Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking freely available human leukocyte antigen typing algorithms across varying genes, coverages and typing resolutions

The human leukocyte antigen (HLA) system is a group of genes coding for proteins that are central to the adaptive immune system and identifying the specific HLA allele combination of a patient is relevant in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation-sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower coverage was evaluated by subsampling and HLA typing 230 WES samples at coverages ranging from 1X to 100X. The typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions, which specifically focus on the peptide binding region. On average, across the five HLA genes, HLA*LA was found to have the highest typing accuracy. For the individual genes, HLA-A, -B and -C, Optitype’s typing accuracy was highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools’ robustness to lower coverage data varied widely and further depended on the specific HLA locus. For all class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the protein) at 50X, but increasing the depth of coverage beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA genes as well as HLA*LA’s typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which often is based on lower quality sequencing data. Interestingly, we found that Optitype’s typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the depth of coverage is sufficiently high.
Rhythmic Information Sampling in the Brain during Visual Recognition

When we fixate an object, visual information is continuously received on the retina. Several studies observed behavioral oscillations in perceptual sensitivity across such stimulus time, and these fluctuations have been linked to brain oscillations. However, whether specific brain areas show oscillations across stimulus time (i.e., different time points of the stimulus being more or less processed, in a rhythmic fashion) has not been investigated. Here, we revealed random areas of face images at random moments across time and recorded the brain activity of male and female human participants using MEG while they performed two recognition tasks. This allowed us to quantify how each snapshot of visual information coming from the stimulus is processed across time and across the brain. Oscillations across stimulus time (rhythmic sampling) were mostly visible in early visual areas, at theta, alpha, and low beta frequencies. We also found that they contributed to brain activity more than previously investigated rhythmic processing (oscillations in the processing of a single snapshot of visual information). Nonrhythmic sampling was also visible at later latencies across the visual cortex, either in the form of a transient processing of early stimulus time points or of a sustained processing of the whole stimulus. Our results suggest that successive cycles of ongoing brain oscillations process stimulus information incoming at successive moments. Together, these results advance our understanding of the oscillatory neural dynamics associated with visual processing and show the importance of considering the temporal dimension of stimuli when studying visual recognition. SIGNIFICANCE STATEMENT Several behavioral studies have observed oscillations in perceptual sensitivity over the duration of stimulus presentation, and these fluctuations have been linked to brain oscillations. However, oscillations across stimulus time in the brain have not been studied. Here, we developed an MEG paradigm to quantify how visual information received at each moment during fixation is processed through time and across the brain. We showed that different snapshots of a stimulus are distinctly processed in many brain areas and that these fluctuations are oscillatory in early visual areas. Oscillations across stimulus time were more prevalent than previously studied oscillations across processing time. These results increase our understanding of how neural oscillations interact with the visual processing of temporal stimuli.
Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryo-EM structure of a PP2A-B56 holoenzyme-PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multi-partite contacts at structured cores to activate the methylesterase. B56-interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56-interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.
Reconstructing the genetic history of Kra-Dai speakers from Thailand

Genetic history of the Thai people and, more generally, speakers of the Kra-Dai languages (also known as Tai-Kadai languages) in Thailand remains a topic of debate. Recently, Kutanan et al.1 analyzed genome-wide genetic data for dozens of present-day human populations from Thailand and surrounding countries and concluded that the Central Thai, Southern Thai, and Malay from Southern Thailand are genetically continuous with Austroasiatic speakers such as Mon, and thus the advent of Kra-Dai and Austronesian languages to Central and Southern Thailand was overwhelmingly a result of cultural rather than genetic diffusion. We re-analyzed the genetic data reported by Kutanan et al.1 using an advanced technique for inferring admixture graph models, using autosomal haplotypes, and other methods. We did not reproduce the results by Kutanan et al.1, and our analyses revealed a more complex picture of the genetic history of Kra-Dai speakers and other populations of Thailand.
Context-dependent transcriptional remodeling of TADs during differentiation

