bims-ginsta 2024-06-09 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024‒06‒09
34 papers selected by
Jinrong Hu, National University of Singapore

Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators.
Capturing totipotency in human cells through spliceosomal repression.
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.
Cell-size-dependent regulation of Ezrin dictates epithelial resilience to stretch by countering myosin-II-mediated contractility.
The ribotoxic stress response drives UV-mediated cell death.
Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells.
FAK regulates tension transmission to the nucleus and endothelial transcriptome independent of kinase activity.
Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency.
IRE1α Mediates the Hypertrophic Growth of Cardiomyocytes Through Facilitating the Formation of Initiation Complex to Promote the Translation of TOP-Motif Transcripts.
Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer.
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development.
Naive pluripotent stem cell-based models capture FGF-dependent human hypoblast lineage specification.
Scaling behaviour and control of nuclear wrinkling.
Cardiac Fibroblastic Niches in Homeostasis and Inflammation.
Single-cell nascent RNA sequencing unveils coordinated global transcription.
Cardiomyocyte βII spectrin plays a critical role in maintaining cardiac function by regulating mitochondrial respiratory function.
Senescent glia link mitochondrial dysfunction and lipid accumulation.
Single-cell and spatiotemporal profile of ovulation in the mouse ovary.
MYCT1 controls environmental sensing in human haematopoietic stem cells.
Extraembryonic gut endoderm cells undergo programmed cell death during development.
TCF3, TCF12 and distinct enhancers regulate oocyte transcription.
SenNet recommendations for detecting senescent cells in different tissues.
Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila.
Runx1 is sufficient but not required for cardiomyocyte cell cycle activation.
Setdb1 protects genome integrity in murine muscle stem cells to allow for regenerative myogenesis and inflammation.
Transient stabilization of human cardiovascular progenitor cells from hPSCs in vitro reflects stage-specific heart development in vivo.
Whole-body replacement of larval myofibers generates permanent adult myofibers in zebrafish.
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts.
CENP-E inhibition induces chromosomal instability and synergizes with diverse microtubule-targeting agents in breast cancer.
Clonal hematopoiesis driven by mutated DNMT3A promotes inflammatory bone loss.
Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics.
Increased endothelial sclerostin caused by elevated DSCAM mediates multiple trisomy 21 phenotypes.
Developmental origin of oligodendrocytes determines their function in the adult brain.
Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging.

Nat Cell Biol. 2024 Jun 05.

Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators.

Bofeng Liu, Yuanlin He, Xiaotong Wu, Zili Lin, Jing Ma, Yuexin Qiu, Yunlong Xiang, Feng Kong, Fangnong Lai, Mrinmoy Pal, Peizhe Wang, Jia Ming, Bingjie Zhang, Qiujun Wang, Jingyi Wu, Weikun Xia, Weimin Shen, Jie Na, Maria-Elena Torres-Padilla, Jing Li, Wei Xie.

Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbour prevalent putative enhancers in fully grown oocytes linked to oocyte-specific genes and repeat activation. Embryo-specific enhancers are primed before zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis, TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting transcription factors that underpin the development of mammalian oocytes and early embryos.

DOI: https://doi.org/10.1038/s41556-024-01422-x
Cell. 2024 Jun 03. pii: S0092-8674(24)00519-1. [Epub ahead of print]

Capturing totipotency in human cells through spliceosomal repression.

Shiyu Li, Min Yang, Hui Shen, Li Ding, Xuehui Lyu, Kexin Lin, Jennie Ong, Peng Du.

  The cleavage of zygotes generates totipotent blastomeres. In human 8-cell blastomeres, zygotic genome activation (ZGA) occurs to initiate the ontogenesis program. However, capturing and maintaining totipotency in human cells pose significant challenges. Here, we realize culturing human totipotent blastomere-like cells (hTBLCs). We find that splicing inhibition can transiently reprogram human pluripotent stem cells into ZGA-like cells (ZLCs), which subsequently transition into stable hTBLCs after long-term passaging. Distinct from reported 8-cell-like cells (8CLCs), both ZLCs and hTBLCs widely silence pluripotent genes. Interestingly, ZLCs activate a particular group of ZGA-specific genes, and hTBLCs are enriched with pre-ZGA-specific genes. During spontaneous differentiation, hTBLCs re-enter the intermediate ZLC stage and further generate epiblast (EPI)-, primitive endoderm (PrE)-, and trophectoderm (TE)-like lineages, effectively recapitulating human pre-implantation development. Possessing both embryonic and extraembryonic developmental potency, hTBLCs can autonomously generate blastocyst-like structures in vitro without external cell signaling. In summary, our study provides key criteria and insights into human cell totipotency.

Keywords:  ZGA-like cells; blastocyst-like structure; blastomere; pluripotent; splicing inhibition; stem cell culture; totipotency; totipotent blastomere-like cells; zygotic genomic activation

DOI:  https://doi.org/10.1016/j.cell.2024.05.010
Dev Cell. 2024 May 30. pii: S1534-5807(24)00327-7. [Epub ahead of print]

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

Brian T Do, Peggy P Hsu, Sidney Y Vermeulen, Zhishan Wang, Taghreed Hirz, Keene L Abbott, Najihah Aziz, Joseph M Replogle, Stefan Bjelosevic, Jonathan Paolino, Samantha A Nelson, Samuel Block, Alicia M Darnell, Raphael Ferreira, Hanyu Zhang, Jelena Milosevic, Daniel R Schmidt, Christopher Chidley, Isaac S Harris, Jonathan S Weissman, Yana Pikman, Kimberly Stegmaier, Sihem Cheloufi, Xiaofeng A Su, David B Sykes, Matthew G Vander Heiden.

  Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.

Keywords:  cancer; cell fate; cell state; dependencies; differentiation; epigenetics; hematopoiesis; metabolism; nucleotides; replication; replication stress

DOI:  https://doi.org/10.1016/j.devcel.2024.05.010
Cell Rep. 2024 May 31. pii: S2211-1247(24)00599-0. [Epub ahead of print]43(6): 114271

Cell-size-dependent regulation of Ezrin dictates epithelial resilience to stretch by countering myosin-II-mediated contractility.

Geetika Chouhan, Natasha Steffi Lewis, Vallari Ghanekar, Sri Rama Koti Ainavarapu, Mandar M Inamdar, Mahendra Sonawane.

