Biology subjects

Sisu, C.

Publications and source records attributed to Sisu, C..

9 recordsLinked to original sources

bioRxiv2025

Comprehensive analysis of pseudogene expression in human and macaque brains compared with other tissues

Although gene expression in the brain has been extensively investigated and compared to other tissues, the activity of pseudogenes has not been comprehensively surveyed. Here, leveraging large-scale RNA-seq data, we construct consistent pseudogene expression profiles in human and macaque brains and compare them to 29 other tissues. We further annotate pseudogenes with potential cellular roles based on co-clustering them with protein-coding genes. Notably, the majority of the expressed pseudogenes show elevated expression in the brain relative to other tissues, and these pseudogenes show broad and consistent expression patterns across brain subregions. Furthermore, spatiotemporal analyses reveal that pseudogenes in different brain subregions have greatly varying temporal trajectories (e.g., increasing vs. decreasing), in contrast to protein-coding genes that tend to be more uniform. Finally, we identify a set of pseudogenes exhibiting significant changes in neuropsychiatric disorders, some of which overlap with known brain eGenes (genes whose expression is associated with expression quantitative trait loci, eQTLs), as well as with genes implicated by genome-wide association studies (GWAS). Together, our study provides a public resource of pseudogene expression in human and macaque brains (in comparison to other tissues) and highlights aspects of pseudogene expression in brain development and pathogenesis.

bioinformatics↗

bioRxiv2024

GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing

Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For more than twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, becoming a foundation for biomedical and genomics communities worldwide. Nevertheless, collections of important yet poorly-understood gene classes like long non-coding RNAs (lncRNAs) remain incomplete and scattered across multiple, uncoordinated catalogs. To address this, GENCODE has undertaken the most comprehensive lncRNA annotation effort to date. This is founded on the manually supervised computational annotation of full-length targeted long-read sequencing, on matched embryonic and adult tissues, of orthologous regions in human and mouse. Altogether 17,931 human genes (140,268 transcripts) and 22,784 mouse genes (136,169 transcripts) have been added to the GENCODE catalog representing a 2-fold and 6-fold growth in transcripts, respectively - the greatest increase in the number of annotated human genes since the sequencing of the human genome. Our targeted design assigned human-mouse orthologs at a rate beyond previous studies, tripling the number of human disease-associated lncRNAs that have mouse orthologs. Novel lncRNA genes consistently exhibit biological signals of functionality, and they greatly enhance the functional interpretability of the human genome. While poorly expressed in bulk RNA-Seq samples, many of them are highly expressed in specific cell populations, maybe even contributing to cell-type determination. The expanded GENCODE lncRNA annotations mark a critical step toward deciphering the human and mouse genomes.

genomics↗

bioRxiv2022

A Meta-analysis of 2D vs. 3D Ovarian Cancer Cellular Models

Three-dimensional (3D) cancer models are revolutionizing research, allowing for the recapitulation of in vivo like response through the use of an in vitro system, more complex and physiologically relevant than traditional mono-layer culture. Cancers such as ovarian (OvCa), are prone to developing resistance and are often lethal, and stand to benefit greatly from the enhanced modelling emulated by 3D culture. However current models often fall short of predicted response where reproducibility is limited owing to the lack of standardized methodology and established protocols. This meta-analysis aims to assess the current scope of 3D OvCa models and the differences in genetic profile presented by a vast array of 3D cultures. A meta-analysis of the literature (Pubmed.gov) spanning 2012 - 2022, was used to identify studies with comparable monolayer (2D) counterparts in addition to RNA sequencing and microarray data. From the data 19 cell lines were found to show differential regulation in their gene expression profiles depending on the bio-scaffold (i.e. agarose, collagen or Matrigel) compared to 2D cell cultures. Top genes differentially expressed 2D vs. 3D include C3, CXCL1, 2 and 8, IL1B, SLP1, FN1, IL6, DDIT4, PI3, LAMC2, CCL20, MMP1, IFI27, CFB, and ANGPTL4. Top Enriched Gene sets for 2D vs. 3D include IFN- and IFN-{gamma} Response, TNF- signalling, IL-6-JAK-STAT3 signalling, angiogenesis, hedgehog signalling, apoptosis, epithelial mesenchymal transition, hypoxia, and inflammatory response. Our transversal comparison of numerous scaffolds allowed us to highlight the variability that can be induced by these scaffolds in the transcriptional landscape as well as identifying key genes and biological processes that are hallmarks of cancer cells grown in 3D cultures. Future studies are needed to identify which is the most appropriate in vitro/preclinical model to study tumour microenvironment. SummaryOvarian cancer is one of the most lethal forms of female cancers. Cell culture is often the go to model to study the molecular processes of cancer. However, this is an oversimplification of the reality. 3D tissue culture has been developed to address the cell culture limitations and to provide a more realistic model of the system studied. Cells grown in 3D represent better the human tumour microenvironment. This meta-analysis is exploring the use of 3D tissue culture as a model of ovarian cancer. Our analysis shows that ovarian cancer cells grown in 3D exhibit enhanced regulation in processes pertinent to tumour development and progression. We identify a panel of genes associated with specific 3D growth conditions that could be used as conditional markers. Finally, we present an overview of the state-of-art of 3D culture with an extensive profile of the genes and pathways enhanced in ovarian cancer models.

bioinformatics↗

bioRxiv2022

Engineered model of t(7;12)(q36;p13) AML recapitulates patient-specific features and gene expression profiles

