bims-ginsta 2024-03-31 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–03–31
37 papers selected by
Jinrong Hu, National University of Singapore

Mechanical strengthening of cell-cell adhesion during mouse embryo compaction.
Global signal peptide profiling reveals principles of selective Sec61 inhibition.
Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.
A stable microtubule bundle formed through an orchestrated multistep process controls quiescence exit.
Mapping single-cell gene expression in the healthy human breast.
Control of cell proliferation by memories of mitosis.
Chromatin compaction by Polycomb group proteins revisited.
Distinct types of intramitochondrial protein aggregates protect mitochondria against proteotoxic stress.
Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism.
Macrophages suppress cardiac reprogramming of fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit.
Cell-fate conversion of intestinal cells in adult Drosophila midgut by depleting a single transcription factor.
Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition.
Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice.
RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication.
How Can Young Extracellular Matrix Promote Cardiac Regeneration? Versi-Can!
Modeling mechanical activation of macrophages during pulmonary fibrogenesis for targeted anti-fibrosis therapy.
Single-cell multiplex chromatin and RNA interactions in ageing human brain.
Lethal Giant Disc is a target of Cdk1 and regulates ESCRT-III localization during germline stem cell abscission.
Initiation of a ZAKα-dependent ribotoxic stress response by the innate immunity endoribonuclease RNase L.
Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche.
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.
Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.
Force-induced tail-autotomy mitochondrial fission and biogenesis of matrix-excluded mitochondrial-derived vesicles for quality control.
Adhesion energy controls lipid binding-mediated endocytosis.
TP53INP2-dependent activation of muscle autophagy ameliorates sarcopenia and promotes healthy aging.
Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis.
Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD.
A cell fate decision map reveals abundant direct neurogenesis bypassing intermediate progenitors in the human developing neocortex.
FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells.
Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA.
Microinterfaces in biopolymer-based bicontinuous hydrogels guide rapid 3D cell migration.
TGFβ1 Drives Integrin Dependent Pericyte Migration and Microvascular Destabilization In Fibrotic Disease.
The HEAT repeat protein HPO-27 is a lysosome fission factor.
Trophoblast organoid systems to study human placentation.
Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Extra centrosomes delay DNA damage-driven tumorigenesis.
Hippo-deficient cardiac fibroblasts differentiate into osteochondroprogenitors.

Biophys J. 2024 Mar 25. pii: S0006-3495(24)00208-X. [Epub ahead of print]

Mechanical strengthening of cell-cell adhesion during mouse embryo compaction.

Ludmilla de Plater, Julie Firmin, Jean-Léon Maître.

Compaction is the first morphogenetic movement of the eutherian mammals and involves a developmentally regulated adhesion process. Previous studies investigated cellular and mechanical aspects of compaction. During mouse and human compaction, cells spread onto each other as a result of a contractility-mediated increase in surface tension pulling at the edges of their cell-cell contacts. However, how compaction may affect the mechanical stability of cell-cell contacts remains unknown. Here, we used a dual pipette aspiration assay on cell doublets to quantitatively analyze the mechanical stability of compacting mouse embryos. We measured increased mechanical stability of contacts with rupture forces growing from 40 to 70 nN, which was highly correlated with cell-cell contact expansion. Analyzing the dynamic molecular reorganization of cell-cell contacts, we find minimal recruitment of the cell-cell adhesion molecule Cdh1 (also known as E-cadherin) to contacts but we observe its reorganization into a peripheral adhesive ring. However, this reorganization is not associated with increased effective bond density, contrary to previous reports in other adhesive systems. Using genetics, we reduce the levels of Cdh1 or replace it with a chimeric adhesion molecule composed of the extracellular domain of Cdh1 and the intracellular domain of Cdh2 (also known as N-cadherin). We find that reducing the levels of Cdh1 impairs the mechanical stability of cell-cell contacts due to reduced contact growth, which nevertheless show higher effective bond density than WT contacts of similar size. On the other hand, chimeric adhesion molecules cannot form large or strong contacts indicating that the intracellular domain of Cdh2 is unable to reorganize contacts and/or is mechanically weaker than the one of Cdh1 in mouse embryos. Together, we find that mouse embryo compaction mechanically strengthens cell-cell adhesion via the expansion of Cdh1 adhesive rings that maintain pre-compaction levels of effective bond density.

DOI: https://doi.org/10.1016/j.bpj.2024.03.028
Nat Chem Biol. 2024 Mar 22.

Global signal peptide profiling reveals principles of selective Sec61 inhibition.

Nicole A Wenzell, Brian B Tuch, Dustin L McMinn, Matthew J Lyons, Christopher J Kirk, Jack Taunton.

Cotransins target the Sec61 translocon and inhibit the biogenesis of an undefined subset of secretory and membrane proteins. Remarkably, cotransin inhibition depends on the unique signal peptide (SP) of each Sec61 client, which is required for cotranslational translocation into the endoplasmic reticulum. It remains unknown how an SP's amino acid sequence and biophysical properties confer sensitivity to structurally distinct cotransins. Here we describe a fluorescence-based, pooled-cell screening platform to interrogate nearly all human SPs in parallel. We profiled two cotransins with distinct effects on cancer cells and discovered a small subset of SPs, including the oncoprotein human epidermal growth factor receptor 3 (HER3), with increased sensitivity to the more selective cotransin, KZR-9873. By comparing divergent mouse and human orthologs, we unveiled a position-dependent effect of arginine on SP sensitivity. Our multiplexed profiling platform reveals how cotransins can exploit subtle sequence differences to achieve SP discrimination.