Metazoan chromosomes are organized into discrete domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between TAD organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow TAD dynamics during development, we used Capture Hi-C to interrogate the TADs around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and sub-domains were formed around some activated genes without changes in CTCF binding. The ectopic induction of one gene was sufficient to recapitulate microdomain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex, but non-universal, chromosome folding patterns that can be important in certain genomic contexts.
CovidOutcome2: a tool for SARS-CoV2 mutation identification and for disease severity prediction

Our goal was to develop a platform, CovidOutcome2, capable of predicting disease severity from viral mutation profiles using automated machine learning (autoML) and deep neural networks applied to the available large corpus of sequenced SARS-CoV2 genomes. CovidOutcome2 accepts either user-submitted genomes or user defined mutation combinations as the input. The output is a predicted severity score plus a list of identified, annotated mutations and their functional effects in VCF format. The best model performance is a ROC-AUC 0.899 for the model including patient age and ROC-AUC 0.83 for the model without patient age. Availability CovidOutcome is freely available online under the URL https://www.covidoutcome. bio-ml.com as well as in a standalone version https://github.com/bio-apps/covid-outcome.
A DARPin-based molecular toolset to probe gephyrin and inhibitory synapse biology

Neuroscience currently requires the use of antibodies to study synaptic proteins, where antibody binding is used as a correlate to define the presence, plasticity, and regulation of synapses. Gephyrin is an inhibitory synaptic scaffolding protein used to mark GABAergic and glycinergic postsynaptic sites. Despite the importance of gephyrin in modulating inhibitory transmission, its study is currently limited by the tractability of available reagents. Designed Ankyrin Repeat Proteins (DARPins) are a class of synthetic protein binder derived from diverse libraries by in vitro selection, and tested by high-throughput screening to produce specific binders. In order to generate a functionally diverse toolset for studying inhibitory synapses, we screened a DARPin library against gephyrin mutants representing both phosphorylated and dephosphorylated states. We validated the robust use of anti-gephyrin DARPin clones for morphological identification of gephyrin clusters in rodent neuron culture and brain tissue, discovering previously overlooked clusters. This DARPin-based toolset includes clones with heterogenous gephyrin binding modes that allowed for identification of the most extensive gephyrin interactome to date, and defined novel classes of putative interactors, creating a framework for understanding gephyrin’s non-synaptic functions. This study demonstrates anti-gephyrin DARPins as a versatile platform for studying inhibitory synapses in an unprecedented manner.
Invasive Streptococcal Infection Can Lead to the Generation of Cross-Strain Opsonic Antibodies

The bacterium Streptococcus pyogenes is a common cause of both mild and severe human diseases resulting in substantial morbidity and mortality each year. No vaccines are available, and our understanding of the antibody response to this human pathogen is still incomplete. ABSTRACT The human pathogen Streptococcus pyogenes causes substantial morbidity and mortality. It is unclear if antibodies developed after infections with this pathogen are opsonic and if they are strain specific or more broadly protective. Here, we quantified the opsonic-antibody response following invasive S. pyogenes infection. Four patients with S. pyogenes bacteremia between 2018 and 2020 at Skåne University Hospital in Lund, Sweden, were prospectively enrolled. Acute- and convalescent-phase sera were obtained, and the S. pyogenes isolates were genome sequenced (emm118, emm85, and two emm1 isolates). Quantitative antibody binding and phagocytosis assays were used to evaluate isolate-dependent opsonic antibody function in response to infection. Antibody binding increased modestly against the infecting isolate and across emm types in convalescent- compared to acute-phase sera for all patients. For two patients, phagocytosis increased in convalescent-phase serum both for the infecting isolate and across types. The increase was only across types for one patient, and one had no improvement. No correlation to the clinical outcomes was observed. Invasive S. pyogenes infections result in a modestly increased antibody binding with differential opsonic capacity, both nonfunctional binding and broadly opsonic binding across types. These findings question the dogma that an invasive infection should lead to a strong type-specific antibody increase rather than a more modest but broadly reactive response, as seen in these patients. Furthermore, our results indicate that an increase in antibody titers might not be indicative of an opsonic response and highlight the importance of evaluating antibody function in S. pyogenes infections. IMPORTANCE The bacterium Streptococcus pyogenes is a common cause of both mild and severe human diseases resulting in substantial morbidity and mortality each year. No vaccines are available, and our understanding of the antibody response to this human pathogen is still incomplete. Here, we carefully analyzed the opsonic antibody response following invasive infection in four patients. Unexpectedly, the patients did not always generate opsonic antibodies against the specific infecting strain. Instead, we found that some patients could generate cross-opsonic antibodies, leading to phagocytosis of bacteria across strains. The emergence of cross-opsonic antibodies is likely important for long-term immunity against S. pyogenes. Our findings question the dogma that mostly strain-specific immunity is developed after infection and add to our overall understanding of how immunity to S. pyogenes can evolve.
Sclerostin influences exercise-induced adaptations in body composition and white adipose tissue morphology in male mice