  The epithelial adaptations to mechanical stress are facilitated by molecular and tissue-scale changes that include the strengthening of junctions, cytoskeletal reorganization, and cell-proliferation-mediated changes in tissue rheology. However, the role of cell size in controlling these properties remains underexplored. Our experiments in the zebrafish embryonic epidermis, guided by theoretical estimations, reveal a link between epithelial mechanics and cell size, demonstrating that an increase in cell size compromises the tissue fracture strength and compliance. We show that an increase in E-cadherin levels in the proliferation-deficient epidermis restores epidermal compliance but not the fracture strength, which is largely regulated by Ezrin-an apical membrane-cytoskeleton crosslinker. We show that Ezrin fortifies the epithelium in a cell-size-dependent manner by countering non-muscle myosin-II-mediated contractility. This work uncovers the importance of cell size maintenance in regulating the mechanical properties of the epithelium and fostering protection against future mechanical stresses.

Keywords:  2D vertex model; CP: Cell biology; CP: Developmental biology; Ezrin; cell adhesion; cell proliferation; cell size; epithelial resilience; epithelium; myosin contractility

DOI:  https://doi.org/10.1016/j.celrep.2024.114271
Cell. 2024 May 31. pii: S0092-8674(24)00527-0. [Epub ahead of print]

The ribotoxic stress response drives UV-mediated cell death.

Niladri K Sinha, Connor McKenney, Zhong Y Yeow, Jeffrey J Li, Ki Hong Nam, Tomer M Yaron-Barir, Jared L Johnson, Emily M Huntsman, Lewis C Cantley, Alban Ordureau, Sergi Regot, Rachel Green.

  While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.

Keywords:  DNA damage response; GCN2; UV radiation; ZAK; apoptosis; collisions; phosphoproteomics; ribosomes; ribotoxic stress; signaling

DOI:  https://doi.org/10.1016/j.cell.2024.05.018
Dev Cell. 2024 May 28. pii: S1534-5807(24)00326-5. [Epub ahead of print]

Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells.

Boyan Huang, Xing Peng, Xuzhao Zhai, Jie Hu, Junyu Chen, Suming Yang, Qingpei Huang, Enze Deng, Huanhuan Li, Tahsin Stefan Barakat, Jiekai Chen, Duanqing Pei, Xiaoying Fan, Ian Chambers, Man Zhang.

  Embryonic stem cells (ESCs) can differentiate into all cell types of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which is not fully understood. Here, we show that treating mouse ESCs with sodium butyrate (NaB) increases the population of 2C-like cells and enables direct reprogramming of ESCs into trophoblast stem cells (TSCs) without a transition through a 2C-like state. Mechanistically, NaB inhibits histone deacetylase activities in the LSD1-HDAC1/2 corepressor complex. This increases acetylation levels in the regulatory regions of both 2C- and TSC-specific genes, promoting their expression. In addition, NaB-treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and form deciduae in vivo. These results identify how epigenetics restrict the totipotent and trophectoderm fate in mouse ESCs.

Keywords:  2C-like cells; ESCs; HDACi; TSCs; blastoids; totipotency; transdifferentiation

DOI:  https://doi.org/10.1016/j.devcel.2024.05.009
Cell Rep. 2024 May 31. pii: S2211-1247(24)00625-9. [Epub ahead of print]43(6): 114297

FAK regulates tension transmission to the nucleus and endothelial transcriptome independent of kinase activity.

Md Zahid Akhter, Pascal Yazbeck, Mohammad Tauseef, Mumtaz Anwar, Faruk Hossen, Sayanti Datta, Vigneshwaran Vellingiri, Jagdish Chandra Joshi, Peter T Toth, Nityanand Srivastava, Stephen Lenzini, Guangjin Zhou, James Lee, Mukesh K Jain, Jae-Won Shin, Dolly Mehta.

  The mechanical environment generated through the adhesive interaction of endothelial cells (ECs) with the matrix controls nuclear tension, preventing aberrant gene synthesis and the transition from restrictive to leaky endothelium, a hallmark of acute lung injury (ALI). However, the mechanisms controlling tension transmission to the nucleus and EC-restrictive fate remain elusive. Here, we demonstrate that, in a kinase-independent manner, focal adhesion kinase (FAK) safeguards tension transmission to the nucleus to maintain EC-restrictive fate. In FAK-depleted ECs, robust activation of the RhoA-Rho-kinase pathway increased EC tension and phosphorylation of the nuclear envelope protein, emerin, activating DNMT3a. Activated DNMT3a methylates the KLF2 promoter, impairing the synthesis of KLF2 and its target S1PR1 to induce the leaky EC transcriptome. Repleting FAK (wild type or kinase dead) or inhibiting RhoA-emerin-DNMT3a activities in damaged lung ECs restored KLF2 transcription of the restrictive EC transcriptome. Thus, FAK sensing and control of tension transmission to the nucleus govern restrictive endothelium to maintain lung homeostasis.

Keywords:  CP: Cell biology; DNA methylation; DNMT3a; FAK; KLF2; S1PR1; emerin; endothelial cell; intracellular tension; stiffness

DOI:  https://doi.org/10.1016/j.celrep.2024.114297
Nat Commun. 2024 Jun 03. 15(1): 4716

Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency.

Liana Goehring, Sarah Keegan, Sudipta Lahiri, Wenxin Xia, Michael Kong, Judit Jimenez-Sainz, Dipika Gupta, Ronny Drapkin, Ryan B Jensen, Duncan J Smith, Eli Rothenberg, David Fenyö, Tony T Huang.

BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.

DOI: https://doi.org/10.1038/s41467-024-48286-1
Circulation. 2024 Jun 05.

IRE1α Mediates the Hypertrophic Growth of Cardiomyocytes Through Facilitating the Formation of Initiation Complex to Promote the Translation of TOP-Motif Transcripts.

Chao Li, Shiqian Li, Guangyu Zhang, Qinfeng Li, Weidan Song, Xiaoding Wang, Jane A Cook, Miesje van der Stoel, Bradley W Wright, Francisco Altamirano, Erica L Niewold, Jungsoo Han, Garrett Kimble, Pengfei Zhang, Xiang Luo, Hery Urra, Herman I May, Anwarul Ferdous, Xue-Nan Sun, Yingfeng Deng, Elina Ikonen, Claudio Hetz, Randal J Kaufman, Kezhong Zhang, Thomas G Gillette, Philipp E Scherer, Joseph A Hill, Jin Chen, Zhao V Wang.