DOI: https://doi.org/10.1038/s41589-024-01592-7
Mol Cell. 2024 Mar 13. pii: S1097-2765(24)00144-8. [Epub ahead of print]

Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.

Erica M Hildebrand, Kirill Polovnikov, Bastiaan Dekker, Yu Liu, Denis L Lafontaine, A Nicole Fox, Ying Li, Sergey V Venev, Leonid A Mirny, Job Dekker.

  The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations, and multi-contact 3C and find that, by contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a topoisomerase-II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias topoisomerase II activity toward decatenation. At the second stage, the loops are released, and the formation of new entanglements is prevented by lower topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed in experiments and models, a normal interphase state cannot be acquired.

Keywords:  G1; chromosome entanglement; chromosome folding; cohesin; fractal globule; genome architecture; genome topology; mitosis; self-catenation; topoisomerase II

DOI:  https://doi.org/10.1016/j.molcel.2024.02.025
Elife. 2024 Mar 25. pii: RP89958. [Epub ahead of print]12

A stable microtubule bundle formed through an orchestrated multistep process controls quiescence exit.

Damien Laporte, Aurelie Massoni-Laporte, Charles Lefranc, Jim Dompierre, David Mauboules, Emmanuel T Nsamba, Anne Royou, Lihi Gal, Maya Schuldiner, Mohan L Gupta, Isabelle Sagot.

  Cells fine-tune microtubule assembly in both space and time to give rise to distinct edifices with specific cellular functions. In proliferating cells, microtubules are highly dynamics, and proliferation cessation often leads to their stabilization. One of the most stable microtubule structures identified to date is the nuclear bundle assembled in quiescent yeast. In this article, we characterize the original multistep process driving the assembly of this structure. This Aurora B-dependent mechanism follows a precise temporality that relies on the sequential actions of kinesin-14, kinesin-5, and involves both microtubule-kinetochore and kinetochore-kinetochore interactions. Upon quiescence exit, the microtubule bundle is disassembled via a cooperative process involving kinesin-8 and its full disassembly is required prior to cells re-entry into proliferation. Overall, our study provides the first description, at the molecular scale, of the entire life cycle of a stable microtubule structure in vivo and sheds light on its physiological function.

Keywords:  S. cerevisiae; cell biology; kinesin; microtubules; quiescence

DOI:  https://doi.org/10.7554/eLife.89958
Nat Genet. 2024 Mar 29.

Mapping single-cell gene expression in the healthy human breast.

DOI: https://doi.org/10.1038/s41588-024-01691-0
Science. 2024 Mar 29. 383(6690): 1441-1448

Control of cell proliferation by memories of mitosis.

Franz Meitinger, Hazrat Belal, Robert L Davis, Mallory B Martinez, Andrew K Shiau, Karen Oegema, Arshad Desai.

Mitotic duration is tightly constrained, and extended mitosis is characteristic of problematic cells prone to chromosome missegregation and genomic instability. We show here that mitotic extension leads to the formation of p53-binding protein 1 (53BP1)-ubiquitin-specific protease 28 (USP28)-p53 protein complexes that are transmitted to, and stably retained by, daughter cells. Complexes assembled through a Polo-like kinase 1-dependent mechanism during extended mitosis and elicited a p53 response in G1 that prevented the proliferation of the progeny of cells that experienced an approximately threefold extended mitosis or successive less extended mitoses. The ability to monitor mitotic extension was lost in p53-mutant cancers and some p53-wild-type (p53-WT) cancers, consistent with classification of TP53BP1 and USP28 as tumor suppressors. Cancers retaining the ability to monitor mitotic extension exhibited sensitivity to antimitotic agents.

DOI: https://doi.org/10.1126/science.add9528
Curr Opin Struct Biol. 2024 Mar 26. pii: S0959-440X(24)00033-2. [Epub ahead of print]86 102806

Chromatin compaction by Polycomb group proteins revisited.

Michael Uckelmann, Chen Davidovich.

The chromatin compaction activity of Polycomb group proteins has traditionally been considered essential for transcriptional repression. However, there is very little information on how Polycomb group proteins compact chromatin at the molecular level and no causal link between the compactness of chromatin and transcriptional repression. Recently, a more complete picture of Polycomb-dependent chromatin architecture has started to emerge, owing to advanced methods for imaging and chromosome conformation capture. Discoveries into Polycomb-driven phase separation add another layer of complexity. Recent observations generally imply that Polycomb group proteins modulate chromatin structure at multiple scales to reduce its dynamics and segregate it from active domains. Hence, it is reasonable to hypothesise that Polycomb group proteins maintain the energetically favourable state of compacted chromatin, rather than actively compact it.

DOI: https://doi.org/10.1016/j.sbi.2024.102806
Cell Rep. 2024 Mar 28. pii: S2211-1247(24)00346-2. [Epub ahead of print]43(4): 114018

Distinct types of intramitochondrial protein aggregates protect mitochondria against proteotoxic stress.

Lea Bertgen, Jan-Eric Bökenkamp, Tim Schneckmann, Christian Koch, Markus Räschle, Zuzana Storchová, Johannes M Herrmann.

