bims-crepig 2022-04-03 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022–04–03
nineteen papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit

Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs.
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer.
MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation.
Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes.
The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation.
H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats.
Rixosomal RNA degradation contributes to silencing of Polycomb target genes.
The role of insulators and transcription in 3D chromatin organization of flies.
CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells.
FOXK2 promotes ovarian cancer stemness by regulating the unfolded protein response pathway.
SHOOT: phylogenetic gene search and ortholog inference.
Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression.
Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma.
BarWare: efficient software tools for barcoded single-cell genomics.
Genome-wide identification and analysis of prognostic features in human cancers.
Complete genomic and epigenetic maps of human centromeres.
classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes.
NFκB activation by hypoxic small extracellular vesicles drives oncogenic reprogramming in a breast cancer microenvironment.

Biophys J. 2022 Mar 29. pii: S0006-3495(22)00237-5. [Epub ahead of print]

Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs.

Charles A Kenworthy, Nayem Haque, Shu-Hao Liou, Panagiotis Chandris, Vincent Wong, Patrycja Dziuba, Luke D Lavis, Wei-Li Liu, Robert H Singer, Robert A Coleman.

  Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF's bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome binding kinetic profiles that mimic chromatin stability. Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF's dynamic bromodomain mediated engagement of a nucleosome may reflect the chromatin remodeling potential of differentially bound chromatin states.

Keywords:  Histone H3.3; Histone acetylation; PBAF; Single Molecule Tracking; bromodomain; chromatin remodeling; nuclear hubs

DOI:  https://doi.org/10.1016/j.bpj.2022.03.027
NAR Cancer. 2022 Mar;4(1): zcac008

Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer.

Oslo Breast Cancer Consortium (OSBREAC)

Aberrant DNA methylation is an early event in breast carcinogenesis and plays a critical role in regulating gene expression. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL) analysis through the integration of DNA methylation and gene expression to identify disease-driving pathways under epigenetic control. By grouping the emQTLs using biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis including regulation of proliferation and tumor-infiltrating fibroblasts. We report genome-wide loss of enhancer methylation at binding sites of proliferation-driving transcription factors including CEBP-β, FOSL1, and FOSL2 with concomitant high expression of proliferation-related genes in aggressive breast tumors as we confirm with scRNA-seq. The identified emQTL-CpGs and genes were found connected through chromatin loops, indicating that proliferation in breast tumors is under epigenetic regulation by DNA methylation. Interestingly, the associations between enhancer methylation and proliferation-related gene expression were also observed within known subtypes of breast cancer, suggesting a common role of epigenetic regulation of proliferation. Taken together, we show that proliferation in breast cancer is linked to loss of methylation at specific enhancers and transcription factor binding and gene activation through chromatin looping.

DOI: https://doi.org/10.1093/narcan/zcac008
iScience. 2022 Apr 15. 25(4): 104058

MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation.

Xiaoming Zhang, Bo-Wen Zhang, Lue Xiang, Hui Wu, Supit Alva Sahiri Alexander, Peipei Zhou, Melvin Zi-Yu Dai, Xiaoyun Wang, Wenjun Xiong, Yan Zhang, Zi-Bing Jin, Lih-Wen Deng.

  Histone methylation, particularly at the H3K4 position, is thought to contribute to the specification of photoreceptor cell fate; however, the mechanisms linking histone methylation with transcription factor transactivation and photoreceptor gene expression have not yet been determined. Here, we demonstrate that MLL5 is abundantly expressed in the mouse retina. Mll5 deficiency impaired electroretinogram responses, alongside attenuated expression of a number of retina genes. Mechanistic studies revealed that MLL5 interacts with the retina-specific transcription factor, CRX, contributing to its binding to photoreceptor-specific gene promoters. Moreover, depletion of MLL5 impairs H3K4 methylation and H3K79 methylation, which subsequently compromises CRX-CBP assembly and H3 acetylation on photoreceptor promoters. Our data support a scenario in which recognition of H3K4 methylation by MLL5 is required for photoreceptor-specific gene transcription through maintaining a permissive chromatin state and proper CRX-CBP recruitment at promoter sites.