  BACKGROUND: Cardiomyocyte growth is coupled with active protein synthesis, which is one of the basic biological processes in living cells. However, it is unclear whether the unfolded protein response transducers and effectors directly take part in the control of protein synthesis. The connection between critical functions of the unfolded protein response in cellular physiology and requirements of multiple processes for cell growth prompted us to investigate the role of the unfolded protein response in cell growth and underlying molecular mechanisms.METHODS: Cardiomyocyte-specific inositol-requiring enzyme 1α (IRE1α) knockout and overexpression mouse models were generated to explore its function in vivo. Neonatal rat ventricular myocytes were isolated and cultured to evaluate the role of IRE1α in cardiomyocyte growth in vitro. Mass spectrometry was conducted to identify novel interacting proteins of IRE1α. Ribosome sequencing and polysome profiling were performed to determine the molecular basis for the function of IRE1α in translational control.
RESULTS: We show that IRE1α is required for cell growth in neonatal rat ventricular myocytes under prohypertrophy treatment and in HEK293 cells in response to serum stimulation. At the molecular level, IRE1α directly interacts with eIF4G and eIF3, 2 critical components of the translation initiation complex. We demonstrate that IRE1α facilitates the formation of the translation initiation complex around the endoplasmic reticulum and preferentially initiates the translation of transcripts with 5' terminal oligopyrimidine motifs. We then reveal that IRE1α plays an important role in determining the selectivity and translation of these transcripts. We next show that IRE1α stimulates the translation of epidermal growth factor receptor through an unannotated terminal oligopyrimidine motif in its 5' untranslated region. We further demonstrate a physiological role of IRE1α-governed protein translation by showing that IRE1α is essential for cardiomyocyte growth and cardiac functional maintenance under hemodynamic stress in vivo.
CONCLUSIONS: These studies suggest a noncanonical, essential role of IRE1α in orchestrating protein synthesis, which may have important implications in cardiac hypertrophy in response to pressure overload and general cell growth under other physiological and pathological conditions.

Keywords:  EGFR protein, mouse; heart failure; hypertrophy; protein synthesis inhibitors

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.067606
Science. 2024 Jun 07. 384(6700): eadk0850

Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer.

Jennifer E Klomp, J Nathaniel Diehl, Jeffrey A Klomp, A Cole Edwards, Runying Yang, Alexis J Morales, Khalilah E Taylor, Kristina Drizyte-Miller, Kirsten L Bryant, Antje Schaefer, Jared L Johnson, Emily M Huntsman, Tomer M Yaron, Mariaelena Pierobon, Elisa Baldelli, Alex W Prevatte, Natalie K Barker, Laura E Herring, Emanuel F Petricoin, Lee M Graves, Lewis C Cantley, Adrienne D Cox, Channing J Der, Clint A Stalnecker.

To delineate the mechanisms by which the ERK1 and ERK2 mitogen-activated protein kinases support mutant KRAS-driven cancer growth, we determined the ERK-dependent phosphoproteome in KRAS-mutant pancreatic cancer. We determined that ERK1 and ERK2 share near-identical signaling and transforming outputs and that the KRAS-regulated phosphoproteome is driven nearly completely by ERK. We identified 4666 ERK-dependent phosphosites on 2123 proteins, of which 79 and 66%, respectively, were not previously associated with ERK, substantially expanding the depth and breadth of ERK-dependent phosphorylation events and revealing a considerably more complex function for ERK in cancer. We established that ERK controls a highly dynamic and complex phosphoproteome that converges on cyclin-dependent kinase regulation and RAS homolog guanosine triphosphatase function (RHO GTPase). Our findings establish the most comprehensive molecular portrait and mechanisms by which ERK drives KRAS-dependent pancreatic cancer growth.

DOI: https://doi.org/10.1126/science.adk0850
Nat Struct Mol Biol. 2024 Jun 04.

XIST dampens X chromosome activity in a SPEN-dependent manner during early human development.

Charbel Alfeghaly, Gaël Castel, Emmanuel Cazottes, Madeleine Moscatelli, Eva Moinard, Miguel Casanova, Juliette Boni, Kasturi Mahadik, Jenna Lammers, Thomas Freour, Louis Chauviere, Carla Piqueras, Ruben Boers, Joachim Boers, Joost Gribnau, Laurent David, Jean-François Ouimette, Claire Rougeulle.

XIST (X-inactive specific transcript) long noncoding RNA (lncRNA) is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female preimplantation embryos without triggering X chromosome silencing. The XACT (X-active coating transcript) lncRNA coaccumulates with XIST on active X chromosomes and may antagonize XIST function. Here, we used human embryonic stem cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during preimplantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and dampens the transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional before XCI, confirms the existence of a transient process of X chromosome dosage compensation and reveals that XCI and dampening rely on the same set of factors.

DOI: https://doi.org/10.1038/s41594-024-01325-3
Cell Stem Cell. 2024 May 24. pii: S1934-5909(24)00180-2. [Epub ahead of print]

Naive pluripotent stem cell-based models capture FGF-dependent human hypoblast lineage specification.

Anish Dattani, Elena Corujo-Simon, Arthur Radley, Tiam Heydari, Yasaman Taheriabkenar, Francesca Carlisle, Simeng Lin, Corin Liddle, Jonathan Mill, Peter W Zandstra, Jennifer Nichols, Ge Guo.

  The hypoblast is an essential extraembryonic tissue set aside within the inner cell mass in the blastocyst. Research with human embryos is challenging. Thus, stem cell models that reproduce hypoblast differentiation provide valuable alternatives. We show here that human naive pluripotent stem cell (PSC) to hypoblast differentiation proceeds via reversion to a transitional ICM-like state from which the hypoblast emerges in concordance with the trajectory in human blastocysts. We identified a window when fibroblast growth factor (FGF) signaling is critical for hypoblast specification. Revisiting FGF signaling in human embryos revealed that inhibition in the early blastocyst suppresses hypoblast formation. In vitro, the induction of hypoblast is synergistically enhanced by limiting trophectoderm and epiblast fates. This finding revises previous reports and establishes a conservation in lineage specification between mice and humans. Overall, this study demonstrates the utility of human naive PSC-based models in elucidating the mechanistic features of early human embryogenesis.

Keywords:  FGF; blastocyst; cell fate; embryo model; human naive pluripotent stem cells; hypoblast

DOI:  https://doi.org/10.1016/j.stem.2024.05.003
Nat Phys. 2023 Dec;19(12): 1927-1935

Scaling behaviour and control of nuclear wrinkling.

Jonathan A Jackson, Nicolas Romeo, Alexander Mietke, Keaton J Burns, Jan F Totz, Adam C Martin, Jörn Dunkel, Jasmin Imran Alsous.

The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly understood due to a lack of direct quantitative measurements. Here, we characterize the onset and dynamics of nuclear wrinkling during egg development in the fruit fly when nurse cell nuclei increase in size and display stereotypical wrinkling behavior. A spectral analysis of three-dimensional high-resolution live imaging data from several hundred nuclei reveals a robust asymptotic power-law scaling of angular fluctuations consistent with renormalization and scaling predictions from a nonlinear elastic shell model. We further demonstrate that nuclear wrinkling can be reversed through osmotic shock and suppressed by microtubule disruption, providing tuneable physical and biological control parameters for probing mechanical properties of the nuclear envelope. Our findings advance the biophysical understanding of nuclear membrane fluctuations during early multicellular development.
Circ Res. 2024 Jun 07. 134(12): 1703-1717

Cardiac Fibroblastic Niches in Homeostasis and Inflammation.

