Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

The status of the human gene catalogue.

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.

Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we developed CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5'capped, full-length transcripts, together with the data processing pipeline LyRic. We benchmarked CapTrap-seq and other popular RNA-seq library preparation protocols in a number of human tissues using both ONT and PacBio sequencing. To assess the accuracy of the transcript models produced, we introduced a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation in RNA spike-in molecules. We found that the vast majority (up to 90%) of transcript models that LyRic derives from CapTrap-seq reads are full-length. This makes it possible to produce highly accurate annotations with minimal human intervention.

Artificial intelligence, big data and heart transplantation: Actualities.

BACKGROUND: As diagnostic and prognostic models developed by traditional statistics perform poorly in real-world, artificial intelligence (AI) and Big Data (BD) may improve the supply chain of heart transplantation (HTx), allocation opportunities, correct treatments, and finally optimize HTx outcome. We explored available studies, and discussed opportunities and limits of medical application of AI to the field of HTx. METHOD: A systematic overview of studies published up to December 31st, 2022, in English on peer-revied journals, have been identified through PUBMED-MEDLINE-WEB of Science, referring to HTx, AI, BD. Studies were grouped in 4 domains based on main studies' objectives and results: etiology, diagnosis, prognosis, treatment. A systematic attempt was made to evaluate studies by the Prediction model Risk Of Bias ASsessment Tool (PROBAST) and the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD). RESULTS: Among the 27 publications selected, none used AI applied to BD. Of the selected studies, 4 fell in the domain of etiology, 6 in the domain of diagnosis, 3 in the domain of treatment, and 17 in that of prognosis, as AI was most frequently used for algorithmic prediction and discrimination of survival, but in retrospective cohorts and registries. AI-based algorithms appeared superior to probabilistic functions to predict patterns, but external validation was rarely employed. Indeed, based on PROBAST, selected studies showed, to some extent, significant risk of bias (especially in the domain of predictors and analysis). In addition, as example of applicability in the real-world, a free-use prediction algorithm developed through AI failed to predict 1-year mortality post-HTx in cases from our center. CONCLUSIONS: While AI-based prognostic and diagnostic functions performed better than those developed by traditional statistics, risk of bias, lack of external validation, and relatively poor applicability, may affect AI-based tools. More unbiased research with high quality BD meant for AI, transparency and external validations, are needed to have medical AI as a systematic aid to clinical decision making in HTx.

The status of the human gene catalogue.

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants.

Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.

Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.

GENCODE: reference annotation for the human and mouse genomes in 2023.

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Big Data in cardiac surgery: real world and perspectives.

Big Data, and the derived analysis techniques, such as artificial intelligence and machine learning, have been considered a revolution in the modern practice of medicine. Big Data comes from multiple sources, encompassing electronic health records, clinical studies, imaging data, registries, administrative databases, patient-reported outcomes and OMICS profiles. The main objective of such analyses is to unveil hidden associations and patterns. In cardiac surgery, the main targets for the use of Big Data are the construction of predictive models to recognize patterns or associations better representing the individual risk or prognosis compared to classical surgical risk scores. The results of these studies contributed to kindle the interest for personalized medicine and contributed to recognize the limitations of randomized controlled trials in representing the real world. However, the main sources of evidence for guidelines and recommendations remain RCTs and meta-analysis. The extent of the revolution of Big Data and new analytical models in cardiac surgery is yet to be determined.

RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.

Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.

Comprehensive evaluation of Impella RP® in right ventricular failure.

Right ventricular failure has a high morbidity and mortality in patients suffering from advanced heart failure, pulmonary hypertension, acute myocardial infarction after cardiac surgery and in left ventricular assist device patients. The Impella RP® catheter is a mechanical circulatory device, positioned from a venous femoral percutaneous access and passing through the tricuspid and pulmonary valves, reaches the pulmonary artery. Impella RP (Abiomed Inc., MA, USA) acts as a direct right ventricle bypass and it provides a flow up to 4.4 liters per minute, unloading the right ventricle. The main contraindications are: thrombi in the vena cava, right atrium and ventricle and pulmonary artery; mechanical tricuspid or pulmonary prostheses. In this review, the principles of operations, clinical applications and results of Impella RP are summarized and evaluated.