  Mitochondria consist of hundreds of proteins, most of which are inaccessible to the proteasomal quality control system of the cytosol. How cells stabilize the mitochondrial proteome during challenging conditions remains poorly understood. Here, we show that mitochondria form spatially defined protein aggregates as a stress-protecting mechanism. Two different types of intramitochondrial protein aggregates can be distinguished. The mitoribosomal protein Var1 (uS3m) undergoes a stress-induced transition from a soluble, chaperone-stabilized protein that is prevalent under benign conditions to an insoluble, aggregated form upon acute stress. The formation of Var1 bodies stabilizes mitochondrial proteostasis, presumably by sequestration of aggregation-prone proteins. The AAA chaperone Hsp78 is part of a second type of intramitochondrial aggregate that transiently sequesters proteins and promotes their folding or Pim1-mediated degradation. Thus, mitochondrial proteins actively control the formation of distinct types of intramitochondrial protein aggregates, which cooperate to stabilize the mitochondrial proteome during proteotoxic stress conditions.

Keywords:  CP: Cell biology; CP: Molecular biology; Hsp78; MitoStores; Pim1 protease; Var1 bodies; aggregates; chaperones; mitochondria; mitoribosome; protein folding; protein import

DOI:  https://doi.org/10.1016/j.celrep.2024.114018
Genome Biol. 2024 Mar 22. 25(1): 77

Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism.

Emily M Pujadas Liwag, Xiaolong Wei, Nicolas Acosta, Lucas M Carter, Jiekun Yang, Luay M Almassalha, Surbhi Jain, Ali Daneshkhah, Suhas S P Rao, Fidan Seker-Polat, Kyle L MacQuarrie, Joe Ibarra, Vasundhara Agrawal, Erez Lieberman Aiden, Masato T Kanemaki, Vadim Backman, Mazhar Adli.

   BACKGROUND: B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology.
RESULTS: Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci, heterochromatin, and chromatin domains.
CONCLUSIONS: Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single-cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.

Keywords:  3D chromatin organization; Auxin-inducible degron system; CRISPR-Sirius; in situ Hi-C; Lamin-associated domains; Nuclear lamina; Partial Wave Spectroscopic Microscopy; Topologically associated domains

DOI:  https://doi.org/10.1186/s13059-024-03212-y
Protein Cell. 2024 Mar 26. pii: pwae013. [Epub ahead of print]

Macrophages suppress cardiac reprogramming of fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit.

Hao Wang, Junbo Yang, Yihong Cai, Yang Zhao.

  Direct conversion of cardiac fibroblasts (CFs) to cardiomyocytes (CMs) in vivo to regenerate heart tissue is an attractive approach. After myocardial infarction (MI), heart repair proceeds with an inflammation stage initiated by monocytes infiltration of the infarct zone establishing an immune microenvironment. However, whether and how the MI microenvironment influences the reprogramming of CFs remains unclear. Here, we found that in comparison with cardiac fibroblasts (CFs) cultured in vitro, CFs that transplanted into infarct region of MI mouse models resisted to cardiac reprogramming. RNA-seq analysis revealed upregulation of interferon (IFN) response genes in transplanted CFs, and subsequent inhibition of the IFN receptors increased reprogramming efficiency in vivo. Macrophage-secreted IFN-β was identified as the dominant upstream signaling factor after MI. CFs treated with macrophage-conditioned medium containing IFN-β displayed reduced reprogramming efficiency, while macrophage depletion or blocking the IFN signaling pathway after MI increased reprogramming efficiency in vivo. Co-IP, BiFC and Cut-tag assays showed that phosphorylated STAT1 downstream of IFN signaling in CFs could interact with the reprogramming factor GATA4 and inhibit the GATA4 chromatin occupancy in cardiac genes. Furthermore, upregulation of IFN-IFNAR-p-STAT1 signaling could stimulate CFs secretion of CCL2/7/12 chemokines, subsequently recruiting IFN-β-secreting macrophages. Together, these immune cells further activate STAT1 phosphorylation, enhancing CCL2/7/12 secretion and immune cell recruitment, ultimately forming a self-reinforcing positive feedback loop between CFs and macrophages via IFN-IFNAR-p-STAT1 that inhibits cardiac reprogramming in vivo. Cumulatively, our findings uncover an intercellular self-stimulating inflammatory circuit as a microenvironmental molecular barrier of in situ cardiac reprogramming that needs to be overcome for regenerative medicine applications.

Keywords:   Ifnar1/2 ; cardiac reprogramming; heart regeneration; microenvironment

DOI:  https://doi.org/10.1093/procel/pwae013
Nat Commun. 2024 Mar 26. 15(1): 2656

Cell-fate conversion of intestinal cells in adult Drosophila midgut by depleting a single transcription factor.

Xingting Guo, Chenhui Wang, Yongchao Zhang, Ruxue Wei, Rongwen Xi.