Nadine Cadosch, Cristina Gil-Cruz, Christian Perez-Shibayama, Burkhard Ludewig.

  Fibroblasts are essential for building and maintaining the structural integrity of all organs. Moreover, fibroblasts can acquire an inflammatory phenotype to accommodate immune cells in specific niches and to provide migration, differentiation, and growth factors. In the heart, balancing of fibroblast activity is critical for cardiac homeostasis and optimal organ function during inflammation. Fibroblasts sustain cardiac homeostasis by generating local niche environments that support housekeeping functions and by actively engaging in intercellular cross talk. During inflammatory perturbations, cardiac fibroblasts rapidly switch to an inflammatory state and actively communicate with infiltrating immune cells to orchestrate immune cell migration and activity. Here, we summarize the current knowledge on the molecular landscape of cardiac fibroblasts, focusing on their dual role in promoting tissue homeostasis and modulating immune cell-cardiomyocyte interaction. In addition, we discuss potential future avenues for manipulating cardiac fibroblast activity during myocardial inflammation.

Keywords:  cardiovascular diseases; endothelial cells; fibroblasts; homeostasis; inflammation; myocarditis

DOI:  https://doi.org/10.1161/CIRCRESAHA.124.323892
Nature. 2024 Jun 05.

Single-cell nascent RNA sequencing unveils coordinated global transcription.

Dig B Mahat, Nathaniel D Tippens, Jorge D Martin-Rufino, Sean K Waterton, Jiayu Fu, Sarah E Blatt, Phillip A Sharp.

Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1,2. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations3. However, fundamental questions about the temporal regulation of transcription and enhancer-gene coordination remain unanswered, primarily because of the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq-a new single-cell nascent RNA sequencing assay that uses click chemistry-and unveil coordinated transcription throughout the genome. We demonstrate the episodic nature of transcription and the co-transcription of functionally related genes. scGRO-seq can estimate burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells and can leverage replication-dependent non-polyadenylated histone gene transcription to elucidate cell cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq enables the identification of networks of enhancers and genes. Our results suggest that the bursting of transcription at super-enhancers precedes bursting from associated genes. By imparting insights into the dynamic nature of global transcription and the origin and propagation of transcription signals, we demonstrate the ability of scGRO-seq to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.

DOI: https://doi.org/10.1038/s41586-024-07517-7
Cardiovasc Res. 2024 Jun 04. pii: cvae116. [Epub ahead of print]

Cardiomyocyte βII spectrin plays a critical role in maintaining cardiac function by regulating mitochondrial respiratory function.

Rongjin Yang, Banjun Ruan, Rutao Wang, Xiaomeng Zhang, Pingping Xing, Congye Li, Yunyun Zhang, Xiaoqian Chang, Haifeng Song, Shun Zhang, Huishou Zhao, Feiyu Zhang, Tao Yin, Tingting Qi, Wenjun Yan, Fuyang Zhang, Guangyu Hu, Shan Wang, Ling Tao.

  AIMS: βII spectrin is a cytoskeletal protein known to be tightly linked to heart development and cardiovascular electrophysiology. However, the roles of βII spectrin in cardiac contractile function and pathological post-myocardial infarction remodeling remain unclear. Here, we investigated whether and how βII spectrin, the most common isoform of non-erythrocytic spectrin in cardiomyocytes, is involved in cardiac contractile function and ischemia/reperfusion (I/R) injury.METHODS AND RESULTS: We observed that the levels of serum βII spectrin breakdown products (βII SBDPs) were significantly increased in patients with acute myocardial infarction (AMI). Concordantly, βII spectrin was degraded into βII SBDPs by calpain in mouse hearts after I/R injury. Using tamoxifen-inducible cardiac-specific βII spectrin knockout mice, we found that deletion of βII spectrin in the adult heart resulted in spontaneous development of cardiac contractile dysfunction, cardiac hypertrophy and fibrosis at 5 weeks after tamoxifen treatment. Moreover, at 1 week after tamoxifen treatment, although spontaneous cardiac dysfunction in cardiac-specific βII spectrin knockout mice had not developed, deletion of βII spectrin in the heart exacerbated I/R-induced cardiomyocyte death and heart failure. Furthermore, restoration of βII spectrin expression via adenoviral small activating RNA (saRNA) delivery into the heart reduced I/R injury. Immunoprecipitation coupled with mass spectrometry (IP-LC-MS/MS) analyses and functional studies revealed that βII spectrin is indispensable for mitochondrial complex I activity and respiratory function. Mechanistically, βII spectrin promotes translocation of NADH:ubiquinone oxidoreductase 75 kDa Fe-S protein 1 (NDUFS1) from the cytosol to mitochondria by crosslinking with actin filaments (F-actin) to maintain F-actin stability.
CONCLUSION: βII spectrin is an essential cytoskeletal element for preserving mitochondrial homeostasis and cardiac function. Defects in βII spectrin exacerbate cardiac I/R injury.

Keywords:  Cardiac function; Cytoskeleton; Mitochondria; Mitochondrial complex I; βII spectrin

DOI:  https://doi.org/10.1093/cvr/cvae116
Nature. 2024 Jun 05.

Senescent glia link mitochondrial dysfunction and lipid accumulation.

China N Byrns, Alexandra E Perlegos, Karl N Miller, Zhecheng Jin, Faith R Carranza, Palak Manchandra, Connor H Beveridge, Caitlin E Randolph, V Sai Chaluvadi, Shirley L Zhang, Ananth R Srinivasan, F C Bennett, Amita Sehgal, Peter D Adams, Gaurav Chopra, Nancy M Bonini.

Senescence is a cellular state linked to ageing and age-onset disease across many mammalian species1,2. Acutely, senescent cells promote wound healing3,4 and prevent tumour formation5; but they are also pro-inflammatory, thus chronically exacerbate tissue decline. Whereas senescent cells are active targets for anti-ageing therapy6-11, why these cells form in vivo, how they affect tissue ageing and the effect of their elimination remain unclear12,13. Here we identify naturally occurring senescent glia in ageing Drosophila brains and decipher their origin and influence. Using Activator protein 1 (AP1) activity to screen for senescence14,15, we determine that senescent glia can appear in response to neuronal mitochondrial dysfunction. In turn, senescent glia promote lipid accumulation in non-senescent glia; similar effects are seen in senescent human fibroblasts in culture. Targeting AP1 activity in senescent glia mitigates senescence biomarkers, extends fly lifespan and health span, and prevents lipid accumulation. However, these benefits come at the cost of increased oxidative damage in the brain, and neuronal mitochondrial function remains poor. Altogether, our results map the trajectory of naturally occurring senescent glia in vivo and indicate that these cells link key ageing phenomena: mitochondrial dysfunction and lipid accumulation.