Right ventricular failure is a severe medical condition characterized by a sudden or a progressive reduction of the function of the right heart. This condition, if left untretated, leads to low blood pressure, reduced oxygen supply to other organs as brain, liver and kidneys, and eventually death. The right ventricular failure can be the consequence of a heart attack or a progressive disease of the heart, such as chronic heart failure, inflammatory diseases or inherited conditions. When medical therapy fails, the function of the right ventricle (RV) can be temporarily replaced by a mechanical device. Impella RP^® is a mechanical device, inserted into the heart without the need of a surgical operation, that bypasses the RV and ensures an adequate blood flow. Impella RP, while replaces the right ventricular function, allows time for the right ventricular recovery. When and if the RV recovers, Impella RP can be removed. As all the medical devices, Impella RP can be associated to adverse effects, mainly bleeding and damage of cardiac structures.

Eculizumab in patients with severe coronavirus disease 2019 (COVID-19) requiring continuous positive airway pressure ventilator support: Retrospective cohort study.

BACKGROUND: Complement activation contributes to lung dysfunction in coronavirus disease 2019 (COVID-19). We assessed whether C5 blockade with eculizumab could improve disease outcome. METHODS: In this single-centre, academic, unblinded study two 900 mg eculizumab doses were added-on standard therapy in ten COVID-19 patients admitted from February 2020 to April 2020 and receiving Continuous-Positive-Airway-Pressure (CPAP) ventilator support from ≤24 hours. We compared their outcomes with those of 65 contemporary similar controls. Primary outcome was respiratory rate at one week of ventilator support. Secondary outcomes included the combined endpoint of mortality and discharge with chronic complications. RESULTS: Baseline characteristics of eculizumab-treated patients and controls were similar. At baseline, sC5b-9 levels, ex vivo C5b-9 and thrombi deposition were increased. Ex vivo tests normalised in eculizumab-treated patients, but not in controls. In eculizumab-treated patients respiratory rate decreased from 26.8±7.3 breaths/min at baseline to 20.3±3.8 and 18.0±4.8 breaths/min at one and two weeks, respectively (p<0.05 for both), but did not change in controls. Between-group changes differed significantly at both time-points (p<0.01). Changes in respiratory rate correlated with concomitant changes in ex vivo C5b-9 deposits at one (rs = 0.706, p = 0.010) and two (rs = 0.751, p = 0.032) weeks. Over a median (IQR) period of 47.0 (14.0-121.0) days, four eculizumab-treated patients died or had chronic complications versus 52 controls [HRCrude (95% CI): 0.26 (0.09-0.72), p = 0.010]. Between-group difference was significant even after adjustment for age, sex and baseline serum creatinine [HRAdjusted (95% CI): 0.30 (0.10-0.84), p = 0.023]. Six patients and 13 controls were discharged without complications [HRCrude (95% CI): 2.88 (1.08-7.70), p = 0.035]. Eculizumab was tolerated well. The main study limitations were the relatively small sample size and the non-randomised design. CONCLUSIONS: In patients with severe COVID-19, eculizumab safely improved respiratory dysfunction and decreased the combined endpoint of mortality and discharge with chronic complications. Findings need confirmation in randomised controlled trials.

Cardiac Toxicity Associated with Cancer Immunotherapy and Biological Drugs.