The manipulation of cell identity by reprograming holds immense potential in regenerative medicine, but is often limited by the inefficient acquisition of fully functional cells. This problem can potentially be resolved by better understanding the reprogramming process using in vivo genetic models, which are currently scarce. Here we report that both enterocytes (ECs) and enteroendocrine cells (EEs) in adult Drosophila midgut show a surprising degree of cell plasticity. Depleting the transcription factor Tramtrack in the differentiated ECs can initiate Prospero-mediated cell transdifferentiation, leading to EE-like cells. On the other hand, depletion of Prospero in the differentiated EEs can lead to the loss of EE-specific transcription programs and the gain of intestinal progenitor cell identity, allowing cell cycle re-entry or differentiation into ECs. We find that intestinal progenitor cells, ECs, and EEs have a similar chromatin accessibility profile, supporting the concept that cell plasticity is enabled by pre-existing chromatin accessibility with switchable transcription programs. Further genetic analysis with this system reveals that the NuRD chromatin remodeling complex, cell lineage confliction, and age act as barriers to EC-to-EE transdifferentiation. The establishment of this genetically tractable in vivo model should facilitate mechanistic investigation of cell plasticity at the molecular and genetic level.

DOI: https://doi.org/10.1038/s41467-024-46956-8
Nat Cardiovasc Res. 2023 Nov;2(11): 1060-1077

Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition.

Yifang Xie, Qiaozi Wang, Yuchen Yang, David Near, Haofei Wang, Marazzano Colon, Christopher Nguyen, Conor Slattery, Benjamin Keepers, Gregory Farber, Tzu-Wen Wang, Sung-Ho Lee, Yen-Yu Ian Shih, Jiandong Liu, Li Qian.

Direct reprogramming of fibroblasts into induced cardiomyocytes holds great promise for heart regeneration. Although considerable progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here, we characterized the translational landscape of iCM reprogramming through integrative ribosome and transcriptomic profiling, and found extensive translatome repatterning during this process. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. In a mouse model of myocardial infarction, removing Ybx1 enhanced in vivo reprogramming, resulting in improved heart function and reduced scar size. Mechanistically, Ybx1 depletion de-repressed the translation of its direct targets SRF and Baf60c, both of which mediated the effect of Ybx1 depletion on iCM generation. Furthermore, removal of Ybx1 allowed single factor Tbx5-mediated iCM conversion. In summary, this study revealed a new layer of regulatory mechanism that controls cardiac reprogramming at the translational level.

DOI: https://doi.org/10.1038/s44161-023-00344-5
Mol Cell. 2024 Mar 11. pii: S1097-2765(24)00173-4. [Epub ahead of print]

Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice.

Oleksandra Sirozh, Anabel Saez-Mas, Bomi Jung, Laura Sanchez-Burgos, Eduardo Zarzuela, Sara Rodrigo-Perez, Ivan Ventoso, Vanesa Lafarga, Oscar Fernandez-Capetillo.

  Nucleolar stress (NS) has been associated with age-related diseases such as cancer or neurodegeneration. To investigate how NS triggers toxicity, we used (PR)n arginine-rich peptides present in some neurodegenerative diseases as inducers of this perturbation. We here reveal that whereas (PR)n expression leads to a decrease in translation, this occurs concomitant with an accumulation of free ribosomal (r) proteins. Conversely, (PR)n-resistant cells have lower rates of r-protein synthesis, and targeting ribosome biogenesis by mTOR inhibition or MYC depletion alleviates (PR)n toxicity in vitro. In mice, systemic expression of (PR)97 drives widespread NS and accelerated aging, which is alleviated by rapamycin. Notably, the generalized accumulation of orphan r-proteins is a common outcome of chemical or genetic perturbations that induce NS. Together, our study presents a general model to explain how NS induces cellular toxicity and provides in vivo evidence supporting a role for NS as a driver of aging in mammals.

Keywords:  aging; nucleolar stress; nucleolus; ribosomal proteins; ribosomopathy

DOI:  https://doi.org/10.1016/j.molcel.2024.02.031
J Clin Invest. 2024 Mar 26. pii: e167419. [Epub ahead of print]

RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication.

Joonyoung Her, Haiyan Zheng, Samuel F Bunting.

  The mammalian SUMO-targeted E3 Ubiquitin Ligase, Rnf4, has been reported to act as a regulator of DNA repair, but the importance of RNF4 as a tumor suppressor has not been tested. Using a conditional-knockout mouse model, we deleted Rnf4 in the B cell lineage to test the importance of RNF4 for growth of somatic cells. Although Rnf4 conditional-knockout B cells exhibited substantial genomic instability, Rnf4 deletion caused no increase in tumor susceptibility. In contrast, Rnf4 deletion extended the healthy lifespan of mice expressing an oncogenic c-myc transgene. Rnf4 activity is essential for normal DNA replication, and in its absence, there was a failure in ATR-CHK1 signaling of replication stress. Factors that normally mediate replication fork stability, including members of the Fanconi Anemia gene family and the helicases, PIF1 and RECQL5, showed reduced accumulation at replication forks in the absence of RNF4. RNF4 deficiency also resulted in an accumulation of hyper-SUMOylated proteins in chromatin, including members of the SMC5/6 complex, which contributes to replication failure by a mechanism dependent on RAD51. These findings indicate that RNF4, which shows increased expression in multiple human tumor types, is a potential target for anti-cancer therapy, especially in tumors expressing c-myc.

Keywords:  Cell stress; Genetics; Lymphomas; Oncology; Ubiquitin-proteosome system

DOI:  https://doi.org/10.1172/JCI167419
Circulation. 2024 Mar 26. 149(13): 1016-1018

How Can Young Extracellular Matrix Promote Cardiac Regeneration? Versi-Can!