Sclerostin is an inhibitor of the osteogenic Wnt/β-catenin signalling pathway that has an endocrine role in regulating adipocyte differentiation and metabolism. Additionally, subcutaneous white adipose tissue (scWAT) sclerostin content decreases following exercise training (EXT). Therefore, we hypothesized that EXT-induced reductions in adipose tissue sclerostin may play a role in regulating adaptations in body composition and whole-body metabolism. To test this hypothesis, 10-week-old male C57BL/6J mice were either sedentary (SED) or performing 1h of treadmill running at ∼65-70% VO2max 5 d/week (EXT) for 4 weeks and had subcutaneous (s.c) injections of either saline (C) or recombinant sclerostin (S) (0.1 mg/kg body mass) 5 d/week; thus, making 4 groups (SED-C, EXT-C, SED-S, and EXT-S; n=12/group). No differences in body mass were observed between experimental groups, while food intake was higher in EXT (p=0.03) and S (p=0.08) groups. There was a higher resting energy expenditure in all groups compared to SED-C. EXT-C had a higher lean mass and lower fat mass percentage compared to SED-C and SED-S. No differences in body composition were observed in either the SED-S or EXT-S groups. Lower scWAT (inguinal), vWAT (epididymal) mass, and scWAT adipocyte cell size and increased percentage of multilocular cells in scWAT were observed in the EXT-C group compared to SED-C, while lower vWAT was only observed in the EXT-S group. EXT mice had increased iWAT Lrp4 and mitochondrial content and sclerostin treatment only inhibited increased Lrp4 content with EXT. Together, these results provide evidence that reductions in resting sclerostin with exercise training may influence associated alterations in energy metabolism and body composition, particularly in scWAT.
Functional analysis of recurrent non-coding variants in human melanoma

Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused in on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in a human A375 melanoma cell line and observed decreased expression of CDC20, changes in migration capabilities, and an altered transcriptional state previously associated with neural crest transcriptional programs and melanoma initiation. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
Non-invasive quantification of contractile dynamics in cardiac cells, spheroids and organs-on-a-chip using high frequency ultrasound

Cell-based models that mimic in vivo heart physiology are poised to make significant advances in cardiac disease modeling and drug discovery. In these systems, cardiomyocyte (CM) contractility is an important functional metric, but current measurement methods are inaccurate, low-throughput, or require complex set-ups. To address this need, we developed a standalone non-invasive, label-free ultrasound technique operating at 40-200 MHz to measure the beat rate, beat rhythm, and force of contraction of cardiac models, ranging from single adult CMs to 3D microtissue constructs in standard cell culture formats. The high temporal resolution of 1000 fps resolved the beat profile of single mouse CMs paced at up to 9 Hz, revealing limitations of lower speed optical based measurements to resolve beat kinetics or characterize aberrant beats. Coupling of ultrasound with traction force microscopy enabled the measurement of CM longitudinal modulus and facile estimation of adult mouse CM contractile forces of 2.34 ± 1.40 μN, comparable to more complex measurement techniques. Similarly, measurements of beat rate, rhythm, and drug responses of CM spheroid and microtissue models were demonstrated. In conclusion, ultrasound can be used for the rapid characterization of CM contractile function in a wide range of commonly-studied configurations ranging from single cells to 3D tissue constructs using standard well plates, with applications in cardiac drug discovery and cardiotoxicity evaluation.
Genome-wide identification and characterization of the HSP gene superfamily in apple snails (Gastropoda: Ampullariidae) and expression analysis under temperature stress