DOI: https://doi.org/10.1038/s41586-024-07516-8
bioRxiv. 2024 May 23. pii: 2024.05.20.594719. [Epub ahead of print]

Single-cell and spatiotemporal profile of ovulation in the mouse ovary.

Ruixu Huang, Caroline Elisabeth Kratka, Jeffrey Pea, Cai McCann, Jack Nelson, John P Bryan, Luhan Tracy Zhou, Daniela D Russo, Emily J Zaniker, Achla H Gandhi, Alex K Shalek, Brian Cleary, Samouil L Farhi, Francesca E Duncan, Brittany A Goods.

Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel single-cell RNA-seq and spatial transcriptomics on paired mouse ovaries across an ovulation time course to map the spatiotemporal profile of ovarian cell types. We show that major ovarian cell types exhibit time-dependent transcriptional states enriched for distinct functions and have specific localization profiles within the ovary. We also identified gene markers for ovulation-dependent cell states and validated these using orthogonal methods. Finally, we performed cell-cell interaction analyses to identify ligand-receptor pairs that may drive ovulation, revealing previously unappreciated interactions. Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.

DOI: https://doi.org/10.1101/2024.05.20.594719
Nature. 2024 Jun 05.

MYCT1 controls environmental sensing in human haematopoietic stem cells.

Júlia Aguadé-Gorgorió, Yasaman Jami-Alahmadi, Vincenzo Calvanese, Maya Kardouh, Iman Fares, Haley Johnson, Valerie Rezek, Feiyang Ma, Mattias Magnusson, Yanling Wang, Juliana E Shin, Karina J Nance, Helen S Goodridge, Simone Liebscher, Katja Schenke-Layland, Gay M Crooks, James A Wohlschlegel, Hanna K A Mikkola.

The processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1-3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.

DOI: https://doi.org/10.1038/s41586-024-07478-x
Nat Cell Biol. 2024 Jun 07.

Extraembryonic gut endoderm cells undergo programmed cell death during development.

Julia Batki, Sara Hetzel, Dennis Schifferl, Adriano Bolondi, Maria Walther, Lars Wittler, Stefanie Grosswendt, Bernhard G Herrmann, Alexander Meissner.

Despite a distinct developmental origin, extraembryonic cells in mice contribute to gut endoderm and converge to transcriptionally resemble their embryonic counterparts. Notably, all extraembryonic progenitors share a non-canonical epigenome, raising several pertinent questions, including whether this landscape is reset to match the embryonic regulation and if extraembryonic cells persist into later development. Here we developed a two-colour lineage-tracing strategy to track and isolate extraembryonic cells over time. We find that extraembryonic gut cells display substantial memory of their developmental origin including retention of the original DNA methylation landscape and resulting transcriptional signatures. Furthermore, we show that extraembryonic gut cells undergo programmed cell death and neighbouring embryonic cells clear their remnants via non-professional phagocytosis. By midgestation, we no longer detect extraembryonic cells in the wild-type gut, whereas they persist and differentiate further in p53-mutant embryos. Our study provides key insights into the molecular and developmental fate of extraembryonic cells inside the embryo.

DOI: https://doi.org/10.1038/s41556-024-01431-w
Nat Cell Biol. 2024 Jun 05.

TCF3, TCF12 and distinct enhancers regulate oocyte transcription.

Qiqi Cao, Edward J Grow.

DOI: https://doi.org/10.1038/s41556-024-01433-8
Nat Rev Mol Cell Biol. 2024 Jun 03.

SenNet recommendations for detecting senescent cells in different tissues.

Vidyani Suryadevara, Adam D Hudgins, Adarsh Rajesh, Alberto Pappalardo, Alla Karpova, Amit K Dey, Ann Hertzel, Anthony Agudelo, Azucena Rocha, Bikem Soygur, Birgit Schilling, Chase M Carver, Cristina Aguayo-Mazzucato, Darren J Baker, David A Bernlohr, Diana Jurk, Dilyana B Mangarova, Ellen M Quardokus, Elizabeth Ann L Enninga, Elizabeth L Schmidt, Feng Chen, Francesca E Duncan, Francesco Cambuli, Gagandeep Kaur, George A Kuchel, Gung Lee, Heike E Daldrup-Link, Helene Martini, Hemali Phatnani, Iman M Al-Naggar, Irfan Rahman, Jia Nie, João F Passos, Jonathan C Silverstein, Judith Campisi, Julia Wang, Kanako Iwasaki, Karina Barbosa, Kay Metis, Kerem Nernekli, Laura J Niedernhofer, Li Ding, Lichao Wang, Lisa C Adams, Liu Ruiyang, Madison L Doolittle, Marcos G Teneche, Marissa J Schafer, Ming Xu, Mohammadjavad Hajipour, Mozhgan Boroumand, Nathan Basisty, Nicholas Sloan, Nikolai Slavov, Olena Kuksenko, Paul Robson, Paul T Gomez, Periklis Vasilikos, Peter D Adams, Priscila Carapeto, Quan Zhu, Ramalakshmi Ramasamy, Rolando Perez-Lorenzo, Rong Fan, Runze Dong, Ruth R Montgomery, Sadiya Shaikh, Sanja Vickovic, Shanshan Yin, Shoukai Kang, Sonja Suvakov, Sundeep Khosla, Vesna D Garovic, Vilas Menon, Yanxin Xu, Yizhe Song, Yousin Suh, Zhixun Dou, Nicola Neretti.

Once considered a tissue culture-specific phenomenon, cellular senescence has now been linked to various biological processes with both beneficial and detrimental roles in humans, rodents and other species. Much of our understanding of senescent cell biology still originates from tissue culture studies, where each cell in the culture is driven to an irreversible cell cycle arrest. By contrast, in tissues, these cells are relatively rare and difficult to characterize, and it is now established that fully differentiated, postmitotic cells can also acquire a senescence phenotype. The SenNet Biomarkers Working Group was formed to provide recommendations for the use of cellular senescence markers to identify and characterize senescent cells in tissues. Here, we provide recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans. We discuss some of the recent advances in detecting and characterizing cellular senescence, including molecular senescence signatures and morphological features, and the use of circulating markers. We aim for this work to be a valuable resource for both seasoned investigators in senescence-related studies and newcomers to the field.

DOI: https://doi.org/10.1038/s41580-024-00738-8
Elife. 2024 Jun 06. pii: RP91572. [Epub ahead of print]12

Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila.