Elad Bassat, Eldad Tzahor.



Keywords:  Editorials; extracellular matrix; myocardial infarction; regeneration

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.068078
Sci Adv. 2024 Mar 29. 10(13): eadj9559

Modeling mechanical activation of macrophages during pulmonary fibrogenesis for targeted anti-fibrosis therapy.

Ying Xu, Linxuan Ying, Jennifer K Lang, Boris Hinz, Ruogang Zhao.

Pulmonary fibrosis is an often fatal lung disease. Immune cells such as macrophages were shown to accumulate in the fibrotic lung, but their contribution to the fibrosis development is unclear. To recapitulate the involvement of macrophages in the development of pulmonary fibrosis, we developed a fibrotic microtissue model with cocultured human macrophages and fibroblasts. We show that profibrotic macrophages seeded on topographically controlled stromal tissues became mechanically activated. The resulting co-alignment of macrophages, collagen fibers, and fibroblasts promoted widespread fibrogenesis in micro-engineered lung tissues. Anti-fibrosis treatment using pirfenidone disrupts the polarization and mechanical activation of profibrotic macrophages, leading to fibrosis inhibition. Pirfenidone inhibits the mechanical activation of macrophages by suppressing integrin αMβ2 and Rho-associated kinase 2. These results demonstrate a potential pulmonary fibrogenesis mechanism at the tissue level contributed by macrophages. The cocultured microtissue model is a powerful tool to study the immune-stromal cell interactions and the anti-fibrosis drug mechanism.

DOI: https://doi.org/10.1126/sciadv.adj9559
Nature. 2024 Mar 27.

Single-cell multiplex chromatin and RNA interactions in ageing human brain.

Xingzhao Wen, Zhifei Luo, Wenxin Zhao, Riccardo Calandrelli, Tri C Nguyen, Xueyi Wan, John Lalith Charles Richard, Sheng Zhong.

Dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA1-3. Chromatin complex compositions change during cellular differentiation and ageing, and are expected to be highly heterogeneous among terminally differentiated single cells4-7. Here we introduce the multinucleic acid interaction mapping in single cells (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression and RNA-chromatin associations within individual nuclei. When applied to 14 human frontal cortex samples from older donors, MUSIC delineated diverse cortical cell types and states. We observed that nuclei exhibiting fewer short-range chromatin interactions were correlated with both an 'older' transcriptomic signature and Alzheimer's disease pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci and a promoter tends to be that in which these cis expression quantitative trait loci specifically affect the expression of their target gene. In addition, female cortical cells exhibit highly heterogeneous interactions between XIST non-coding RNA and chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploration of chromatin architecture and transcription at cellular resolution in complex tissues.

DOI: https://doi.org/10.1038/s41586-024-07239-w
Development. 2024 Mar 21. pii: dev.202306. [Epub ahead of print]

Lethal Giant Disc is a target of Cdk1 and regulates ESCRT-III localization during germline stem cell abscission.

Catherine Hermant, Neuza Reis Matias, Pascale Michel-Hissier, Jean-René Huynh, Juliette Mathieu.

  Abscission is the final step of cytokinesis which allows the physical separation of sister cells through the scission of the cellular membrane. This deformation is driven by ESCRT-III proteins which can bind membranes and form dynamic helices. A crucial step in abscission is the recruitment of ESCRT-III proteins at the right time and place. Alix is one of the best characterized proteins that recruits ESCRT-III proteins from yeast to mammals. However, recent studies in vivo revealed that pathways acting independently or redundantly with Alix are also required at abscission sites in different cellular contexts. Here, we show that Lgd acts redundantly with Alix to properly localize ESCRT-III to the abscission site in Germline Stem Cells (GSCs) during Drosophila oogenesis. We further demonstrate that Lgd is phosphorylated at multiple sites by the CycB/Cdk1 kinase. We found that these phosphorylation events potentiate the activity of Shrub, a Drosophila ESCRT-III, during abscission of GSCs. Our study reveals that redundancy between Lgd and Alix, and coordination with the cell cycle kinase Cdk1, confers robust and timely abscission of Drosophila germline stem cells.

Keywords:  ALIX; CC2D1; CHMP4; ESCRT-III; Germline stem cell; Lgd; Shrub

DOI:  https://doi.org/10.1242/dev.202306
Cell Rep. 2024 Mar 28. pii: S2211-1247(24)00326-7. [Epub ahead of print]43(4): 113998

Initiation of a ZAKα-dependent ribotoxic stress response by the innate immunity endoribonuclease RNase L.

Jiajia Xi, Goda Snieckute, José Francisco Martínez, Frederic Schrøder Wenzel Arendrup, Abhishek Asthana, Christina Gaughan, Anders H Lund, Simon Bekker-Jensen, Robert H Silverman.

  RNase L is an endoribonuclease of higher vertebrates that functions in antiviral innate immunity. Interferons induce oligoadenylate synthetase enzymes that sense double-stranded RNA of viral origin leading to the synthesis of 2',5'-oligoadenylate (2-5A) activators of RNase L. However, it is unknown precisely how RNase L remodels the host cell transcriptome. To isolate effects of RNase L from other effects of double-stranded RNA or virus, 2-5A is directly introduced into cells. Here, we report that RNase L activation by 2-5A causes a ribotoxic stress response involving the MAP kinase kinase kinase (MAP3K) ZAKα, MAP2Ks, and the stress-activated protein kinases JNK and p38α. RNase L activation profoundly alters the transcriptome by widespread depletion of mRNAs associated with different cellular functions but also by JNK/p38α-stimulated induction of inflammatory genes. These results show that the 2-5A/RNase L system triggers a protein kinase cascade leading to proinflammatory signaling and apoptosis.

