Biology subjects

Galante, P. A. F.

Publications and source records attributed to Galante, P. A. F..

18 recordsLinked to original sources

bioRxiv2026

Transposable elements shape olaparib response according to BRCA1 status in triple-negative breast cancer

BackgroundTriple-negative breast cancer (TNBC) is an aggressive subtype with limited therapeutic options. While PARP inhibitors, such as olaparib, show promise in BRCA1-deficient TNBC through synthetic lethality, up to 50% of patients fail to respond, highlighting the need to understand the molecular mechanisms underlying PARP inhibitors efficacy. Transposable elements (TEs), particularly LINE-1 elements, are increasingly recognized as modulators of genomic instability associated with DNA repair processes and potential key players in synthetic lethality. Here, we investigate the functional relationship between TE activity and olaparib treatment in TNBC with distinct BRCA1 functional status. MethodsWe performed comprehensive multi-OMICs analysis of four TNBC cell lines (two BRCA1-deficient: SUM1315 and MDA-MB-436; two BRCA1-proficient: MDA-MB-468 and BT549) treated with olaparib. We analyzed expression and differential expression of protein-coding genes, TEs, and gene-TE chimeric transcripts. Long-read whole-genome sequencing was employed to detect de novo TE insertions, complemented by a functional assay to quantify LINE-1 retrotransposition activity in olaparib-treated cells. ResultsOlaparib treatment induces extensive transcriptomic and genomic disorganization mediated by TEs, especially LINE-1, exclusively in BRCA1-deficient cells. We observed aberrant overexpression of both genes and TEs, including gene-TE chimeric transcripts harboring poison exons within tumorigenic genes and multi-exonic TE-TE chimeras capable of forming immunostimulatory double-stranded RNA (dsRNA) structures. Functional enrichment analyses revealed activation of antiviral immune pathways linked to LINE-1 activity. Consistently, orthogonal assays confirmed LINE-1 retrotransposition in BRCA1-deficient cells following olaparib exposure. ConclusionsOur findings demonstrate that olaparib treatment induces TE activation especially in BRCA1-deficient cells, a novel mechanism that may underlie synthetic lethality in TNBC. This TE activation triggers immune responses and genomic instability, providing new therapeutic opportunities through immunotherapy combinations and suggesting that TE activity may serve as a potential biomarker for treatment stratification of TNBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/738694v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1cf6ecorg.highwire.dtl.DTLVardef@19725f7org.highwire.dtl.DTLVardef@3d9597org.highwire.dtl.DTLVardef@127f0bb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing

Transposable elements (TEs) not only account for half of the human genome sequence but also generate transcripts that contribute to transcriptomic diversity. Yet, their repetitive nature has hindered accurate quantification of the full TE-derived transcriptome, a challenge that long-read sequencing can overcome. Here, we combined multiplexed arrays isoform sequencing (MAS-ISO-seq) with a dedicated computational framework (TEscape) to perform an in-depth annotation of the human TE transcriptome. To capture the breadth of human transcriptome diversity, we profiled six representative cell types spanning three distinct biological contexts, including metabolism with, primary patient-derived adipogenic cells at two differentiation stages, and iPSC derived hepatic progenitor cells; the nervous system with iPSC-derived neurons, neural progenitor cells (NPCs), and pluripotency using induced pluripotent stem cells (iPSCs). Together, these datasets yielded over 235 million full-length long reads. First, to assess data coverage and transcriptome depth, we quantified protein-coding gene expression, detecting 14,312 genes (73.6% of all annotated protein-coding genes), which is a level consistent with deep and comprehensive transcriptome representation. Second, focusing on TE-derived transcripts, we identified >83,000 previously unannotated isoforms, the vast majority (84%) originating from a complex combination of multi-TEs. We also identified solo TEs, which are predominantly from LINE1 (14%). We confirmed that TE-transcripts are able to be exemplified by signatures detected in Liver Hepatocellular Carcinoma (LICH). Together, MAS-ISO-seq and TEscape establish the first long-read-based, high-resolution atlas of transcribed human TEs, providing a foundational resource for integrative transcriptome analyses and for investigating TE expression and regulation in health and disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/737305v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18158aeorg.highwire.dtl.DTLVardef@e51fdforg.highwire.dtl.DTLVardef@8f9504org.highwire.dtl.DTLVardef@804113_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioinformatics↗