Keywords:  Biological sciences; Molecular biology; Molecular neuroscience; Neuroscience; Omics

DOI:  https://doi.org/10.1016/j.isci.2022.104058
Cell Rep. 2022 Mar 29. pii: S2211-1247(22)00349-7. [Epub ahead of print]38(13): 110601

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.

Andrea Esposito, Simona Bianco, Andrea M Chiariello, Alex Abraham, Luca Fiorillo, Mattia Conte, Raffaele Campanile, Mario Nicodemi.

  The mammalian genome has a complex, functional 3D organization. However, it remains largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we infer from only Hi-C the cell-type-specific arrangement of DNA binding sites sufficient to recapitulate, through polymer physics, contact patterns genome wide. Our model is validated by its predictions in a set of duplications at Sox9 against available independent data. The binding site types fall in classes that well match chromatin states from segmentation studies, yet they have an overlapping, combinatorial organization along chromosomes necessary to accurately explain contact specificity. The chromatin signatures of the binding site types return a code linking chromatin states to 3D architecture. The code is validated by extensive de novo predictions of Hi-C maps in an independent set of chromosomes. Overall, our results shed light on how 3D information is encrypted in 1D chromatin via the specific combinatorial arrangement of binding sites.

Keywords:  3D genome organization; CP: Molecular biology; biophysics; chromatin architecture; computer simulations; epigenomics; machine learning; polymer-physics

DOI:  https://doi.org/10.1016/j.celrep.2022.110601
J Cell Sci. 2022 Apr 01. pii: jcs.259456. [Epub ahead of print]

The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes.

Ludmila Recoules, Alexandre Heurteau, Flavien Raynal, Nezih Karasu, Fatima Moutahir, Fabienne Bejjani, Isabelle Jariel-Encontre, Olivier Cuvier, Thomas Sexton, Anne-Claire Lavigne, Kerstin Bystricky.

  The histone variant macroH2A1.1 plays a role in cancer development and metastasis. To determine the underlying molecular mechanisms, we mapped the genome-wide localization of endogenous macroH2A1.1 in the human breast cancer cell line MDA-MB 231. We demonstrate that macroH2A1.1 specifically binds to active promoters and enhancers in addition to facultative heterochromatin. Selective knock-down of macroH2A1.1 deregulates expression of hundreds of highly active genes. Depending on the chromatin landscape, macroH2A1.1 acts through two distinct molecular mechanisms. The first mitigates excessive transcription by binding over domains including the promoter and the gene body. The second stimulates expression of RNA Polymerase II (Pol II) paused genes, including genes regulating mammary tumor cell migration. In contrast to the first one, macroH2A1.1 specifically associates with the TSS of Pol II paused genes. These processes occur in a predefined local 3D genome landscape but do not require rewiring of enhancer-promoter contacts. We thus propose that macroH2A1.1 serves as a transcriptional modulator with a potential role in assisting the conversion of promoter-locked into a productive and elongating Pol II.

Keywords:  Breast cancer; Cellular migration; Chromatin structure; Gene expression; Histone variants; RNA Polymerase II paused genes

DOI:  https://doi.org/10.1242/jcs.259456
Sci Adv. 2022 Apr;8(13): eabj8360

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation.

Lorenzo Rinaldi, Gregory Fettweis, Sohyoung Kim, David A Garcia, Saori Fujiwara, Thomas A Johnson, Theophilus T Tettey, Laurent Ozbun, Gianluca Pegoraro, Michele Puglia, Blagoy Blagoev, Arpita Upadhyaya, Diana A Stavreva, Gordon L Hager.

The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.

DOI: https://doi.org/10.1126/sciadv.abj8360
Genes Dev. 2022 Mar 31.

H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats.

Francesco Gualdrini, Sara Polletti, Marta Simonatto, Elena Prosperini, Francesco Pileri, Gioacchino Natoli.

  Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification controlling constitutive heterochromatin, gene repression, and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin domains to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the impact of SETDB1 on stimulus-inducible gene expression in macrophages, we found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE B2 repeats enhanced insulation at hundreds of sites and increased loop formation within topological domains containing lipopolysaccharide-inducible genes, which correlated with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with an impact on chromatin organization and gene regulation.

Keywords:  CTCF; H3K9me3; histone methylation; macrophages; topological domains; transposable elements

DOI:  https://doi.org/10.1101/gad.349282.121
Nature. 2022 Mar 30.

Rixosomal RNA degradation contributes to silencing of Polycomb target genes.

Haining Zhou, Chad B Stein, Tiasha A Shafiq, Gergana Shipkovenska, Marian Kalocsay, Joao A Paulo, Jiuchun Zhang, Zhenhua Luo, Steven P Gygi, Karen Adelman, Danesh Moazed.

Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are histone-modifying and -binding complexes that mediate the formation of facultative heterochromatin and are required for silencing of developmental genes and maintenance of cell fate1-3. Multiple pathways of RNA decay work together to establish and maintain heterochromatin in fission yeast, including a recently identified role for a conserved RNA-degradation complex known as the rixosome or RIX1 complex4-6. Whether RNA degradation also has a role in the stability of mammalian heterochromatin remains unknown. Here we show that the rixosome contributes to silencing of many Polycomb targets in human cells. The rixosome associates with human PRC complexes and is enriched at promoters of Polycomb target genes. Depletion of either the rixosome or Polycomb results in accumulation of paused and elongating RNA polymerase at Polycomb target genes. We identify point mutations in the RING1B subunit of PRC1 that disrupt the interaction between PRC1 and the rixosome and result in diminished silencing, suggesting that direct recruitment of the rixosome to chromatin is required for silencing. Finally, we show that the RNA endonuclease and kinase activities of the rixosome and the downstream XRN2 exoribonuclease, which degrades RNAs with 5' monophosphate groups generated by the rixosome, are required for silencing. Our findings suggest that rixosomal degradation of nascent RNA is conserved from fission yeast to human, with a primary role in RNA degradation at facultative heterochromatin in human cells.

DOI: https://doi.org/10.1038/s41586-022-04598-0
Genome Res. 2022 Mar 30.

The role of insulators and transcription in 3D chromatin organization of flies.

Keerthi T Chathoth, Liudmila A Mikheeva, Gilles Crevel, Jareth C Wolfe, Ioni Hunter, Saskia Beckett-Doyle, Sue Cotterill, Hongsheng Dai, Andrew Harrison, Nicolae Radu Zabet.

The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.

DOI: https://doi.org/10.1101/gr.275809.121
PLoS One. 2022 ;17(3): e0262378

CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells.

Archana Bommi-Reddy, Sungmi Park-Chouinard, David N Mayhew, Esteban Terzo, Aparna Hingway, Michael J Steinbaugh, Jonathan E Wilson, Robert J Sims, Andrew R Conery.

Therapeutic targeting of the estrogen receptor (ER) is a clinically validated approach for estrogen receptor positive breast cancer (ER+ BC), but sustained response is limited by acquired resistance. Targeting the transcriptional coactivators required for estrogen receptor activity represents an alternative approach that is not subject to the same limitations as targeting estrogen receptor itself. In this report we demonstrate that the acetyltransferase activity of coactivator paralogs CREBBP/EP300 represents a promising therapeutic target in ER+ BC. Using the potent and selective inhibitor CPI-1612, we show that CREBBP/EP300 acetyltransferase inhibition potently suppresses in vitro and in vivo growth of breast cancer cell line models and acts in a manner orthogonal to directly targeting ER. CREBBP/EP300 acetyltransferase inhibition suppresses ER-dependent transcription by targeting lineage-specific enhancers defined by the pioneer transcription factor FOXA1. These results validate CREBBP/EP300 acetyltransferase activity as a viable target for clinical development in ER+ breast cancer.

DOI: https://doi.org/10.1371/journal.pone.0262378
J Clin Invest. 2022 Mar 29. pii: e151591. [Epub ahead of print]

FOXK2 promotes ovarian cancer stemness by regulating the unfolded protein response pathway.

