenced by host genotype or landscape composition.

We collected multiple honeybees from 64 colonies, and sequenced the V4 region of the 16S rRNA gene to characterise the mid- and hindgut bacterial communities. We characterised the genotype of each individual honeybee, and also the land cover surrounding each colony.

The literature-defined core taxa consistently dominated across the region, despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained a large proportion of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There was a trend for colonies in more similar landscapes to have more similar microbiota, whilst bees from more urban landscapes had a slightly less diverse microbiota than those from less urban landscapes.

Our study provides, to our knowledge, the first demonstration for any species that the gut bacterial communities of individuals can be influenced by the genotypes of other conspecifics in the population. This is particularly important for social organisms, such as honeybees, as colony rather than individual genetic diversity appears to drive gut microbial diversity, a factor related to colony health.