Cancer immunotherapy significantly contributed to an improvement in the prognosis of cancer patients. Immunotherapy, including human epidermal growth factor receptor 2 (HER2)-targeted therapies, immune checkpoint inhibitors (ICI), and chimeric antigen receptor-modified T (CAR-T), share the characteristic to exploit the capabilities of the immune system to kill cancerous cells. Trastuzumab is a monoclonal antibody against HER2 that prevents HER2-mediated signaling; it is administered mainly in HER2-positive cancers, such as breast, colorectal, biliary tract, and non-small-cell lung cancers. Immune checkpoint inhibitors (ICI) inhibit the binding of CTLA-4 or PD-1 to PDL-1, allowing T cells to kill cancerous cells. ICI can be used in melanomas, non-small-cell lung cancer, urothelial, and head and neck cancer. There are two main types of T-cell transfer therapy: tumor-infiltrating lymphocytes (or TIL) therapy and chimeric antigen receptor-modified T (CAR-T) cell therapy, mainly applied for B-cell lymphoma and leukemia and mantle-cell lymphoma. HER2-targeted therapies, mainly trastuzumab, are associated with left ventricular dysfunction, usually reversible and rarely life-threatening. PD/PDL-1 inhibitors can cause myocarditis, rare but potentially fulminant and associated with a high fatality rate. CAR-T therapy is associated with several cardiac toxic effects, mainly in the context of a systemic adverse effect, the cytokines release syndrome.

Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).

Metazoan genomes produce thousands of long-noncoding RNAs (lncRNAs), of which just a small fraction have been well characterized. Understanding their biological functions requires accurate annotations, or maps of the precise location and structure of genes and transcripts in the genome. Current lncRNA annotations are limited by compromises between quality and size, with many gene models being fragmentary or uncatalogued. To overcome this, the GENCODE consortium has developed RNA capture long-read sequencing (CLS), an approach combining targeted RNA capture with third-generation long-read sequencing. CLS provides accurate annotations at high-throughput rates. It eliminates the need for noisy transcriptome assembly from short reads, and requires minimal manual curation. The full-length transcript models produced are of quality comparable to present-day manually curated annotations. Here we describe a detailed CLS protocol, from probe design through long-read sequencing to creation of final annotations.

GENCODE 2021.

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation.

The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass testing, which has been a critical measure to contain the infection in several countries. Through this article, we share our experiences and learnings as a group of volunteers at the Centre for Genomic Regulation (CRG) in Barcelona, Spain. As members of the ORFEU project, an initiative by the Government of Catalonia to achieve mass testing of people at risk and contain the epidemic in Spain, we share our motivations, challenges and the key lessons learnt, which we feel will help better prepare the global society to address similar situations in the future.

GENCODE reference annotation for the human and mouse genomes.

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

Nupela species (Naviculales: Bacillariophyceae) from Colombian lowland waters including N. acaciensis nov. sp. and N. catatumbensis nov. sp.

The genus Nupela comprises ca. 50 species that generally have a distribution restricted by bioclimatic frontiers. As part of an integrated analysis of the diatom flora of Colombia, in this study we focused our interest on the genus Nupela from lowland waters. Periphyton samples were collected from 150 sites of lotic water bodies in Colombia, taking into account hidrogeomorfological variability. In each sampling station, periphyton samples were obtained by scraping, and temperature, pH, dissolved oxygen and conductivity variables were measured. Samples were processed by both light microscopy (LM; Carl Zeiss Axio Scope.A1) and scanning electron microscopy (SEM; FEI-Quanta 450 and a Jeol JSM-6360 LV). The genus Nupela was found in 28 sites. Five taxa were identified, described and illustrated from tropical or subtropical environments: N. lesothensis, N. praecipua y N. subpallavicinii; these were new records for Colombia, and N. acaciensis and N. catatumbensis two new species for science. N. acaciensis is characterized by raphe branches of both valves equally long combined with cymbelloid symmetry, striae built by 2 transapically elongated areolae that delimit a longitudinal line at each hemivalve. N. catatumbensis is characterized by the presence of a well developed raphe in both valves; valves lanceolate with subcapitated to capitated ends and cymbelloid symmetry, striae built by 3-4 transapically elongated areolae, interestriae elevated as transapical ribs and internal proximal raphe ends hook-shaped. The genus Nupela was widely distributed in the studied basins but showed different distribution patterns: N. acaciensis and N. subpallavicini had a restricted distribution, while N. catatumbensis, N. lesothensis and N. praecipua had a wider distribution, and were collected in sites with significant variations in their ecomorphology, altitude, temperature, pH and electrolyte content.