Keywords:  2-5A; CP: Immunology; OAS; RNase L; ZAKalpha; innate immunity; ribotoxic stress response

DOI:  https://doi.org/10.1016/j.celrep.2024.113998
Nat Aging. 2024 Mar 29.

Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche.

Lucy Xu, Julliana Ramirez-Matias, Max Hauptschein, Eric D Sun, Judith C Lunger, Matthew T Buckley, Anne Brunet.

Partial reprogramming (pulsed expression of reprogramming transcription factors) improves the function of several tissues in old mice. However, it remains largely unknown how partial reprogramming impacts the old brain. Here we use single-cell transcriptomics to systematically examine how partial reprogramming influences the subventricular zone neurogenic niche in aged mouse brains. Whole-body partial reprogramming mainly improves neuroblasts (cells committed to give rise to new neurons) in the old neurogenic niche, restoring neuroblast proportion to more youthful levels. Interestingly, targeting partial reprogramming specifically to the neurogenic niche also boosts the proportion of neuroblasts and their precursors (neural stem cells) in old mice and improves several molecular signatures of aging, suggesting that the beneficial effects of reprogramming are niche intrinsic. In old neural stem cell cultures, partial reprogramming cell autonomously restores the proportion of neuroblasts during differentiation and blunts some age-related transcriptomic changes. Importantly, partial reprogramming improves the production of new neurons in vitro and in old brains. Our work suggests that partial reprogramming could be used to rejuvenate the neurogenic niche and counter brain decline in old individuals.

DOI: https://doi.org/10.1038/s43587-024-00594-3
Nat Genet. 2024 Mar 28.

A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.

Austin D Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J Kunz, Linsey J Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J Q Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J Gomm, Valerie Speirs, J Louise Jones, John C Marioni, Walid T Khaled.

Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mastectomies. From more than 800,000 cells we identified 41 cell subclusters across the epithelial, immune and stromal compartments. The contribution of these different clusters varied according to the natural history of the tissue. Age, parity and germline mutations, known to modulate the risk of developing breast cancer, affected the homeostatic cellular state of the breast in different ways. We found that immune cells from BRCA1 or BRCA2 carriers had a distinct gene expression signature indicative of potential immune exhaustion, which was validated by immunohistochemistry. This suggests that immune-escape mechanisms could manifest in non-cancerous tissues very early during tumor initiation. This atlas is a rich resource that can be used to inform novel approaches for early detection and prevention of breast cancer.

DOI: https://doi.org/10.1038/s41588-024-01688-9
Nat Cell Biol. 2024 Mar 28.

Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.

Yick Hin Ling, Ziyang Ye, Chloe Liang, Chuofan Yu, Giho Park, Jeffry L Corden, Carl Wu.

Efficient gene expression requires RNA polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in three-dimensional nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. In the present study, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation and reduces transcription bursting. The present study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.

DOI: https://doi.org/10.1038/s41556-024-01382-2
Proc Natl Acad Sci U S A. 2024 Apr 02. 121(14): e2217019121

Force-induced tail-autotomy mitochondrial fission and biogenesis of matrix-excluded mitochondrial-derived vesicles for quality control.

Xiaoying Liu, Linyu Xu, Yutong Song, Zhihao Zhao, Xinyu Li, Cheuk-Yiu Wong, Rong Chen, Jianxiong Feng, Yitao Gou, Yajing Qi, Hei-Man Chow, Shuhuai Yao, Yi Wang, Song Gao, Xingguo Liu, Liting Duan.

  Mitochondria constantly fuse and divide for mitochondrial inheritance and functions. Here, we identified a distinct type of naturally occurring fission, tail-autotomy fission, wherein a tail-like thin tubule protrudes from the mitochondrial body and disconnects, resembling autotomy. Next, utilizing an optogenetic mitochondria-specific mechanostimulator, we revealed that mechanical tensile force drives tail-autotomy fission. This force-induced fission involves DRP1/MFF and endoplasmic reticulum tubule wrapping. It redistributes mitochondrial DNA, producing mitochondrial fragments with or without mitochondrial DNA for different fates. Moreover, tensile force can decouple outer and inner mitochondrial membranes, pulling out matrix-excluded tubule segments. Subsequent tail-autotomy fission separates the matrix-excluded tubule segments into matrix-excluded mitochondrial-derived vesicles (MDVs) which recruit Parkin and LC3B, indicating the unique role of tail-autotomy fission in segregating only outer membrane components for mitophagy. Sustained force promotes fission and MDV biogenesis more effectively than transient one. Our results uncover a mechanistically and functionally distinct type of fission and unveil the role of tensile forces in modulating fission and MDV biogenesis for quality control, underscoring the heterogeneity of fission and mechanoregulation of mitochondrial dynamics.

Keywords:  mitochondrial fission; mitochondrial quality control; optogenetics; photoactivatable proteins; tensile force

DOI:  https://doi.org/10.1073/pnas.2217019121
Nat Commun. 2024 Mar 29. 15(1): 2767

Adhesion energy controls lipid binding-mediated endocytosis.