Andrew Liu, Jessica O'Connell, Farley Wall, Richard W Carthew.

  The atypical cadherins Fat and Dachsous (Ds) signal through the Hippo pathway to regulate growth of numerous organs, including the Drosophila wing. Here, we find that Ds-Fat signaling tunes a unique feature of cell proliferation found to control the rate of wing growth during the third instar larval phase. The duration of the cell cycle increases in direct proportion to the size of the wing, leading to linear-like growth during the third instar. Ds-Fat signaling enhances the rate at which the cell cycle lengthens with wing size, thus diminishing the rate of wing growth. We show that this results in a complex but stereotyped relative scaling of wing growth with body growth in Drosophila. Finally, we examine the dynamics of Fat and Ds protein distribution in the wing, observing graded distributions that change during growth. However, the significance of these dynamics is unclear since perturbations in expression have negligible impact on wing growth.

Keywords:  D. melanogaster; cadherins; cell cycle; developmental biology; growth control; hippo pathway

DOI:  https://doi.org/10.7554/eLife.91572
Am J Physiol Heart Circ Physiol. 2024 Jun 07.

Runx1 is sufficient but not required for cardiomyocyte cell cycle activation.

Kaelin A Akins, Michael A Flinn, Samantha K Swift, Smrithi V Chanjeevaram, Alexandra L Purdy, Tyler Buddell, Mary E Kolell, Kaitlyn G Andresen, Samantha Paddock, Sydney L Buday, Caitlin C O'Meara, Matthew B Veldman, Michaela Patterson.

  Factors responsible for cardiomyocyte proliferation could serve as potential therapeutics to stimulate endogenous myocardial regeneration following insult, such as ischemic injury. A previously published forward genetics approach on cardiomyocyte cell cycle and ploidy led us to the transcription factor, RUNX1. Here, we examine the effect of Runx1 on cardiomyocyte cell cycle during postnatal development and cardiac regeneration using cardiomyocyte-specific gain- and loss-of-function mouse models. RUNX1 is expressed in cardiomyocytes during early postnatal life, decreases to negligible levels by 3 weeks of age, and increases upon myocardial injury, all consistent with observed rates of cardiomyocyte cell cycle activity. Loss of Runx1 transiently stymied cardiomyocyte cell cycle activity during normal postnatal development, a result that corrected itself and did not extend to the context of neonatal heart regeneration. On the other hand, cardiomyocyte-specific Runx1 overexpression resulted in an expansion of diploid cardiomyocytes in uninjured hearts and expansion of 4N cardiomyocytes in the context of neonatal cardiac injury, suggesting Runx1 overexpression is sufficient to induce cardiomyocyte cell cycle responses. Persistent overexpression of Runx1 for >1 month continued to promote cardiomyocyte cell cycle activity resulting in substantial hyperpolyploidization (≥8N DNA content). This persistent cell cycle activation was accompanied by ventricular dilation and adverse remodeling, raising the concern that continued cardiomyocyte cell cycling can have detrimental effects.

Keywords:  Cardiomyocyte; Ploidy; Runx1; endomitosis; proliferation

DOI:  https://doi.org/10.1152/ajpheart.00782.2023
Dev Cell. 2024 Jun 05. pii: S1534-5807(24)00329-0. [Epub ahead of print]

Setdb1 protects genome integrity in murine muscle stem cells to allow for regenerative myogenesis and inflammation.

Pauline Garcia, William Jarassier, Caroline Brun, Lorenzo Giordani, Fany Agostini, Wai Hing Kung, Cécile Peccate, Jade Ravent, Sidy Fall, Valentin Petit, Tom H Cheung, Slimane Ait-Si-Ali, Fabien Le Grand.

  The histone H3 lysine 9 methyltransferase SETDB1 controls transcriptional repression to direct stem cell fate. Here, we show that Setdb1 expression by adult muscle stem cells (MuSCs) is required for skeletal muscle regeneration. We find that SETDB1 represses the expression of endogenous retroviruses (ERVs) in MuSCs. ERV de-repression in Setdb1-null MuSCs prevents their amplification following exit from quiescence and promotes cell death. Multi-omics profiling shows that chromatin decompaction at ERV loci activates the DNA-sensing cGAS-STING pathway, entailing cytokine expression by Setdb1-null MuSCs. This is followed by aberrant infiltration of inflammatory cells, including pathological macrophages. The ensuing histiocytosis is accompanied by myofiber necrosis, which, in addition to progressive MuSCs depletion, completely abolishes tissue repair. In contrast, loss of Setdb1 in fibro-adipogenic progenitors (FAPs) does not impact immune cells. In conclusion, genome maintenance by SETDB1 in an adult somatic stem cell is necessary for both its regenerative potential and adequate reparative inflammation.

Keywords:  SETDB1; cGAS-STING pathway; endogeneous retrovirus; inflammation; muscle regeneration; muscle stem cells; necrosis; transposable element

DOI:  https://doi.org/10.1016/j.devcel.2024.05.012
Cardiovasc Res. 2024 Jun 05. pii: cvae118. [Epub ahead of print]

Transient stabilization of human cardiovascular progenitor cells from hPSCs in vitro reflects stage-specific heart development in vivo.

Bolesani Emiliano, Bornhorst Dorothee, Lavanya M Iyer, Zawada Dorota, Friese Nina, Morgan Michael, Lange Lucas, Gonzalez David, Schrode Nadine, Leffler Andreas, Julian Wunder, Franke Annika, Drakhlis Lika, Robert Sebra, Schambach Axel, Goedel Alexander, Dubois Nicole, Dobreva Gergana, Moretti Alessandra, Laura C Zelarayán, Abdelilah-Seyfried Salim, Zweigerdt Robert.

AIM: Understanding the molecular identity of human pluripotent stem cell (hPSC)-derived cardiac progenitors and mechanisms controlling their proliferation and differentiation, is valuable for developmental biology and regenerative medicine.METHODS AND RESULTS: Here we show that chemical modulation of Histone Acetyl Transferases (HATs; by IQ-1) and WNT (by CHIR99021), synergistically enable the transient and reversible block of directed cardiac differentiation progression on hPSCs. The resulting stabilized cardiovascular progenitors (SCPs) are characterized by ISL1pos/KI-67pos/NKX2-5neg expression. In the presence of the chemical inhibitors, SCPs maintain a proliferation quiescent state. Upon small molecules removal SCPs resume proliferation and concomitant NKX2-5 upregulation triggers cell-autonomous differentiation into cardiomyocytes. Directed differentiation of SCPs into the endothelial and smooth muscle lineages confirms their full developmental potential typical of bona fide cardiovascular progenitors. Single-cell RNAseq-based transcriptional profiling of our in vitro generated human SCPs notably reflects the dynamic cellular composition of E8.25-E9.25 posterior second heart field (pSHF) of mouse hearts, hallmarked by NR2F2 expression. Investigating molecular mechanisms of SCP stabilization, we found that the cell-autonomously regulated Retinoic Acid (RA) and BMP signaling is governing SCPs transition from quiescence towards proliferation and cell-autonomous differentiation, reminiscent of a niche-like behavior.
CONCLUSION: The chemically defined and reversible nature our stabilization approach provides an unprecedented opportunity to dissect mechanisms of cardiovascular progenitors' specification and reveal their cellular and molecular properties.

