Telomeric RNAs are essential to maintain telomeres

Telomeres are transcribed generating long non-coding RNAs known as TERRA. Deciphering the role of TERRA has been one of the unsolved issues of telomere biology in the past decade. This has been, in part, due to lack of knowledge on the TERRA loci, thus preventing functional genetic studies. Here, we describe that long non-coding RNAs with TERRA features are transcribed from the human 20q and Xp subtelomeres. Deletion of the 20q locus by using the CRISPR-Cas9 technology causes a dramatic decrease in TERRA levels, while deletion of the Xp locus does not result in decreased TERRA levels. Strikingly, 20q-TERRA ablation leads to dramatic loss of telomere sequences and the induction of a massive DNA damage response. These findings identify chromosome 20q as a main TERRA locus in human cells and represent the first demonstration in any organism of the essential role of TERRA in the maintenance of telomeres.We are indebted to R. Torres and S. Rodriguez for advice in the CRISPR-Cas9 technology and helpful discussions. We thank D. Megías for the quantification of confocal imagesignals and to O. Dominguez for troubleshooting with cloning and sequencing. We thank S. Llanos for the p21 promoter reporter (described in ref. 33). Research in the Blasco lab is funded by the Spanish Ministry of Economy and Competitiveness Project (SAF2013-45111-R), the Madrid Regional Government Project S2010/BMD-2303 (ReCaRe),Fundacio´n Botı´n (Spain) and AXA Research Fund (AXA 2011, Spain).S

The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues

Cohesin, which in somatic vertebrate cells consists of SMC1, SMC3, RAD21 and either SA1 or SA2, mediates higher-order chromatin organization. To determine how cohesin contributes to the establishment of tissue-specific transcriptional programs, we compared genome-wide cohesin distribution, gene expression and chromatin architecture in cerebral cortex and pancreas from adult mice. More than one third of cohesin binding sites differ between the two tissues and these show reduced overlap with CCCTC-binding factor (CTCF) and are enriched at the regulatory regions of tissue-specific genes. Cohesin/CTCF sites at active enhancers and promoters contain, at least, cohesin-SA1. Analyses of chromatin contacts at the Protocadherin (Pcdh) and Regenerating islet-derived (Reg) gene clusters, mostly expressed in brain and pancreas, respectively, revealed remarkable differences that correlate with the presence of cohesin. We could not detect significant changes in the chromatin contacts at the Pcdh locus when comparing brains from wild-type and SA1 null embryos. In contrast, reduced dosage of SA1 altered the architecture of the Reg locus and decreased the expression of Reg genes in the pancreas of SA1 heterozygous mice. Given the role of Reg proteins in inflammation, such reduction may contribute to the increased incidence of pancreatic cancer observed in these animals.The Spanish Ministry of Economy and Competitiveness (MINECO) [BFU2013-48481-R to A.L.]; 'Ramon y Cajal' Contract [RYC-2010-06122 to A.C.]; Fundacion La Caixa [PhD Fellowship to S.R.]. Funding for open access charge: The Spanish Ministry of Economy and Competitiveness (MINECO) [BFU2013-48481-R]S

Hsa-miR-139-5p is a prognostic thyroid cancer marker involved in HNRNPF-mediated alternative splicing.

It is critical to identify biomarkers and functional networks associated with aggressive thyroid cancer to anticipate diseaseprogression and facilitate personalized patient management. We performed miRNome sequencing of 46 thyroid tumorsenriched with advanced disease patients with a median follow-up of 96 months. MiRNome profiles correlated with tumor-specific histopathological and molecular features, such as stromal cell infiltration and tumor driver mutation. Differentialexpression analysis revealed a consistent hsa-miR-139-5p downexpression in primary carcinomas from patients withrecurrent/metastatic disease compared to disease-free patients, sustained in paired local metastases and validated in publiclypost-print1,62 M

Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data

Transposable elements (TE) have played a major role in configuring the structures of mammalian genomes through evolution. In normal conditions, expression of these elements is repressed by different epigenetic regulation mechanisms such as DNA methylation, histone modification and regulation by small RNAs. TE re-activation is associated with stemness potential acquisition, regulation of innate immunity, and disease, such as cancer. However, the vast majority of current knowlededge in the field is based on bulk expression studies and very little is known on cell type- or state-specific expression of TE derived transcripts. Therefore, cost-efficient single cell-resolution TE expression analytical approaches are needed. We have implemented an analytical approach based on pseudoalignment to consensus sequences to incorporate TE expression information to scRNAseq data. All the data and code implemented is available as Supplementary data and in: https://github.com/jmzvillarreal/kallisto_TE_scRNAseq. Supplementary data are available at Bioinformatics online