bioRxiv2026

Processed pseudogenes as dynamic substrates of vertebrate genome evolution

Pseudogenes, gene copies presumed nonfunctional, are widespread products of genome evolution, yet their retention under selection and functional significance across vertebrate diversity remain poorly understood. Here, by analyzing 244 high-quality, chromosome-scale genomes from the Vertebrate Genomes Project spanning seven major vertebrate lineages, we show that the most abundant class of pseudogenes, processed pseudogenes (retrocopies), is a dynamic substrate for evolutionary innovation rather than an inert relic. Retrocopy abundance varies by more than an order of magnitude across lineages, closely tracks autonomous retrotransposon content, and a considerable fraction retains intact open reading frames under purifying selection. We establish a two-stage model in which a conserved formation bias toward highly expressed housekeeping genes is followed by lineage-specific selective filtering that shapes distinct functional repertoires. Testing this model, we show that the mammalian X chromosome exports retrocopies to autosomes at significantly elevated rates enriched for functionally constrained copies, establishing meiotic sex chromosome inactivation as the selective driver. Furthermore, tumor suppressor gene retrocopies accumulate preferentially over oncogene retrocopies in large-bodied and long-lived mammalian lineages, identifying retrocopy-mediated tumor suppressor dosage expansion as a previously unrecognized genomic correlate of Petos paradox. Beyond cancer-related dynamics, retrocopy abundance itself correlates with key mammalian life-history traits, including brain mass, generation length, and reproductive timing, which suggests that retrocopy turnover is broadly coupled to organismal pace-of-life. These findings recast retrocopies as a major axis of vertebrate genome evolution and provide a comprehensive resource for studying gene duplicate innovation.

genomics↗

bioRxiv2025

The complete genome of a songbird

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding [~]90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

genomics↗

bioRxiv2025

Transcriptomic entropy reveals tissue-specific patterns in aging and predicts cancer progression

ABSTRACTAging and cancer share complex molecular mechanisms, yet distinguishing between causative factors and byproducts remains challenging. Here, we investigated the role of transcriptomic entropy in aging and cancer processes by analyzing RNA-sequencing data from thousands of human and mouse samples. We found that entropy changes during aging are highly tissue-specific, with some tissues showing increased entropy while others exhibit decreased or stable entropy levels. Transcriptomic entropy strongly correlates with age-related processes, showing positive associations with proliferation, cellular senescence, and somatic mutation burden, while negatively correlating with stemness. Surprisingly, cellular reprogramming also increases transcriptomic entropy. In cancer, we observed that primary tumors generally display higher entropy than normal tissue, with entropy levels further increasing in metastatic stages. Notably, treatment-resistant tumors showed distinct entropy patterns, with acquired resistance associated with increased entropy, while primary resistance and immediate post-treatment responses showed decreased entropy. Higher entropy levels predicted poor survival outcomes in multiple cancer types, suggesting its potential as a prognostic marker. Furthermore, differential expression analysis revealed that entropy-associated genes are enriched in developmental processes and depleted in metabolic pathways, indicating a possible link to cellular dedifferentiation. Finally, we found increased entropy in various age-related diseases beyond cancer, suggesting that transcriptomic disorder may be a common feature in age-related pathologies. Our findings establish transcriptomic entropy as a fundamental parameter in aging and cancer progression, offering new insights into disease mechanisms and challenging the current view that increased disorder is always detrimental.

genomics↗

bioRxiv2024

FREDDIE: A comprehensive tool for detecting exonization of retrotransposable elements in short and long RNA sequencing data

BackgroundTransposable elements (TEs) constitute a significant portion of mammalian genomes, accounting for about 50% of the total DNA. Intragenic TEs are of particular interest as they are co-transcribed with their host genes in pre-mRNA, potentially leading to the formation of novel chimeric transcripts and the exonization of TEs. The abundance of RNA sequencing data currently available offers a unique opportunity to explore transcriptomic variations. However, a significant limitation is the capability of existing computational tools. Here, we introduce FREDDIE, an innovative algorithm designed to detect the exonization of retrotransposable elements using RNA-seq data. FREDDIE can process short and long RNA sequencing data, assemble and quantify transcripts, evaluate coding potential, and identify protein domains in chimeric transcripts involving exonized TEs and retrocopies. ResultsTo demonstrate the efficacy of FREDDIE, we analyzed and validated TE exonization in two human cancer cell lines, K562 and U251. We have identified 322 chimeric transcripts, of which 126 were from K562, and 196 were from U251. Among these chimeric transcripts, there were 35 that showed similar exonization patterns and host genes. These transcripts involve protein-coding genes of the host and exonization of LINE-1 (L1), Alu elements, and retrocopies of coding genes. We have selected some candidates and validated them experimentally through RT-PCR. The validation rate for these candidates was 70%, later confirmed by long-read sequencing. Additionally, we applied FREDDIE to analyze TE exonization across 157 glioblastoma samples, identifying 1,010 chimeric transcripts. The majority of these transcripts involved the exonization of Alu elements (69.8%), followed by L1 (20.6%) and retrocopies (9.6%). Notably, we discovered a highly expressed L1 exonization within the ROS gene, resulting in a truncated open reading frame (ORF) with the deletion of two protein domains. ConclusionsFREDDIE is an efficient and user-friendly tool for identifying chimeric transcripts that involve exonization of intragenic TEs. Overall, FREDDIE enables comprehensive investigations into the contributions of TEs to transcriptome evolution, variation, and disease-associated abnormalities, and it operates effectively on standard computing systems. FREDDIE is publicly available: https://github.com/galantelab/freddie