DOI: https://doi.org/10.1093/cvr/cvae118
EMBO J. 2024 Jun 05.

Whole-body replacement of larval myofibers generates permanent adult myofibers in zebrafish.

Uday Kumar, Chun-Yi Fang, Hsiao-Yuh Roan, Shao-Chun Hsu, Chung-Han Wang, Chen-Hui Chen.

  Drastic increases in myofiber number and size are essential to support vertebrate post-embryonic growth. However, the collective cellular behaviors that enable these increases have remained elusive. Here, we created the palmuscle myofiber tagging and tracking system for in toto monitoring of the growth and fates of ~5000 fast myofibers in developing zebrafish larvae. Through live tracking of individual myofibers within the same individuals over extended periods, we found that many larval myofibers readily dissolved during development, enabling the on-site addition of new and more myofibers. Remarkably, whole-body surveillance of multicolor-barcoded myofibers further unveiled a gradual yet extensive elimination of larval myofiber populations, resulting in near-total replacement by late juvenile stages. The subsequently emerging adult myofibers are not only long-lasting, but also morphologically and functionally distinct from the larval populations. Furthermore, we determined that the elimination-replacement process is dependent on and driven by the autophagy pathway. Altogether, we propose that the whole-body replacement of larval myofibers is an inherent yet previously unnoticed process driving organismic muscle growth during vertebrate post-embryonic development.

Keywords:  Fast Myofiber; Live Imaging; Post-embryonic Growth; Zebrafish

DOI:  https://doi.org/10.1038/s44318-024-00136-y
Nat Genet. 2024 Jun 05.

A single-cell transcriptome atlas of human euploid and aneuploid blastocysts.

Shengpeng Wang, Lizhi Leng, Quanlei Wang, Yifan Gu, Jinlu Li, Yanru An, Qiuting Deng, Pingyuan Xie, Can Cheng, Xueqin Chen, Qinwei Zhou, Jia Lu, Fang Chen, Longqi Liu, Huanming Yang, Jian Wang, Xun Xu, Yong Hou, Fei Gong, Liang Hu, Guangxiu Lu, Zhouchun Shang, Ge Lin.

Aneuploidy is frequently detected in early human embryos as a major cause of early pregnancy failure. However, how aneuploidy affects cellular function remains elusive. Here, we profiled the transcriptomes of 14,908 single cells from 203 human euploid and aneuploid blastocysts involving autosomal and sex chromosomes. Nearly all of the blastocysts contained four lineages. In aneuploid chromosomes, 19.5% ± 1.2% of the expressed genes showed a dosage effect, and 90 dosage-sensitive domains were identified. Aneuploidy leads to prevalent genome-wide transcriptome alterations. Common effects, including apoptosis, were identified, especially in monosomies, partially explaining the lower cell numbers in autosomal monosomies. We further identified lineage-specific effects causing unstable epiblast development in aneuploidies, which was accompanied by the downregulation of TGF-β and FGF signaling, which resulted in insufficient trophectoderm maturation. Our work provides crucial insights into the molecular basis of human aneuploid blastocysts and may shed light on the cellular interaction during blastocyst development.

DOI: https://doi.org/10.1038/s41588-024-01788-6
Cancer Res. 2024 Jun 04.

CENP-E inhibition induces chromosomal instability and synergizes with diverse microtubule-targeting agents in breast cancer.

John B Tucker, Caleb L Carlsen, Christina M Scribano, Srishrika M Pattaswamy, Mark E Burkard, Beth A Weaver.

Drugs that perturb microtubules are commonly used to treat breast cancers of all subtypes in both early stage and metastatic disease, but they are only effective in approximately 50% of patients. High concentrations of microtubule-targeting agents can elicit mitotic arrest in cell culture models; however, recent evidence from primary and metastatic breast cancers revealed that they only accumulate at intratumoral levels capable of inducing abnormal multipolar mitotic spindles, not mitotic arrest. While maintenance of multipolar spindles can generate cytotoxic rates of chromosomal instability (CIN), focusing of aberrant multipolar spindles into normal bipolar spindles dramatically reduces CIN and confers resistance to microtubule poisons. Here, we showed that inhibition of the mitotic kinesin CENP-E overcomes resistance caused by focusing multipolar spindles. Clinically relevant microtubule-targeting agents used a mechanistically conserved pathway to induce multipolar spindles without requiring centrosome amplification. Focusing could occur at any point in mitosis, with earlier focusing conferring greater resistance to anti-microtubule agents. CENP-E inhibition increased CIN on focused spindles by generating chromosomes that remained misaligned at spindle poles during anaphase, which substantially increased death in the resulting daughter cells. CENP-E inhibition synergized with diverse, clinically relevant microtubule poisons to potentiate cell death in cell lines and suppress tumor growth in orthotopic tumor models. These results suggest that primary resistance to microtubule-targeting drugs can be overcome by simultaneous inhibition of CENP-E.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3332
Cell. 2024 May 30. pii: S0092-8674(24)00492-6. [Epub ahead of print]

Clonal hematopoiesis driven by mutated DNMT3A promotes inflammatory bone loss.

Hui Wang, Kimon Divaris, Bohu Pan, Xiaofei Li, Jong-Hyung Lim, Gundappa Saha, Marko Barovic, Danai Giannakou, Jonathan M Korostoff, Yu Bing, Souvik Sen, Kevin Moss, Di Wu, James D Beck, Christie M Ballantyne, Pradeep Natarajan, Kari E North, Mihai G Netea, Triantafyllos Chavakis, George Hajishengallis.

