Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis.

The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.

The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.

The Swedish Childhood Tumor Biobank (BTB) is a nonprofit national infrastructure for collecting tissue samples and genomic data from pediatric patients diagnosed with central nervous system (CNS) and other solid tumors. The BTB is built on a multidisciplinary network established to provide the scientific community with standardized biospecimens and genomic data, thereby improving knowledge of the biology, treatment and outcome of childhood tumors. As of 2022, over 1100 fresh-frozen tumor samples are available for researchers. We present the workflow of the BTB from sample collection and processing to the generation of genomic data and services offered. To determine the research and clinical utility of the data, we performed bioinformatics analyses on next-generation sequencing (NGS) data obtained from a subset of 82 brain tumors and patient blood-derived DNA combined with methylation profiling to enhance the diagnostic accuracy and identified germline and somatic alterations with potential biological or clinical significance. The BTB procedures for collection, processing, sequencing, and bioinformatics deliver high-quality data. We observed that the findings could impact patient management by confirming or clarifying the diagnosis in 79 of the 82 tumors and detecting known or likely driver mutations in 68 of 79 patients. In addition to revealing known mutations in a broad spectrum of genes implicated in pediatric cancer, we discovered numerous alterations that may represent novel driver events and specific tumor entities. In summary, these examples reveal the power of NGS to identify a wide number of actionable gene alterations. Making the power of NGS available in healthcare is a challenging task requiring the integration of the work of clinical specialists and cancer biologists; this approach requires a dedicated infrastructure, as exemplified here by the BTB.

Rapid evolution of the primate larynx?

Tissue vibrations in the larynx produce most sounds that comprise vocal communication in mammals. Larynx morphology is thus predicted to be a key target for selection, particularly in species with highly developed vocal communication systems. Here, we present a novel database of digitally modeled scanned larynges from 55 different mammalian species, representing a wide range of body sizes in the primate and carnivoran orders. Using phylogenetic comparative methods, we demonstrate that the primate larynx has evolved more rapidly than the carnivoran larynx, resulting in a pattern of larger size and increased deviation from expected allometry with body size. These results imply fundamental differences between primates and carnivorans in the balance of selective forces that constrain larynx size and highlight an evolutionary flexibility in primates that may help explain why we have developed complex and diverse uses of the vocal organ for communication.

Vocal tract allometry in a mammalian vocal learner.

Acoustic allometry occurs when features of animal vocalisations can be predicted from body size measurements. Despite this being considered the norm, allometry sometimes breaks, resulting in species sounding smaller or larger than expected for their size. A recent hypothesis suggests that allometry-breaking mammals cluster into two groups: those with anatomical adaptations to their vocal tracts and those capable of learning new sounds (vocal learners). Here, we tested which mechanism is used to escape from acoustic allometry by probing vocal tract allometry in a proven mammalian vocal learner, the harbour seal (Phoca vitulina). We tested whether vocal tract structures and body size scale allometrically in 68 young individuals. We found that both body length and body mass accurately predict vocal tract length and one tracheal dimension. Independently, body length predicts vocal fold length while body mass predicts a second tracheal dimension. All vocal tract measures are larger in weaners than in pups and some structures are sexually dimorphic within age classes. We conclude that harbour seals do comply with anatomical allometric constraints. However, allometry between body size and vocal fold length seems to emerge after puppyhood, suggesting that ontogeny may modulate the anatomy-learning distinction previously hypothesised as clear cut. We suggest that seals, and perhaps other species producing signals that deviate from those expected from their vocal tract dimensions, may break allometry without morphological adaptations. In seals, and potentially other vocal learning mammals, advanced neural control over vocal organs may be the main mechanism for breaking acoustic allometry.

Developing an Artificial Intelligence (A.I)-based descriptor of facial appearance that fits with the assessments of makeup experts.