Heat shock proteins (HSPs) play important roles in the response to various stresses as molecular chaperones. Apple snails from the family Ampullariidae have become economically important due to several species mainly from the genus Pomacea were invasive. The recent release of the genomes of ampullariids (P. canaliculata, P. maculata, Lanistes nyassanus, and Marisa cornuarietis) has opened the opportunity for a comprehensive analysis of the HSP superfamily. We identified that the number of HSP from P. canaliculata (PcaHSPs) was greater than that from the other three species. A total of 42 PcaHSPs were distributed on 12 chromosomes and were classified into the families of HSP90, HSP70, HSP60, HSP40, HSP20, and HSP10. Each family formed a monophyletic clade on the phylogenetic trees, except for the HSP40 family. We identified tandem duplication of paralogous genes in PcaHSP70 and PcaHSP20. The RNA-seq data show that the expression profiles of PcaHSPs in different tissues have similar patterns, except that several PcaHSP20 genes revealed tissue-specific expression levels. Moreover, we identified that there were more HSP genes with stronger induction levels in response to hot than cold stress. Our findings will be helpful for future studies on stress response and adaptation focusing on HSPs in apple snails.
Decisive Roles of Sequence Distributions in the Generalizability of de novo Deep Learning Models for RNA Secondary Structure Prediction

The availability of sizeable RNA structure databases and powerful deep learning (DL) frameworks has prompted recent developments of DL models for RNA secondary structure prediction. Taking RNA sequences as the only inputs, the class of de novo DL models has demonstrated far superior performances than traditional algorithms. However, key questions remain over the statistical underpinning of such DL models which make no use of co-evolutionary information or physical laws of RNA folding. Here we present a quantitative study of the capacity and generalizability of a series of de novo DL models, with a minimal two-module architecture and no post-processing, under varied sequence distributions of seen and unseen datasets. Excellent performances are observed from our models with as few as 16K parameters, affirming their remarkable learning capacity. Our DL models show to generalize well over non-identical unseen sequences, but the model generalizability degrades rapidly as the sequence distributions between the seen and unseen become dissimilar. Examinations of RNA family-specific behaviors manifest not only disparate family-dependent model performances but substantial generalization gaps within the same RNA family. We further determine how model generalization decreases with the decrease of sequence similarity via pairwise sequence alignment, providing quantitative insights into the limitations of statistical learning. Model generalizability thus poses major hurdles for practical uses of current single-sequence-based DL models and we discuss avenues for future advances of such de novo DL models for RNA secondary structure prediction.
Polyunsaturated fatty acids alter the formation of lipid droplets and eicosanoid production in Leishmania promatigotes

Leishmania parasites contain lipid droplets (LD, or lipid bodies) and the molecular machinery responsible for synthesizing prostaglandins (PGs) and other bioactive lipids. We studied the effects of polyunsaturated fatty acids (PUFA) on LD biogenesis and eicosanoid production in distinct Leishmania species associated with different clinical forms of leishmaniasis. We also compared structural models of human-like cyclooxygenase-2 (GP63) and prostaglandin F synthase (PGFS) proteins of Leishmania, and we evaluated their enzymatic production in logarithmic and stationary growth phases of procyclic L. amazonensis, L. braziliensis and L. infantum. PUFAs modulate the formation of LDs in L. braziliensis and L. infantum. Leishmania species with equivalent clinical manifestations and tissue tropism had same protein mutations in GP63 and PGFS. No differences in GP63 production were observed among L. amazonensis, L. braziliensis and L. infantum, however increased PGFS production was detected during the parasite differentiation. Stimulation with arachidonic acid resulted in highly elevated production of hydroxyeicosatetraenoic acids compared to prostaglandins quantified by LC-MS/MS. The present findings open new perspectives on the role of eicosanoid metabolism in Leishmania and could contribute to the development of novel antiparasitic drugs.