miR-203 drives breast cancer cell differentiation

Breast cancer; Cell differentiationCáncer de mama; Diferenciación celularCàncer de mama; Diferenciació cel·lularA hallmark of many malignant tumors is dedifferentiated (immature) cells bearing slight or no resemblance to the normal cells from which the cancer originated. Tumor dedifferentiated cells exhibit a higher capacity to survive to chemo and radiotherapies and have the ability to incite tumor relapse. Inducing cancer cell differentiation would abolish their self-renewal and invasive capacity and could be combined with the current standard of care, especially in poorly differentiated and aggressive tumors (with worst prognosis). However, differentiation therapy is still in its early stages and the intrinsic complexity of solid tumor heterogeneity demands innovative approaches in order to be efficiently translated into the clinic. We demonstrate here that microRNA 203, a potent driver of differentiation in pluripotent stem cells (ESCs and iPSCs), promotes the differentiation of mammary gland tumor cells. Combining mouse in vivo approaches and both mouse and human-derived tridimensional organoid cultures, we report that miR-203 influences the self-renewal capacity, plasticity and differentiation potential of breast cancer cells and prevents tumor cell growth in vivo. Our work sheds light on differentiation-based antitumor therapies and offers miR-203 as a promising tool for directly confronting the tumor-maintaining and regeneration capability of cancer cells.This work has been in part financed by the crowdfunding project “Match point against breast cancer” (PRECIPITA PR242, 2019; FECYT; Spanish Ministry of Science and Innovation, MICINN, led by MS-R) and donations to Asociación Española contra el Cáncer (AECC). The work has been funded also by the Comunidad de Madrid (Y2020/BIO-6519 and S2022/BMD-7437) to MM, the Spanish Ministry of Science and Innovation through CNS2022-135364 to MS-R and PID2021-128726 to MM and the Spanish Ministry of Economy and Competitiveness by Instituto de Salud Carlos III (ISC III) through PI20/00590 to CS and co-funded by the European Union. MS-R was supported by AECC (AIOA120833SALA and INVES18005SALA), a Juan de la Cierva Incorporación and a Ramón y Cajal contract (RYC2020-028929-I, from the MICINN, FSE/ Agencia Estatal de Investigación). NGM-I was supported by AECC (PRDMA19003GARC)

Inactivation of Capicua in adult mice causes T-cell lymphoblastic lymphoma

CIC (also known as Capicua) is a transcriptional repressor negatively regulated by RAS/MAPK signaling. Whereas the functions of Cic have been well characterized in Drosophila, little is known about its role in mammals. CIC is inactivated in a variety of human tumors and has been implicated recently in the promotion of lung metastases. Here, we describe a mouse model in which we inactivated Cic by selectively disabling its DNA-binding activity, a mutation that causes derepression of its target genes. Germline Cic inactivation causes perinatal lethality due to lung differentiation defects. However, its systemic inactivation in adult mice induces T-cell acute lymphoblastic lymphoma (T-ALL), a tumor type known to carry CIC mutations, albeit with low incidence. Cic inactivation in mice induces T-ALL by a mechanism involving derepression of its well-known target, Etv4 Importantly, human T-ALL also relies on ETV4 expression for maintaining its oncogenic phenotype. Moreover, Cic inactivation renders T-ALL insensitive to MEK inhibitors in both mouse and human cell lines. Finally, we show that Ras-induced mouse T-ALL as well as human T-ALL carrying mutations in the RAS/MAPK pathway display a genetic signature indicative of Cic inactivation. These observations illustrate that CIC inactivation plays a key role in this human malignancy.We are grateful to Carol MacKintosh (University of Dundee, UK) for the pcDNA5/FRT/TO-GFP-CIC plasmid, and Huda Zoghbi (Baylor College of Medicine, Houston, TX) and Yoontae Lee (University of Pohang, Korea) for Cic antisera. We thank Scott Brown and Robert Holt (University of Vancouver, Canada) for their help with TCR abundance calculations. We also thank Carmen G. Lechuga, Marta San Roman, Raquel Villar, Beatriz Jimenez, and Nuria Cabrera for excellent technical assistance. We value the support of Sagrario Ortega (Transgenic Mice Core Unit, CNIO) for help in generating the Cic mutant mice, Orlando Dominguez (Genomics Core Unit, CNIO) for the RNA-seq analysis, and the Histopathology Core Unit. This work was supported by grants from the Fundacio La Marato de TV3 (20131730/1) to G.J. and M.B., and the European Research Council (ERC-AG/250297-RAS AHEAD), the EU-Framework Programme (HEALTH-F2-2010-259770/LUNGTARGET and HEALTH-2010-260791/EUROCANPLATFORM), the Spanish Ministry of Economy and Competitiveness (SAF2014-59864-R), the Autonomous Community of Madrid (S2011/BDM-2470/ONCOCYCLE), and the Asociacion Espanola contra el Cancer (AECC) (GC16173694BARB) to M.B. M.B. is the recipient of an Endowed Chair from the AXA Research Fund. L.S.-C. was supported by a fellowship from the Programa de Formacion de Personal Investigator (FPI) of the Spanish Ministry of Economy and Competitiveness. M.D. and M.B. conceived and designed the study. L.S.-C., O.G., G.J., M.D., and M.B. developed the methodology. L.S.-C., O.G., M.S., and M.D. acquired the data. L.S.-C., O.G., M.S., H.K.C.J., G.J., M.D., and M.B. analyzed and interpreted the data. L.S-C., O.G., G.J., M.D., and M.B. wrote, reviewed, and/or revised the manuscript. G.J. provided material support. A. G. analyzed the T-ALL sequencing. M.D. and M.B. supervised the study.S