OBJECTIVE: To develop an A.I-based automatic descriptor that detects and grades, from selfie pictures, 23 facial signs, hairs included, as a help to making-up procedures. MATERIAL AND METHODS: The selfie images taken in very different conditions by 3326 women and men were used to create (90% of dataset) and validate (10% of dataset) a new algorithm architecture to appraise and grade 23 different facial signs such as lips, nose, eye color, eyebrows, eyelashes, and hair color as defined by makeup artists. Each selfie image was annotated by 12 experts and defined references to train Artificial Intelligence (A.I)-based algorithm. RESULTS: As some the 23 signs present a continuous or discontinuous feature, these were analyzed by two different statistical approaches. The results provided by the automatic descriptor system were not only in good agreement with the expert's assessments but were even found of a better precision and reproducibility. This automatic descriptor system has proven a good and robust accuracy despite the very variable conditions in the acquisition of selfie pictures. CONCLUSION: Such automatic descriptor system seems providing a valuable help in making-up procedures and may extend to other activities such as Skincare or Haircare. As such it should allow large investigations to better evaluate the consumers' needs of esthetical improvements.

Acoustic allometry and vocal learning in mammals.

Acoustic allometry is the study of how animal vocalizations reflect their body size. A key aim of this research is to identify outliers to acoustic allometry principles and pinpoint the evolutionary origins of such outliers. A parallel strand of research investigates species capable of vocal learning, the experience-driven ability to produce novel vocal signals through imitation or modification of existing vocalizations. Modification of vocalizations is a common feature found when studying both acoustic allometry and vocal learning. Yet, these two fields have only been investigated separately to date. Here, we review and connect acoustic allometry and vocal learning across mammalian clades, combining perspectives from bioacoustics, anatomy and evolutionary biology. Based on this, we hypothesize that, as a precursor to vocal learning, some species might have evolved the capacity for volitional vocal modulation via sexual selection for 'dishonest' signalling. We provide preliminary support for our hypothesis by showing significant associations between allometric deviation and vocal learning in a dataset of 164 mammals. Our work offers a testable framework for future empirical research linking allometric principles with the evolution of vocal learning.

Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes.

Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.

Japanese macaque phonatory physiology.

Although the call repertoire and its communicative function are relatively well explored in Japanese macaques (Macaca fuscata), little empirical data are available on the physics and the physiology of this species' vocal production mechanism. Here, a 6 year old female Japanese macaque was trained to phonate under an operant conditioning paradigm. The resulting 'coo' calls and spontaneously uttered 'growl' and 'chirp' calls were recorded with sound pressure level (SPL) calibrated microphones and electroglottography (EGG), a non-invasive method for assessing the dynamics of phonation. A total of 448 calls were recorded, complemented by ex vivo recordings on an excised Japanese macaque larynx. In this novel multidimensional investigative paradigm, in vivo and ex vivo data were matched via comparable EGG waveforms. Subsequent analysis suggests that the vocal range (range of fundamental frequency and SPL) of the macaque was comparable to that of a 7-10 year old human, with the exception of low intensity chirps, the production of which may be facilitated by the species' vocal membranes. In coo calls, redundant control of fundamental frequency in relation to SPL was also comparable to that in humans. EGG data revealed that growls, coos and chirps were produced by distinct laryngeal vibratory mechanisms. EGG further suggested changes in the degree of vocal fold adduction in vivo, resulting in spectral variation within the emitted coo calls, ranging from 'breathy' (including aerodynamic noise components) to 'non-breathy'. This is again analogous to humans, corroborating the notion that phonation in humans and non-human primates is based on universal physical and physiological principles.

Honest signaling in domestic piglets (Sus scrofa domesticus): vocal allometry and the information content of grunt calls.