Yaqi Zhang, Yinu Wang, Guangyuan Zhao, Edward J Tanner, Mazhar Adli, Daniela Matei.

  Understanding the regulatory programs enabling cancer stem cells (CSCs) to self-renew and drive tumorigenicity could identify new treatments. Through comparative chromatin state and gene expression analyses in ovarian CSCs vs. non-CSCs, we identified FOXK2 as a highly expressed stemness-specific transcription factor in ovarian cancer. Its genetic depletion diminished stemness features and reduced tumor initiation capacity. Our mechanistic studies highlight that FOXK2 directly regulated IRE1α (ERN1 gene) expression, a key sensor for the unfolded protein response (UPR). Chromatin immunoprecipitation-sequencing revealed that FOXK2 bound to an intronic regulatory element of ERN1. Blocking FOXK2 from binding to this enhancer by using a catalytically inactive CRISPR/Cas9 (dCas9) diminished IRE1α transcription. At the molecular level, FOXK2-driven upregulation of IRE1α led to alternative XBP1 splicing and activation of stemness pathways, while genetic or pharmacological blockade of this sensor of the UPR inhibited ovarian CSCs. Collectively, these data establish a new function for FOXK2 as a key transcriptional regulator of CSCs and a mediator of the UPR, providing insight into potentially targetable new pathways in CSCs.

Keywords:  Cancer; Cell Biology; Cell stress; Oncology; Transcription

DOI:  https://doi.org/10.1172/JCI151591
Genome Biol. 2022 Mar 28. 23(1): 85

SHOOT: phylogenetic gene search and ortholog inference.

David Mark Emms, Steven Kelly.

  Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional tree inference, and it can identify orthologs with high accuracy. In summary, SHOOT is a fast and accurate tool for phylogenetic analyses of novel query sequences. It is available online at www.shoot.bio .

Keywords:  Orthology inference; Phylogenetic tree inference; Sequence similarity search

DOI:  https://doi.org/10.1186/s13059-022-02652-8
Mol Cell. 2022 Mar 22. pii: S1097-2765(22)00213-1. [Epub ahead of print]

Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression.

William Garland, Iris Müller, Mengjun Wu, Manfred Schmid, Katsutoshi Imamura, Leonor Rib, Albin Sandelin, Kristian Helin, Torben Heick Jensen.

  Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous "nuclear exosome targeting" (NEXT) and "human silencing hub" (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs.

Keywords:  HUSH complex; NEXT complex; RNA decay; RNA exosome; retrotransposons; transposable elements

DOI:  https://doi.org/10.1016/j.molcel.2022.03.004
Nat Commun. 2022 Mar 30. 13(1): 1677

Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma.

Karin D Prummel, Helena L Crowell, Susan Nieuwenhuize, Eline C Brombacher, Stephan Daetwyler, Charlotte Soneson, Jelena Kresoja-Rakic, Agnese Kocere, Manuel Ronner, Alexander Ernst, Zahra Labbaf, David E Clouthier, Anthony B Firulli, Héctor Sánchez-Iranzo, Sundar R Naganathan, Rebecca O'Rourke, Erez Raz, Nadia Mercader, Alexa Burger, Emanuela Felley-Bosco, Jan Huisken, Mark D Robinson, Christian Mosimann.

The mesothelium lines body cavities and surrounds internal organs, widely contributing to homeostasis and regeneration. Mesothelium disruptions cause visceral anomalies and mesothelioma tumors. Nonetheless, the embryonic emergence of mesothelia remains incompletely understood. Here, we track mesothelial origins in the lateral plate mesoderm (LPM) using zebrafish. Single-cell transcriptomics uncovers a post-gastrulation gene expression signature centered on hand2 in distinct LPM progenitor cells. We map mesothelial progenitors to lateral-most, hand2-expressing LPM and confirm conservation in mouse. Time-lapse imaging of zebrafish hand2 reporter embryos captures mesothelium formation including pericardium, visceral, and parietal peritoneum. We find primordial germ cells migrate with the forming mesothelium as ventral migration boundary. Functionally, hand2 loss disrupts mesothelium formation with reduced progenitor cells and perturbed migration. In mouse and human mesothelioma, we document expression of LPM-associated transcription factors including Hand2, suggesting re-initiation of a developmental program. Our data connects mesothelium development to Hand2, expanding our understanding of mesothelial pathologies.