Nupela species (Naviculales: Bacillariophyceae) from Colombian lowland waters including N. acaciensis nov. sp. and N. catatumbensis nov. sp. / Especies de Nupela (Naviculales: Bacillariophyceae) en aguas de tierras bajas de Colombia que incluyen a N. acaciensis nov. sp. y N. catatumbensis nov. sp.

The genus Nupela comprises ca. 50 species that generally have a distribution restricted by bioclimatic frontiers. As part of an integrated analysis of the diatom flora of Colombia, in this study we focused our interest on the genus Nupela from lowland waters. Periphyton samples were collected from 150 sites of lotic water bodies in Colombia, taking into account hidrogeomorfological variability. In each sampling station, periphyton samples were obtained by scraping, and temperature, pH, dissolved oxygen and conductivity variables were measured. Samples were processed by both light microscopy (LM; Carl Zeiss Axio Scope.A1) and scanning electron microscopy (SEM; FEI-Quanta 450 and a Jeol JSM-6360 LV). The genus Nupela was found in 28 sites. Five taxa were identified, described and illustrated from tropical or subtropical environments: N. lesothensis, N. praecipua y N. subpallavicinii; these were new records for Colombia, and N. acaciensis and N. catatumbensis two new species for science. N. acaciensis is characterized by raphe branches of both valves equally long combined with cymbelloid symmetry, striae built by 2 transapically elongated areolae that delimit a longitudinal line at each hemivalve. N. catatumbensis is characterized by the presence of a well developed raphe in both valves; valves lanceolate with subcapitated to capitated ends and cymbelloid symmetry, striae built by 3-4 transapically elongated areolae, interestriae elevated as transapical ribs and internal proximal raphe ends hook-shaped. The genus Nupela was widely distributed in the studied basins but showed different distribution patterns: N. acaciensis and N. subpallavicini had a restricted distribution, while N. catatumbensis, N. lesothensis and N. praecipua had a wider distribution, and were collected in sites with significant variations in their ecomorphology, altitude, temperature, pH and electrolyte content.

El género Nupela comprende alrededor de 50 especies que tienen en general una distribución restringida por fronteras bioclimáticas. Como parte de un estudio integral de la flora diatomológica de Colombia, en este trabajo focalizamos nuestro interés en el género Nupela en cuerpos de agua de tierras bajas. Muestras de perifiton fueron recolectadas en 150 sitios en cuerpos de agua lóticos seleccionados por su variabilidad hidrogeomorfológica. En cada estación de muestreo se obtuvieron muestras por raspado de varios sustratos, y adicionalmente se registraron: temperatura, pH, oxígeno disuelto y conductividad. Las muestras fueron procesadas para su análisis con microscopio óptico (MO, Carl Zeiss Axio Scope. A1) y de barrido (MEB; FEI- Quanta 450 and a Jeol JSM-6360 LV). El género Nupela fue hallado en 28 sitios. Cinco especies fueron identificadas, descritas e ilustradas, tres de ellas: N. lesothensis, N. praecipua y N. subpallavicinii fueron descritas para ambientes tropicales y subtropicales y representan nuevas citas para Colombia. Además fueron descritas N. acaciensis y N. catatumbensis, dos especies nuevas para la ciencia. N. acaciensis se caracteriza por poseer rafe desarrollado en ambas valvas, simetría cymbelloide, estrías formadas por dos aréolas transapicalmente alargadas que definen una línea longitudinal en cada hemivalva. N. catatumbensis se caracteriza poseer rafe desarrollado en ambas valvas. Valvas lanceoladas con extremos subcapitados a capitados y simetría cymbelloide. Estrías formadas por 3-4 aréolas transapicalmente alargadas, interestrías elevadas a modo de costillas transapicales y extremos proximales internos del rafe en forma de gancho. El género Nupela estuvo ampliamente representado en el área de estudio, sin embargo, las especies mostraron diferentes patrones de distribución. N. acaciensis y N. subpallavicini estuvieron presentes en una única cuenca, mientras que N. catatumbensis, N. lesothensis y N. praecipua presentaron una distribución más amplia, y fueron recolectadas en sitios con variaciones significativas en ecomorfología, altitud, temperatura, pH y contenido electrolítico.