Acute myeloid leukaemia carrying the translocation t(7;12)(q36;p13) is an adverse-risk leukaemia uniquely observed in infants. Despite constituting up to 30% of cases in under 2-year-olds, it remains poorly understood. Known molecular features are ectopic overexpression of the MNX1 gene and generation of a fusion transcript in 50% of patients. Lack of research models has hindered understanding of t(7;12) biology, which has historically focused on MNX1 overexpression rather than the cytogenetic entity itself. Here, we employed CRISPR/Cas9 to generate t(7;12) in the human K562 cell line, and in healthy CD34+ haematopoietic progenitors where the translocation was not sustained in long-term cultures or through serial replating. In contrast, in K562 cells, t(7;12) was propagated in self-renewing clonogenic assays, with sustained myeloid bias in colony formation and baseline depletion of erythroid signatures. Nuclear localisation analysis revealed repositioning of the translocated MNX1 locus to the interior of t(7;12)-harbouring K562 nuclei - a known phenomenon in t(7;12) patients which associates with ectopic overexpression of MNX1. Crucially, the K562-t(7;12) model successfully recapitulated the transcriptional landscape of t(7;12) patient leukaemia. In summary, we engineered a clinically-relevant model of t(7;12) acute myeloid leukaemia with the potential to unravel targetable molecular mechanisms of disease.

cancer biology↗

bioRxiv2020

Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression.

H2A.Z is a H2A-type histone variant essential for many aspects of cell biology ranging from gene expression to genome stability. From deuterostomes, H2A.Z evolved into two paralogues H2A.Z.1 and H2A.Z.2 that differ by only three amino acids and are encoded by different genes (H2AFZ and H2AFV respectively). Despite the importance of this histone variant in development and cellular homeostasis, very little is known about the individual functions of each paralogue in mammals. Here we investigated the distinct roles of two paralogues in cell cycle regulation. Using a specific siRNA approach for each paralogue in human cells, we unveiled non-redundant functions for H2A.Z.1 and H2A.Z.2 in cell division: H2A.Z.1 regulates the expression of important cell cycle genes (including Myc and Ki-67) and its depletion leads to a G1 arrest, whereas H2A.Z.2 is essential for centromere integrity and function, thus playing a key role in chromosome segregation.

cell biology↗

bioRxiv2018

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

Pseudogenes are ideal markers of genome remodeling. In turn, the mouse is an ideal platform for studying them, particularly with the availability of developmental transcriptional data and the sequencing of 18 strains. Here, we present a comprehensive genome-wide annotation of the pseudogenes in the mouse reference genome and associated strains. We compiled this by combining manual curation of over 10,000 pseudogenes with results from automatic annotation pipelines. Also, by comparing the human and mouse, we annotated 165 unitary pseudogenes in mouse, and 303 unitaries in human. We make all our annotation available through mouse.pseudogene.org. The overall mouse pseudogene repertoire (in the reference and strains) is similar to human in terms of overall size, biotype distribution (~80% processed/~20% duplicated) and top family composition (with many GAPDH and ribosomal pseudogenes). However, notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of the pseudogenes are unique, reflecting strain-specific functions and evolution. Additionally, we find that ~15% of the pseudogenes are transcribed, a fraction similar to that for human, and that pseudogene transcription exhibits greater tissue and strain specificity compared to protein-coding genes. Finally, we show that highly transcribed parent genes tend to give rise to processed pseudogenes.

genomics↗

bioRxiv2018

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

In a 2018 paper posted to bioRxiv, Pertea et al. presented the CHESS database, a new catalog of human gene annotations that includes 1,178 new protein-coding predictions. These are based on evidence of transcription in human tissues and homology to earlier annotations in human and other mammals. Here, we reanalyze the evidence used by CHESS, and find that nearly all protein-coding predictions are false positives. We find that 86% overlap transposons marked by RepeatMasker that are known to frequently result in false positive protein-coding predictions. More than half are homologous to only nine Alu-derived primate sequences corresponding to an erroneous and previously withdrawn Pfam protein domain. The entire set shows poor evolutionary conservation and PhyloCSF protein-coding evolutionary signatures indistinguishable from noncoding RNAs, indicating lack of protein-coding constraint. Only four predictions are supported by mass spectrometry evidence, and even those matches are inconclusive. Overall, the new protein-coding predictions are unsupported by any credible experimental or evolutionary evidence of function, result primarily from homology to genes incorrectly classified as protein-coding, and are unlikely to encode functional proteins.

genomics↗

bioRxiv2018

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most widely used inbred strains and reveal for the first time extensive strain-specific haplotype variation. We identify and characterise 2,567 regions on the current Genome Reference Consortium mouse reference genome exhibiting the greatest sequence diversity between strains. These regions are enriched for genes involved in defence and immunity, and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. Several immune related loci, some in previously identified QTLs for disease response have novel haplotypes not present in the reference that may explain the phenotype. We used these genomes to improve the mouse reference genome resulting in the completion of 10 new gene structures, and 62 new coding loci were added to the reference genome annotation. Notably this high quality collection of genomes revealed a previously unannotated gene (Efcab3-like) encoding 5,874 amino acids, one of the largest known in the rodent lineage. Interestingly, Efcab3-like-/- mice exhibit severe size anomalies in four regions of the brain suggesting a mechanism of Efcab3-like regulating brain development.

genomics↗

bioRxiv2017

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

genomics↗