DOI: https://doi.org/10.1038/s41467-022-29311-7
BMC Bioinformatics. 2022 Mar 27. 23(1): 106

BarWare: efficient software tools for barcoded single-cell genomics.

Elliott Swanson, Julian Reading, Lucas T Graybuck, Peter J Skene.

   BACKGROUND: Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are additional complications in the data deconvolution steps required to assign each cell to their originating samples.
RESULTS: To meet computational needs for efficient sample deconvolution, we developed the tools BarCounter and BarMixer that compute barcode counts and deconvolute mixed single-cell data into sample-specific files, respectively. Together, these tools are implemented as the BarWare pipeline to support demultiplexing from large sequencing projects with many wells of hashed 10x Genomics scRNA-seq data.
CONCLUSIONS: BarWare is a modular set of tools linked by shell scripting: BarCounter, a computationally efficient barcode sequence quantification tool implemented in C; and BarMixer, an R package for identification of barcoded populations, merging barcoded data from multiple wells, and quality-control reporting related to scRNA-seq data. These tools and a self-contained implementation of the pipeline are freely available for non-commercial use at https://github.com/AllenInstitute/BarWare-pipeline .

Keywords:  Cell hashing; Demultiplexing; Genomics; Single-cell RNA-seq

DOI:  https://doi.org/10.1186/s12859-022-04620-2
Cell Rep. 2022 Mar 29. pii: S2211-1247(22)00313-8. [Epub ahead of print]38(13): 110569

Genome-wide identification and analysis of prognostic features in human cancers.

Joan C Smith, Jason M Sheltzer.

  Clinical decisions in cancer rely on precisely assessing patient risk. To improve our ability to identify the most aggressive malignancies, we constructed genome-wide survival models using gene expression, copy number, methylation, and mutation data from 10,884 patients. We identified more than 100,000 significant prognostic biomarkers and demonstrate that these genomic features can predict patient outcomes in clinically ambiguous situations. While adverse biomarkers are commonly believed to represent cancer driver genes and promising therapeutic targets, we show that cancer features associated with shorter survival times are not enriched for either oncogenes or for successful drug targets. Instead, the strongest adverse biomarkers represent widely expressed cell-cycle and housekeeping genes, and, correspondingly, nearly all therapies directed against these features have failed in clinical trials. In total, our analysis establishes a rich resource for prognostic biomarker analysis and clarifies the use of patient survival data in preclinical cancer research and therapeutic development.

Keywords:  CP: Cancer; CP: Molecular biology; biomarkers; cancer genomics; drug targets

DOI:  https://doi.org/10.1016/j.celrep.2022.110569
Science. 2022 Apr;376(6588): eabl4178

Complete genomic and epigenetic maps of human centromeres.

Nicolas Altemose, Glennis A Logsdon, Andrey V Bzikadze, Pragya Sidhwani, Sasha A Langley, Gina V Caldas, Savannah J Hoyt, Lev Uralsky, Fedor D Ryabov, Colin J Shew, Michael E G Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R Vollger, Arang Rhie, Ann M McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Julian K Lucas, Sergey Aganezov, Daniel Olson, Leonardo Gomes de Lima, Tamara Potapova, Gabrielle A Hartley, Marina Haukness, Peter Kerpedjiev, Fedor Gusev, Kristof Tigyi, Shelise Brooks, Alice Young, Sergey Nurk, Sergey Koren, Sofie R Salama, Benedict Paten, Evgeny I Rogaev, Aaron Streets, Gary H Karpen, Abby F Dernburg, Beth A Sullivan, Aaron F Straight, Travis J Wheeler, Jennifer L Gerton, Evan E Eichler, Adam M Phillippy, Winston Timp, Megan Y Dennis, Rachel J O'Neill, Justin M Zook, Michael C Schatz, Pavel A Pevzner, Mark Diekhans, Charles H Langley, Ivan A Alexandrov, Karen H Miga.