bioinformatics↗

bioRxiv2024

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1s interactome, uncovered novel roles in splicing, cell division and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimers brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.

genomics↗

bioRxiv2023

RCPedia: A global resource for studying and exploring retrocopies in diverse species

MotivationGene retrocopies, or processed pseudogenes, arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species. ResultsHere, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtle, lizard, frog, zebrafish, and drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology and transposable elements. In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species. AvailabilityRCPedia is available at https://www.rcpediadb.org

bioinformatics↗

bioRxiv2023

TRANSPOSABLE ELEMENTS ALTER GENE EXPRESSION AND MAY IMPACT RESPONSE TO CISPLATIN THERAPY IN OVARIAN CANCER

Cisplatin is widely employed for cancer treatment; therefore, understanding resistance to this drug is critical for therapeutic practice. While studies have delved into differential gene expression in the context of cisplatin resistance, findings remain somewhat scant. In this study, we employed RNA-seq, ATAC-seq, and in-depth bioinformatics analyses to perform a detailed investigation of the cellular transcriptome, centering on Transposable Elements (TEs) expression in ovarian cancer cell lines both sensitive and resistant to cisplatin treatment. Our results reveal that cisplatin therapy alters the expression of protein-coding genes, but also key TEs, including LINE1, Alu, and endogenous retroviruses, in both cisplatin-sensitive and -resistant cell lines. By co-expressing with downstream genes or by creating chimeric transcripts with host genes at their insertion sites, these TEs seem to control the expression of protein-coding genes, including tumor-related genes. Notably, our model uncovers TEs influencing the expression of cancer genes and cancer pathways. Collectively, our findings indicate that TEs alterations associated with cisplatin treatment occur in critical cancer genes and cellular pathways synergically. In conclusion, this research highlights the importance of considering the entire spectrum of transcribed elements in the genome, especially TE expression, for a complete understanding of complex models like cancer response to treatment.

cancer biology↗

bioRxiv2023

Unveiling the role of SRY in male-biased cancers: Insights into the molecular basis of sex disparities in high-grade glioma and melanoma

Sex disparities have been observed in many tumor types affecting non-reproductive organs. Typically, the incidence and mortality rates of such cancers are higher in men. Although differences in lifestyle and environmental exposures are known contributors, knowledge of the molecular mechanisms driving sexual dimorphism in tumor development and therapy response remains limited. To address this question, we comprehensively studied the sex-determining region Y (SRY) gene, a male-specific gene that is critical in development. First, we screened 2,448 samples from 11 cancer types to identify those with a higher incidence in men and increased expression of SRY. In cases of high-grade glioma and melanoma, men with tumors exhibiting high SRY expression had a worse prognosis. Our results suggest that SRY target genes show altered expression when SRY is overexpressed. These gene sets are linked to cell growth, epithelial-mesenchymal transition, inflammation, and repression of tumor suppressor pathways. In summary, we present the first comprehensive investigation of SRY expression and its association with clinical outcomes in men with high-grade glioma and melanoma. Our results shed light on the molecular basis for sex disparities and lay the foundation for investigation of various target genes and novel cancer treatments in men with high-grade glioma and melanoma.

cancer biology↗

bioRxiv2023

Retro-miRs: Novel and functional miRNAs originated from mRNA retrotransposition

BackgroundReverse transcribed gene copies, or retrocopies, have emerged as a major source of evolutionary novelties. MicroRNAs (miRNAs) are small, highly conserved RNAs molecules among species that serve as key post-transcriptional regulators of gene expression. The birth and subsequent evolution of miRNAs have been addressed, but not fully. ResultsIn this study, we carried out a comprehensive investigation of miRNAs origination through retroduplicated mRNA sequences (retrocopies). We identified 17 retroduplicated miRNAs (retro-miRs) that emerged from mRNAs retrocopies. Four of these retro-miRs had de novo origination within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and were duplicated along with their host mRNAs. We found that retro-miRs are primates specific, including 5 retro-miRs conserved among all primates and two human-specific retro-miRs. All of the retro-miRs were expressed and had predicted and experimentally validated target genes, with the exception of miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes, such as metabolic processes, cell signaling and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs have a potential oncogenic role in cancer, targeting key cancer genes and being overexpressed in several cancer types, including Liver Hepatocellular Carcinoma and Stomach Adenocarcinoma. ConclusionOur findings demonstrate that mRNAs retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play roles in cancer.