Compi: a framework for portable and reproducible pipelines

Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii) application packaging, with compi-dk, which is a version-control-friendly tool to package the pipeline application and its dependencies into a Docker image; and (iii) application distribution provided through a public repository of Compi pipelines, named Compi Hub, which allows users to discover, browse and reuse them easily. By addressing these three aspects, Compi goes beyond traditional workflow engines, having been specially designed for researchers who want to take advantage of common workflow engine features (such as automatic job scheduling or logging, among others) while keeping the simplicity and readability of shell scripts without the need to learn a new programming language. Here we discuss the design of various pipelines developed with Compi to describe its main functionalities, as well as to highlight the similarities and differences with similar tools that are available. An open-source distribution under the Apache 2.0 License is available from GitHub (available at https://github.com/sing-group/compi). Documentation and installers are available from https://www.sing-group.org/compi. A specific repository for Compi pipelines is available from Compi Hub (available at https://www.sing-group.org/compihub

Luminal Rank loss decreases cell fitness leading to basal cell bipotency in parous mammary glands

Rank signaling pathway regulates mammary gland homeostasis and epithelial cell differentiation. Although Rank receptor is expressed by basal cells and luminal progenitors, its role in each individual cell lineage remains unclear. By combining temporal/lineage specific Rank genetic deletion with lineage tracing techniques, we found that loss of luminal Rank reduces the luminal progenitor pool and leads to aberrant alveolar-like differentiation with high protein translation capacity in virgin mammary glands. These Rank-deleted luminal cells are unable to expand during the first pregnancy, leading to lactation failure and impairment of protein synthesis potential in the parous stage. The unfit parous Rank-deleted luminal cells in the alveoli are progressively replaced by Rank-proficient cells early during the second pregnancy, thereby restoring lactation. Transcriptomic analysis and functional assays point to the awakening of basal bipotency after pregnancy by the induction of Rank/NF-kappa B signaling in basal parous cell to restore lactation and tissue homeostasis. Rocha and co-authors show that loss of luminal Rank signaling causes abnormal alveolar differentiation and lactation failure. Subsequent pregnancies activate bipotency in basal cells, replacing unfit luminal cells, and restoring lactation

Somatic genome editing with the RCAS-TVA-CRISPR-Cas9 system for precision tumor modeling

To accurately recapitulate the heterogeneity of human diseases, animal models require to recreate multiple complex genetic alterations. Here, we combine the RCAS-TVA system with the CRISPR-Cas9 genome editing tools for precise modeling of human tumors. We show that somatic deletion in neural stem cells of a variety of known tumor suppressor genes (Trp53, Cdkn2a, and Pten) leads to high-grade glioma formation. Moreover, by simultaneous delivery of pairs of guide RNAs we generate different gene fusions with oncogenic potential, either by chromosomal deletion (Bcan-Ntrk1) or by chromosomal translocation (Myb-Qk). Lastly, using homology-directed-repair, we also produce tumors carrying the homologous mutation to human BRAF V600E, frequently identified in a variety of tumors, including different types of gliomas. In summary, we have developed an extremely versatile mouse model for in vivo somatic genome editing, that will elicit the generation of more accurate cancer models particularly appropriate for pre-clinical testing.A.C.-G is recipient of a Severo-Ochoa PhD fellowship. C.M. and V.M. are recipients of a "La Caixa "PhD fellowship. We thank A.J. Schuhmacher for the initial assistance with the intracranial injections in adult mice and C.S. Clemente-Troncone for the technical support. We thank Carmen Blanco, David Olmeda, and Marisol Soengas for sharing reagents and Orlando Dominguez for the help with the design of the BRAF high- throughput sequencing. We sincerely thank Dr. José Luis Rodríguez Peralto (Hospital U. 12 de Octubre Madrid) for the BRAF V600 IHCs staining. This research was supported by funds from the Acción Estratégica en Salud Spanish National Research and Development Plan, Instituto de Salud Carlos III (ISCIII), cofounder by FEDER (ERDF) (PI14/01884) to S.R.-P., by a 017 Leonardo Grant for Researchers and Cultural Creators from the BBVA Foundation and a grant from the Seve Ballesteros Foundation to M.S.S