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

DOI: https://doi.org/10.1126/science.abl4178
BMC Bioinformatics. 2022 Mar 31. 23(1): 114

classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes.

Gerard P Quinn, Tamas Sessler, Baharak Ahmaderaghi, Shauna Lambe, Harper VanSteenhouse, Mark Lawler, Mark Wappett, Bruce Seligmann, Daniel B Longley, Simon S McDade.

   BACKGROUND: Transcriptionally informed predictions are increasingly important for sub-typing cancer patients, understanding underlying biology and to inform novel treatment strategies. For instance, colorectal cancers (CRCs) can be classified into four CRC consensus molecular subgroups (CMS) or five intrinsic (CRIS) sub-types that have prognostic and predictive value. Breast cancer (BRCA) has five PAM50 molecular subgroups with similar value, and the OncotypeDX test provides transcriptomic based clinically actionable treatment-risk stratification. However, assigning samples to these subtypes and other transcriptionally inferred predictions is time consuming and requires significant bioinformatics experience. There is no "universal" method of using data from diverse assay/sequencing platforms to provide subgroup classification using the established classifier sets of genes (CMS, CRIS, PAM50, OncotypeDX), nor one which in provides additional useful functional annotations such as cellular composition, single-sample Gene Set Enrichment Analysis, or prediction of transcription factor activity.
RESULTS: To address this bottleneck, we developed classifieR, an easy-to-use R-Shiny based web application that supports flexible rapid single sample annotation of transcriptional profiles derived from cancer patient samples form diverse platforms. We demonstrate the utility of the " classifieR" framework to applications focused on the analysis of transcriptional profiles from colorectal (classifieRc) and breast (classifieRb). Samples are annotated with disease relevant transcriptional subgroups (CMS/CRIS sub-types in classifieRc and PAM50/inferred OncotypeDX in classifieRb), estimation of cellular composition using MCP-counter and xCell, single-sample Gene Set Enrichment Analysis (ssGSEA) and transcription factor activity predictions with Discriminant Regulon Expression Analysis (DoRothEA).
CONCLUSIONS: classifieR provides a framework which enables labs without access to a dedicated bioinformation can get information on the molecular makeup of their samples, providing an insight into patient prognosis, druggability and also as a tool for analysis and discovery. Applications are hosted online at https://generatr.qub.ac.uk/app/classifieRc and https://generatr.qub.ac.uk/app/classifieRb after signing up for an account on https://generatr.qub.ac.uk .

Keywords:  Cancer Subtype; Colorectal Shiny CMS CRIS Immune; Functional Annotation; Gene expression; Shiny application

DOI:  https://doi.org/10.1186/s12859-022-04641-x
Oncogene. 2022 Mar 30.

NFκB activation by hypoxic small extracellular vesicles drives oncogenic reprogramming in a breast cancer microenvironment.

Irene Bertolini, Michela Perego, Jagadish C Ghosh, Andrew V Kossenkov, Dario C Altieri.

Small extracellular vesicles (sEV) contribute to the crosstalk between tumor cells and stroma, but the underlying signals are elusive. Here, we show that sEV generated by breast cancer cells in hypoxic (sEVHYP), but not normoxic (sEVNORM) conditions activate NFκB in recipient normal mammary epithelial cells. This increases the production and release of inflammatory cytokines, promotes mitochondrial dynamics leading to heightened cell motility and disrupts 3D mammary acini architecture with aberrant cell proliferation, reduced apoptosis and EMT. Mechanistically, Integrin-Linked Kinase packaged in sEVHYP via HIF1α is sufficient to activate NFκB in the normal mammary epithelium, in vivo. Therefore, sEVHYP activation of NFκB drives multiple oncogenic steps of inflammation, mitochondrial dynamics, and mammary gland morphogenesis in a breast cancer microenvironment.

DOI: https://doi.org/10.1038/s41388-022-02280-3