genomics↗

bioRxiv2022

The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes

The exon junction complex (EJC) plays key roles throughout the lifespan of RNA and is particularly relevant in the nervous system. We investigated the roles of two EJC members, the paralogs MAGOH and MAGOHB, with respect to brain tumor development. High MAGOH/MAGOHB expression was observed in 14 tumor types; glioblastoma (GBM) showed the greatest difference compared to normal tissue. Increased MAGOH/MAGOHB expression was associated with poor prognosis in glioma patients, while knockdown of MAGOH/MAGOHB affected different cancer phenotypes. Reduced MAGOH/MAGOHB expression in GBM cells caused alterations in the splicing profile, including re-splicing and skipping of multiple exons. The binding profiles of EJC proteins indicated that exons affected by MAGOH/MAGOHB knockdown accumulated fewer complexes on average, providing a possible explanation for their sensitivity to MAGOH/MAGOHB knockdown. Transcripts (genes) showing alterations in the splicing profile are mainly implicated in cell division, cell cycle, splicing, and translation. We propose that high MAGOH/MAGOHB levels are required to safeguard the splicing of genes in high demand in scenarios requiring increased cell proliferation (brain development and GBM growth), ensuring efficient cell division, cell cycle regulation, and gene expression (splicing and translation). Since differentiated neuronal cells do not require increased MAGOH/MAGOHB expression, targeting these paralogs is a potential option for treating GBM.

cancer biology↗

bioRxiv2022

Acute myeloid leukemia expresses a specific group of olfactory receptors

Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults. Although new drugs for specific molecular subsets of AML have recently emerged, the 5-year overall survival rate is still approximately 25%. The treatment options for AML have remained stagnant for decades, and novel molecular targets for this disease are needed. Olfactory receptors (ORs) are seven transmembrane G-protein coupled receptors preferentially expressed in sensory neurons, in which they play a critical role in recognizing odorant molecules. Recent studies have revealed ectopic expression and putative function of ORs in nonolfactory tissues and pathologies, including AML. Here, we comprehensively investigated OR expression in 151 AML samples, 51 healthy tissues (approximately 11,200 samples), and 15 other cancer types (6,400 samples). Our analyses identified a group of 19 ORs with a distinct and major expression pattern in AML. The expression of these ORs was experimentally validated in an independent set of AML samples and cell lines. We also identified an OR signature with prognostic value for AML patients. Finally, we identified cancer-related genes that were coexpressed with the ORs in the AML samples. In summary, we conducted a high-throughput computational study to identify ORs that can be used as novel biomarkers for the diagnosis of AML and as potential drug targets. The same approach may be used to investigate OR expression in other types of cancer.

cancer biology↗

bioRxiv2021

piRNAdb: A piwi-interacting RNA database

MotivationFound in several metazoan species, piwi-interacting RNAs (piRNAs) regulate the expression of a wide variety of transposable elements and genes associated with cellular development, differentiation, and growth. Despite their importance, piRNAs are not well known and are still underexplored. To facilitate piRNA research, a comprehensive and easy-to-use piRNA database is still needed. ResultsHere, we present piRNAdb, an integrative and user-friendly database designed to encompass several aspects of piRNAs. We selected piRNAs from four reliable human RNA-sequencing datasets to start our database. After data processing, we displayed these sequences, their genomic location, clustering information, putative targets on known genes and transposable elements, as well as direct links to other databases. In this first release, piRNAdb catalogues 27,329 piRNAs, as well as 23,380 genes that are putative targets and 47,060 associated gene ontology terms, both of which are organized and linked to each respective piRNA. Finally, to improve information exchange and increase the confidence of sequences, a feedback system is provided to users of piRNAdb. ConclusionThe inclusion of new features to facilitate piRNA analyses, data visualization, and integration is the major pillar of piRNAdb. Our main goal was to make this database an easy interface between the data and the user. We believe that this web tool achieves this objective by providing a streamlined and well-organized data repository for piRNAs and that it will be extremely useful to those already studying piRNAs and to the broader community. AvailabilitypiRNAdb is available freely and is compatible with smartphones and tablets: https://www.pirnadb.org/