  Clonal hematopoiesis of indeterminate potential (CHIP) arises from aging-associated acquired mutations in hematopoietic progenitors, which display clonal expansion and produce phenotypically altered leukocytes. We associated CHIP-DNMT3A mutations with a higher prevalence of periodontitis and gingival inflammation among 4,946 community-dwelling adults. To model DNMT3A-driven CHIP, we used mice with the heterozygous loss-of-function mutation R878H, equivalent to the human hotspot mutation R882H. Partial transplantation with Dnmt3aR878H/+ bone marrow (BM) cells resulted in clonal expansion of mutant cells into both myeloid and lymphoid lineages and an elevated abundance of osteoclast precursors in the BM and osteoclastogenic macrophages in the periphery. DNMT3A-driven clonal hematopoiesis in recipient mice promoted naturally occurring periodontitis and aggravated experimentally induced periodontitis and arthritis, associated with enhanced osteoclastogenesis, IL-17-dependent inflammation and neutrophil responses, and impaired regulatory T cell immunosuppressive activity. DNMT3A-driven clonal hematopoiesis and, subsequently, periodontitis were suppressed by rapamycin treatment. DNMT3A-driven CHIP represents a treatable state of maladaptive hematopoiesis promoting inflammatory bone loss.

Keywords:  DNMT3A; T cells; arthritis; bone marrow; clonal hematopoiesis of indeterminate potential; hematopoietic stem and progenitor cells; inflammation; neutrophils; osteoclastogenesis; periodontitis

DOI:  https://doi.org/10.1016/j.cell.2024.05.003
Circ Res. 2024 Jun 07. 134(12): 1681-1702

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics.

Jack A Palmer, Nadia Rosenthal, Sarah A Teichmann, Monika Litvinukova.

  Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.

Keywords:  cardiovascular diseases; genomics; heart; human; single-cell analysis; spatial analysis

DOI:  https://doi.org/10.1161/CIRCRESAHA.124.323672
J Clin Invest. 2024 Jun 03. pii: e167811. [Epub ahead of print]134(11):

Increased endothelial sclerostin caused by elevated DSCAM mediates multiple trisomy 21 phenotypes.

Pediatric Cardiac Genomics Consortium Investigators

  Trisomy 21 (T21), a recurrent aneuploidy occurring in 1:800 births, predisposes to congenital heart disease (CHD) and multiple extracardiac phenotypes. Despite a definitive genetic etiology, the mechanisms by which T21 perturbs development and homeostasis remain poorly understood. We compared the transcriptome of CHD tissues from 49 patients with T21 and 226 with euploid CHD (eCHD). We resolved cell lineages that misexpressed T21 transcripts by cardiac single-nucleus RNA sequencing and RNA in situ hybridization. Compared with eCHD samples, T21 samples had increased chr21 gene expression; 11-fold-greater levels (P = 1.2 × 10-8) of SOST (chr17), encoding the Wnt inhibitor sclerostin; and 1.4-fold-higher levels (P = 8.7 × 10-8) of the SOST transcriptional activator ZNF467 (chr7). Euploid and T21 cardiac endothelial cells coexpressed SOST and ZNF467; however, T21 endothelial cells expressed 6.9-fold more SOST than euploid endothelial cells (P = 2.7 × 10-27). Wnt pathway genes were downregulated in T21 endothelial cells. Expression of DSCAM, residing within the chr21 CHD critical region, correlated with SOST (P = 1.9 × 10-5) and ZNF467 (P = 2.9 × 10-4). Deletion of DSCAM from T21 endothelial cells derived from human induced pluripotent stem cells diminished sclerostin secretion. As Wnt signaling is critical for atrioventricular canal formation, bone health, and pulmonary vascular homeostasis, we concluded that T21-mediated increased sclerostin levels would inappropriately inhibit Wnt activities and promote Down syndrome phenotypes. These findings imply therapeutic potential for anti-sclerostin antibodies in T21.

Keywords:  Bone development; Cardiology; Cardiovascular disease; Genetic diseases; Genetics

DOI:  https://doi.org/10.1172/JCI167811
Nat Neurosci. 2024 Jun 07.

Developmental origin of oligodendrocytes determines their function in the adult brain.

Sarah Foerster, Elisa M Floriddia, David van Bruggen, Petra Kukanja, Bastien Hervé, Shangli Cheng, Eosu Kim, Benjamin U Phillips, Christopher J Heath, Richa B Tripathi, Cody Call, Theresa Bartels, Katherine Ridley, Björn Neumann, Laura López-Cruz, Abbe H Crawford, Cian J Lynch, Manuel Serrano, Lisa Saksida, David H Rowitch, Wiebke Möbius, Klaus-Armin Nave, Matthew N Rasband, Dwight E Bergles, Nicoletta Kessaris, William D Richardson, Timothy J Bussey, Chao Zhao, Gonçalo Castelo-Branco, Robin J M Franklin.

In the mouse embryonic forebrain, developmentally distinct oligodendrocyte progenitor cell populations and their progeny, oligodendrocytes, emerge from three distinct regions in a spatiotemporal gradient from ventral to dorsal. However, the functional importance of this oligodendrocyte developmental heterogeneity is unknown. Using a genetic strategy to ablate dorsally derived oligodendrocyte lineage cells (OLCs), we show here that the areas in which dorsally derived OLCs normally reside in the adult central nervous system become populated and myelinated by OLCs of ventral origin. These ectopic oligodendrocytes (eOLs) have a distinctive gene expression profile as well as subtle myelination abnormalities. The failure of eOLs to fully assume the role of the original dorsally derived cells results in locomotor and cognitive deficits in the adult animal. This study reveals the importance of developmental heterogeneity within the oligodendrocyte lineage and its importance for homeostatic brain function.

DOI: https://doi.org/10.1038/s41593-024-01666-8
Aging Cell. 2024 Jun 02. e14197

Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging.

Cristobal F Rivera, Yasmeen M Farra, Michele Silvestro, Steven Medvedovsky, Jacqueline Matz, Muhammad Yogi Pratama, John Vlahos, Bhama Ramkhelawon, Chiara Bellini.

  Aortic stiffening is an inevitable manifestation of chronological aging, yet the mechano-molecular programs that orchestrate region- and layer-specific adaptations along the length and through the wall of the aorta are incompletely defined. Here, we show that the decline in passive cyclic distensibility is more pronounced in the ascending thoracic aorta (ATA) compared to distal segments of the aorta and that collagen content increases in both the medial and adventitial compartments of the ATA during aging. The single-cell RNA sequencing of aged ATA tissues reveals altered cellular senescence, remodeling, and inflammatory responses accompanied by enrichment of T-lymphocytes and rarefaction of vascular smooth muscle cells, compared to young samples. T lymphocyte clusters accumulate in the adventitia, while the activation of mechanosensitive Piezo-1 enhances vasoconstriction and contributes to the overall functional decline of ATA tissues. These results portray the immuno-mechanical aging of the ATA as a process that culminates in a stiffer conduit permissive to the accrual of multi-gerogenic signals priming to disease development.

Keywords:  Piezo‐1; collagen remodeling; distensibility; elastic energy; inflammation; tissue stiffness; vasoconstriction

DOI:  https://doi.org/10.1111/acel.14197