The information conveyed in acoustic signals is a central topic in mammal vocal communication research. Body size is one form of information that can be encoded in calls. Acoustic allometry aims to identify the specific acoustic correlates of body size within the vocalizations of a given species, and formants are often a useful acoustic cue in this context. We conducted a longitudinal investigation of acoustic allometry in domestic piglets (Sus scrofa domesticus), asking whether formants of grunt vocalizations provide information concerning the caller's body size over time. On four occasions, we recorded grunts from 20 kunekune piglets, measured their vocal tract length by means of radiographs (X-rays) and weighed them. Controlling for effects of age and sex, we found that body weight strongly predicts vocal tract length, which in turn determines formant frequencies. We conclude that grunt formant frequencies could allow domestic pigs to assess a signaler's body size as it grows. Further research using playback experiments is needed to determine the perceptual role of formants in domestic pig communication.

Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins.

Pancreatic ductal adenocarcinoma (PDAC) is a very aggressive malignancy characterized by an excessive resistance to all known anticancer therapies, a still largely elusive phenomenon. To identify original mechanisms, we have explored the role of post-translational modifications (PTMs) mediated by members of the ubiquitin family. Although alterations of these pathways have been reported in different cancers, no methodical search for these kinds of anomalies has been performed so far. Therefore, we studied the ubiquitin-, Nedd8-, and SUMO1-specific proteomes of a pancreatic cancer cell line (MiaPaCa-2) and identified changes induced by gemcitabine, the standard PDAC's chemotherapeutic drug. These PTMs profiles contained both known major substrates of all three modifiers as well as original ones. Gemcitabine treatment altered the PTM profile of proteins involved in various biological functions, some known cancer associated genes, many potentially cancer-associated genes, and several cancer-signaling networks, including canonical and noncanonical WNT and PI3K/Akt/MTOR pathways. Some of these altered PTMs formed groups of functionally and physically associated proteins. Importantly, we could validate the gemcitabine-induced PTMs variations of relevant candidates and we could demonstrate the biological significance of such altered PTMs by studying in detail the sumoylation of SNIP1, one of these new targets.

Response of red deer stags (Cervus elaphus) to playback of harsh versus common roars.

Red deer stags (Cervus elaphus) give two distinct types of roars during the breeding season, the "common roar" and the "harsh roar." Harsh roars are more frequent during contexts of intense competition, and characterized by a set of features that increase their perceptual salience, suggesting that they signal heightened arousal. While common roars have been shown to encode size information and mediate both male competition and female choice, to our knowledge, the specific function of harsh roars during male competition has not yet been studied. Here, we investigate the hypothesis that the specific structure of male harsh roars signals high arousal to competitors. We contrast the behavioral responses of free ranging, harem-holding stags to the playback of harsh roars from an unfamiliar competitor with their response to the playback of common roars from the same animal. We show that males react less strongly to sequences of harsh roars than to sequences of common roars, possibly because they are reluctant to escalate conflicts with highly motivated and threatening unfamiliar males in the absence of visual information. While future work should investigate the response of stags to harsh roars from familiar opponents, our observations remain consistent with the hypothesis that harsh roars may signal motivation during male competition, and illustrate how intrasexual selection can contribute to the diversification of male vocal signals.

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery.

DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.

Interactome-transcriptome integration for predicting distant metastasis in breast cancer.

MOTIVATION: High-throughput gene expression profiling yields genomic signatures that allow the prediction of clinical conditions including patient outcome. However, these signatures have limitations, such as dependency on the training set, and worse, lack of generalization. RESULTS: We propose a novel algorithm called ITI (interactome-transcriptome integration), to extract a genomic signature predicting distant metastasis in breast cancer by superimposition of large-scale protein-protein interaction data over a compendium of several gene expression datasets. Training on two different compendia showed that the estrogen receptor-specific signatures obtained are more stable (11-35% stability), can be generalized on independent data and performs better than previously published methods (53-74% accuracy). AVAILABILITY: The ITI algorithm source code from analysis are available under CeCILL from the ITI companion website: http://bioinformatique.marseille.inserm.fr/iti. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Domestic cat larynges can produce purring frequencies without neural input.