bioinformatics↗

bioRxiv2021

Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the Spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures to contain the spread of the disease in many countries has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread and whether they can cause a more severe disease remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (KD) values using surface plasmon resonance (SPR) assays of three fastspreading SARS-CoV-2 variants, Alpha, Beta and Gamma ones, as well as genetic factors in the host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased Spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN and TMPRSS2), may have few contributions to the SARS-CoV-2 variants infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than wild-type. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗

bioRxiv2020

Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis

Nowadays, the massive amount of data generated by modern sequencing technologies provides an unprecedented opportunity to find genes associated with cancer patient prognosis, connecting basic and translational research. However, treating high dimensionality of gene expression data and integrating it with clinical variables are major challenges to carry out these analyses. Here, we present Reboot, an original and efficient algorithm to find genes and splicing isoforms associated with cancer patient survival, disease progression, or other clinical endpoints. Reboot innovates by using a multivariate strategy with penalized Cox regression (LASSO method) combined with a bootstrap approach, in addition to statistical tests for supporting the findings, which are automatically plotted. Applying Reboot on data from 154 glioblastoma patients, we identified a three-gene signature (IKBIP, OSMR, PODNL1) whose increased derived risk score was significantly associated with worse patients prognosis, even in conjunction with other well-established clinical parameters. Similarly, Reboot was able to find a seven-splicing isoforms signature (CENPF-201; MLKL-202; NUP54-201; MCF2L-201; TFDP1-207; BBS1-206; HTT-202) related to worse overall survival in 177 pancreatic adenocarcinoma patients with elevated risk scores after uni- and multivariate analyses. In summary, Reboot is an efficient, intuitive, and straightforward way for finding genes or splicing isoforms (transcripts) signatures relevant to patient prognosis, which can democratize this kind of analysis and shed light on still under-investigated sets of cancer-related genes. Reboot effectively runs on either servers or personal computers and it is freely available at github.com/galantelab/reboot.

bioinformatics↗

bioRxiv2020

sideRETRO: a pipeline for identifying somatic and dimorphic insertions of processed pseudogenes or retrocopies

Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or dimorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need. Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity, and genomic context and classifying them as somatic or dimorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them (93.2% accuracy), in addition to identifying dimorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of retroCNVs. AvailabilitysideRETRO is available at https://github.com/galantelab/sideRETRO

bioinformatics↗

bioRxiv2019

Depletion of Ric-8B leads to reduced mTORC2 activity

mTOR, a serine/threonine protein kinase that is involved in a series of critical cellular processes, can be found in two functionally distinct complexes, mTORC1 and mTORC2. In contrast to mTORC1, little is known about the mechanisms that regulate mTORC2. Here we show that mTORC2 activity is reduced in mice with a hypomorphic mutation of the Ric-8B gene. Ric-8B is a highly conserved protein that acts as a non-canonical guanine nucleotide exchange factor (GEF) for heterotrimeric Gs/olf type subunits. We found that Ric-8B hypomorph embryos are smaller than their wild type littermates, fail to close the neural tube in the cephalic region and die during mid-embryogenesis. Comparative transcriptome analysis revealed that signaling pathways involving GPCRs and G proteins are dysregulated in the Ric-8B mutant embryos. Interestingly, this analysis also revealed an unexpected impairment of the mTOR signaling pathway.\n\nPhosphorylation of Akt at Ser 473 is downregulated in the Ric-8B mutant embryos, indicating a decreased activity of mTORC2. In contrast, phosphorylation of S6, a downstream target of mTORC1, is unaltered. Knockdown of the endogenous Ric-8B gene in HEK293T cells leads to reduced phosphorylation levels of Akt at Ser 473, but not of S6, further supporting the selective involvement of Ric-8B in mTORC2 activity. Our results reveal a crucial role for Ric-8B in development and provide novel insights into the signals that regulate mTORC2 activity.\n\nAuthor SummaryGene inactivation in mice can be used to identify genes that are involved in important biological processes and that may contribute to disease. By using this approach, we found that the Ric-8B gene is essential for embryogenesis and for the normal development of the nervous system. Ric-8B mutant mouse embryos are smaller than their wild type littermates and show neural tube defects at the cranial region. This approach also allowed us to identify the biological pathways that are involved in the observed phenotypes, the G protein and mTORC2 signaling pathways. mTORC2 plays particular important roles also in the adult brain, and has been implicated in neurological disorders. Ric-8B is highly conserved in mammals, including humans. Our mutant mice provide a model to study the complex molecular and cellular processes underlying the interplay between Ric-8B and mTORC2 in neuronal function.

molecular biology↗