Most mammals produce vocal sounds according to the myoelastic-aerodynamic (MEAD) principle, through self-sustaining oscillation of laryngeal tissues.1,2 In contrast, cats have long been believed to produce their low-frequency purr vocalizations through a radically different mechanism involving active muscle contractions (AMC), where neurally driven electromyographic burst patterns (typically at 20-30 Hz) cause the intrinsic laryngeal muscles to actively modulate the respiratory airflow. Direct empirical evidence for this AMC mechanism is sparse.3 Here, the fundamental frequency (fo) ranges of eight domestic cats (Felis silvestris catus) were investigated in an excised larynx setup, to test the prediction of the AMC hypothesis that vibration should be impossible without neuromuscular activity, and thus unattainable in excised larynx setups, which are based on MEAD principles. Surprisingly, all eight excised larynges produced self-sustained oscillations at typical cat purring rates. Histological analysis of cat larynges revealed the presence of connective tissue masses, up to 4 mm in diameter, embedded in the vocal fold.4 This vocal fold specialization appears to allow the unusually low fo values observed in purring. While our data do not fully reject the AMC hypothesis for purring, they show that cat larynges can easily produce sounds in the purr regime with fundamental frequencies of 25 to 30 Hz without neural input or muscular contraction. This strongly suggests that the physical and physiological basis of cat purring involves the same MEAD-based mechanisms as other cat vocalizations (e.g., meows) and most other vertebrate vocalizations but is potentially augmented by AMC.

A cross-species framework to identify vocal learning abilities in mammals.

Vocal production learning (VPL) is the experience-driven ability to produce novel vocal signals through imitation or modification of existing vocalizations. A parallel strand of research investigates acoustic allometry, namely how information about body size is conveyed by acoustic signals. Recently, we proposed that deviation from acoustic allometry principles as a result of sexual selection may have been an intermediate step towards the evolution of vocal learning abilities in mammals. Adopting a more hypothesis-neutral stance, here we perform phylogenetic regressions and other analyses further testing a potential link between VPL and being an allometric outlier. We find that multiple species belonging to VPL clades deviate from allometric scaling but in the opposite direction to that expected from size exaggeration mechanisms. In other words, our correlational approach finds an association between VPL and being an allometric outlier. However, the direction of this association, contra our original hypothesis, may indicate that VPL did not necessarily emerge via sexual selection for size exaggeration: VPL clades show higher vocalization frequencies than expected. In addition, our approach allows us to identify species with potential for VPL abilities: we hypothesize that those outliers from acoustic allometry lying above the regression line may be VPL species. Our results may help better understand the cross-species diversity, variability and aetiology of VPL, which among other things is a key underpinning of speech in our species. This article is part of the theme issue 'Voice modulation: from origin and mechanism to social impact (Part II)'.

Immune Checkpoint Inhibitor-Induced Myositis/Myocarditis with Myasthenia Gravis-like Misleading Presentation: A Case Series in Intensive Care Unit.

INTRODUCTION: Immune checkpoint inhibitors (ICIs) are a major breakthrough in cancer treatment. Their increasingly frequent use leads to an uprising incidence of immune-related adverse events (irAEs). Among those, myocarditis is the most reported fatal cardiovascular irAE, frequently associated with ICI-related myositis. CASE SERIES: Here, we report three cases of ICI-induced myocarditis/myositis with an extremely severe myasthenia gravis-like (MG-like) presentation, highlighting the main challenges in irAEs management. These patients were over 60 years old and presented an ongoing melanoma, either locally advanced or metastatic, treated with ICI combinations. Shortly after the first or second ICI infusion, they were admitted in an intensive care unit (ICU) for grade 3 ICI-induced MG-like symptoms leading to acute respiratory failure (ARF) requiring invasive mechanical ventilation (IMV). The initial misdiagnosis was later corrected to severe ICI-induced seronegative myocarditis/myositis upon biological results and histopathology from muscular/endomyocardial biopsies. All of them received urgent high-dose corticosteroids pulses. The oldest patient died prematurely, but the two others received targeted therapies leading to complete recovery for one of them. DISCUSSION: These cases highlight the four main challenges of irAEs, encompassing the lack of knowledge among physicians, the risk of misdiagnosis due to numerous and non-specific symptoms, the frequent overlapping forms of irAEs, and the extremely rare MG-like misleading presentation of myocarditis/myositis. The exact pathophysiology of irAEs remains unclear, although a major involvement of the lymphoid compartment (specifically T lymphocytes) was evidenced. Therapeutic management is based on urgent high-dose corticosteroids. For the severest forms of irAEs, case-by-case targeted immunosuppressive therapies should be urgently administered upon multidisciplinary meetings. CONCLUSION: These cases highlight the lack of knowledge of irAEs among physicians, aggravated by misleading overlapping forms, requiring specific management in trained units and multidisciplinary care. Severe MG-like presentation of irAEs constitutes an absolute therapeutic emergency with high-dose corticosteroids and targeted immunosuppressive therapy.

Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance.

Mechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5'-untranslated region. As a result, we find that sustained translation of IGF-1R mRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that "man-made" fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes.

Effect of Ventricular Folds on Vocalization Fundamental Frequency in Domestic Pigs (Sus scrofa domesticus).

This study investigates the effect of the ventricular folds on fundamental frequency (fo) in the voice production of domestic pigs (Sus scrofa domesticus). The excised larynges of six subadult pigs were phonated in two preparation stages, with the ventricular folds present (PS1) and removed (PS2). Vocal fold resonances were tested with a laser vibrometer, and a four-mass computational model was created. Highly significant fo differences were found between PS1 and PS2 (means at 93.7 and 409.3 Hz, respectively). Two tissue resonances were found at 115 Hz and 250-290 Hz. The computational model had unique solutions for abducted and adducted ventricular folds at about 150 and 400 Hz, roughly matching the fo measured ex vivo for PS1 and PS2. The differing fo encountered across preparation stages PS1 and PS2 is explained by distinct activation of either a high or a low eigenfrequency mode, depending on the engagement of the ventricular folds. The inability of the investigated larynges to vibrate at frequencies below 250 Hz in PS2 suggests that in vivo low-frequency calls of domestic pigs (pre-eminently grunts) are likely produced with engaged ventricular folds. Allometric comparison suggests that the special, mechanically coupled "double oscillator" has evolved to prevent signaling disadvantages. Given these traits, the porcine larynx might - apart from special applications relating to the involvement of ventricular folds - not be an ideal candidate for emulating human voice production in excised larynx experimentation.

Study of intracellular anabolism of 5-fluorouracil and incorporation in nucleic acids based on an LC-HRMS method.

5-Fluorouracil (5-FU) is an anticancer drug extensively used for different cancers. Intracellular metabolic activation leads to several nucleoside and nucleotide metabolites essential to exert its cytotoxic activity on multiple cellular targets such as enzymes, DNA and RNA. In this paper, we describe the development of a method based on liquid chromatography coupled with high resolution mass spectrometry suitable for the simultaneous determination of the ten anabolic metabolites (nucleoside, nucleotide and sugar nucleotide) of 5-FU. The chromatographic separation was optimized on a porous graphitic carbon column allowing the analysis of the metabolites of 5-FU as well as endogenous nucleotides. The detection was performed on an Orbitrap® tandem mass spectrometer. Linearity of the method was verified in intracellular content and in RNA extracts. The limit of detection was equal to 12 pg injected on column for nucleoside metabolites of 5-FU and 150 pg injected on column for mono- and tri-phosphate nucleotide metabolites. Matrix effect was evaluated in cellular contents, DNA and RNA extracts for nucleoside and nucleotides metabolites. The method was successfully applied to i) measure the proportion of each anabolic metabolite of 5-FU in cellular contents, ii) follow the consequence of inhibition of enzymes on the endogenous nucleotide pools, iii) study the incorporation of metabolites of 5-FU into RNA and DNA, and iv) to determine the incorporation rate of 5-FUrd into 18 S and 28 S sub-units of rRNA.