Raluca Groza, Kita Valerie Schmidt, Paul Markus Müller, Paolo Ronchi, Claire Schlack-Leigers, Ursula Neu, Dmytro Puchkov, Rumiana Dimova, Claudia Matthaeus, Justin Taraska, Thomas R Weikl, Helge Ewers.

Several bacterial toxins and viruses can deform membranes through multivalent binding to lipids for clathrin-independent endocytosis. However, it remains unclear, how membrane deformation and endocytic internalization are mechanistically linked. Here we show that many lipid-binding virions induce membrane deformation and clathrin-independent endocytosis, suggesting a common mechanism based on multivalent lipid binding by globular particles. We create a synthetic cellular system consisting of a lipid-anchored receptor in the form of GPI-anchored anti-GFP nanobodies and a multivalent globular binder exposing 180 regularly-spaced GFP molecules on its surface. We show that these globular, 40 nm diameter, particles bind to cells expressing the receptor, deform the plasma membrane upon adhesion and become endocytosed in a clathrin-independent manner. We explore the role of the membrane adhesion energy in endocytosis by using receptors with affinities varying over 7 orders of magnitude. Using this system, we find that once a threshold in adhesion energy is overcome to allow for membrane deformation, endocytosis occurs reliably. Multivalent, binding-induced membrane deformation by globular binders is thus sufficient for internalization to occur and we suggest it is the common, purely biophysical mechanism for lipid-binding mediated endocytosis of toxins and pathogens.

DOI: https://doi.org/10.1038/s41467-024-47109-7
Autophagy. 2024 Mar 28. 1-10

TP53INP2-dependent activation of muscle autophagy ameliorates sarcopenia and promotes healthy aging.

David Sebastián, Marc Beltrà, Andrea Irazoki, David Sala, Pilar Aparicio, Cecilia Aris, Esmaeil Alibakhshi, Maria Rubio-Valera, Manuel Palacín, Juan Castellanos, Luis Lores, Antonio Zorzano.

  Sarcopenia is a major contributor to disability in older adults, and thus, it is key to elucidate the mechanisms underlying its development. Increasing evidence suggests that impaired macroautophagy/autophagy contributes to the development of sarcopenia. However, the mechanisms leading to reduced autophagy during aging remain largely unexplored, and whether autophagy activation protects from sarcopenia has not been fully addressed. Here we show that the autophagy regulator TP53INP2/TRP53INP2 is decreased during aging in mouse and human skeletal muscle. Importantly, chronic activation of autophagy by muscle-specific overexpression of TRP53INP2 prevents sarcopenia and the decline of muscle function in mice. Acute re-expression of TRP53INP2 in aged mice also improves muscle atrophy, enhances mitophagy, and reduces ROS production. In humans, high levels of TP53INP2 in muscle are associated with increased muscle strength and healthy aging. Our findings highlight the relevance of an active muscle autophagy in the maintenance of muscle mass and prevention of sarcopenia.Abbreviation: ATG7: autophagy related 7; BMI: body mass index; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ROS: reactive oxygen species; TP53INP2: tumor protein p53 inducible nuclear protein 2; WT: wild type.

Keywords:  Sarcopenia; aging; autophagy; mitophagy; muscle atrophy

DOI:  https://doi.org/10.1080/15548627.2024.2333717
Science. 2024 Mar 29. 383(6690): 1484-1492

Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis.

Umakant Sahu, Elodie Villa, Colleen R Reczek, Zibo Zhao, Brendan P O'Hara, Michael D Torno, Rohan Mishra, William D Shannon, John M Asara, Peng Gao, Ali Shilatifard, Navdeep S Chandel, Issam Ben-Sahra.

Cellular purines, particularly adenosine 5'-triphosphate (ATP), fuel many metabolic reactions, but less is known about the direct effects of pyrimidines on cellular metabolism. We found that pyrimidines, but not purines, maintain pyruvate oxidation and the tricarboxylic citric acid (TCA) cycle by regulating pyruvate dehydrogenase (PDH) activity. PDH activity requires sufficient substrates and cofactors, including thiamine pyrophosphate (TPP). Depletion of cellular pyrimidines decreased TPP synthesis, a reaction carried out by TPP kinase 1 (TPK1), which reportedly uses ATP to phosphorylate thiamine (vitamin B1). We found that uridine 5'-triphosphate (UTP) acts as the preferred substrate for TPK1, enabling cellular TPP synthesis, PDH activity, TCA-cycle activity, lipogenesis, and adipocyte differentiation. Thus, UTP is required for vitamin B1 utilization to maintain pyruvate oxidation and lipogenesis.

DOI: https://doi.org/10.1126/science.adh2771
Cell. 2024 Mar 14. pii: S0092-8674(24)00234-4. [Epub ahead of print]

Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD.

S Sebastian Pineda, Hyeseung Lee, Maria J Ulloa-Navas, Raleigh M Linville, Francisco J Garcia, Kyriakitsa Galani, Erica Engelberg-Cook, Monica C Castanedes, Brent E Fitzwalter, Luc J Pregent, Mahammad E Gardashli, Michael DeTure, Diana V Vera-Garcia, Andre T S Hucke, Bjorn E Oskarsson, Melissa E Murray, Dennis W Dickson, Myriam Heiman, Veronique V Belzil, Manolis Kellis.

  Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) share many clinical, pathological, and genetic features, but a detailed understanding of their associated transcriptional alterations across vulnerable cortical cell types is lacking. Here, we report a high-resolution, comparative single-cell molecular atlas of the human primary motor and dorsolateral prefrontal cortices and their transcriptional alterations in sporadic and familial ALS and FTLD. By integrating transcriptional and genetic information, we identify known and previously unidentified vulnerable populations in cortical layer 5 and show that ALS- and FTLD-implicated motor and spindle neurons possess a virtually indistinguishable molecular identity. We implicate potential disease mechanisms affecting these cell types as well as non-neuronal drivers of pathogenesis. Finally, we show that neuron loss in cortical layer 5 tracks more closely with transcriptional identity rather than cellular morphology and extends beyond previously reported vulnerable cell types.

Keywords:  ALS; Betz cell; FTLD; frontotemporal dementia; motor neuron; neurodegeneration; single cell; spindle neuron; von Economo

DOI:  https://doi.org/10.1016/j.cell.2024.02.031
Nat Cell Biol. 2024 Mar 28.

A cell fate decision map reveals abundant direct neurogenesis bypassing intermediate progenitors in the human developing neocortex.

Laure Coquand, Clarisse Brunet Avalos, Anne-Sophie Macé, Sarah Farcy, Amandine Di Cicco, Marusa Lampic, Ryszard Wimmer, Betina Bessières, Tania Attie-Bitach, Vincent Fraisier, Pierre Sens, Fabien Guimiot, Jean-Baptiste Brault, Alexandre D Baffet.

The human neocortex has undergone strong evolutionary expansion, largely due to an increased progenitor population, the basal radial glial cells. These cells are responsible for the production of a diversity of cell types, but the successive cell fate decisions taken by individual progenitors remain unknown. Here we developed a semi-automated live/fixed correlative imaging method to map basal radial glial cell division modes in early fetal tissue and cerebral organoids. Through the live analysis of hundreds of dividing progenitors, we show that basal radial glial cells undergo abundant symmetric amplifying divisions, and frequent self-consuming direct neurogenic divisions, bypassing intermediate progenitors. These direct neurogenic divisions are more abundant in the upper part of the subventricular zone. We furthermore demonstrate asymmetric Notch activation in the self-renewing daughter cells, independently of basal fibre inheritance. Our results reveal a remarkable conservation of fate decisions in cerebral organoids, supporting their value as models of early human neurogenesis.

DOI: https://doi.org/10.1038/s41556-024-01393-z
Nat Commun. 2024 Mar 23. 15(1): 2599

FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells.

Ke Cong, Nathan MacGilvary, Silviana Lee, Shannon G MacLeod, Jennifer Calvo, Min Peng, Arne Nedergaard Kousholt, Tovah A Day, Sharon B Cantor.

The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in creating single-stranded DNA gaps and inducing sensitivity requires the FANCJ DNA helicase. Yet, how FANCJ relates to PARP1 inhibition or trapping, which contribute to PARPi toxicity, remains unclear. Here, we find PARPi effectiveness hinges on S-phase PARP1 activity, which is reduced in FANCJ deficient cells as G-quadruplexes sequester PARP1 and MSH2. Additionally, loss of the FANCJ-MLH1 interaction diminishes PARP1 activity; however, depleting MSH2 reinstates PARPi sensitivity and gaps. Indicating sequestered and trapped PARP1 are distinct, FANCJ loss increases PARPi resistance in cells susceptible to PARP1 trapping. However, with BRCA1 deficiency, the loss of FANCJ mirrors PARP1 loss or inhibition, with the detrimental commonality being loss of S-phase PARP1 activity. These insights underline the crucial role of PARP1 activity during DNA replication in BRCA1 deficient cells and emphasize the importance of understanding drug mechanisms for enhancing therapeutic response.

DOI: https://doi.org/10.1038/s41467-024-46824-5
Nat Commun. 2024 Mar 28. 15(1): 2725

Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA.

Daan M K van Soest, Paulien E Polderman, Wytze T F den Toom, Janneke P Keijer, Markus J van Roosmalen, Tim M F Leyten, Johannes Lehmann, Susan Zwakenberg, Sasha De Henau, Ruben van Boxtel, Boudewijn M T Burgering, Tobias B Dansen.

Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of chromosomal DNA mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondria can directly damage nuclear DNA is largely lacking. In this study, we investigated the effects of H2O2 released by mitochondria or produced at the nucleosomes using a titratable chemogenetic approach. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2. Nuclear H2O2 gives rise to DNA damage and mutations and a subsequent p53 dependent cell cycle arrest. Mitochondrial H2O2 release shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. We conclude that H2O2 released from mitochondria is unlikely to directly damage nuclear genomic DNA, limiting its contribution to oncogenic transformation and aging.

DOI: https://doi.org/10.1038/s41467-024-47008-x
Nat Commun. 2024 Mar 29. 15(1): 2766

Microinterfaces in biopolymer-based bicontinuous hydrogels guide rapid 3D cell migration.

Karen L Xu, Nikolas Di Caprio, Hooman Fallahi, Mohammad Dehghany, Matthew D Davidson, Lorielle Laforest, Brian C H Cheung, Yuqi Zhang, Mingming Wu, Vivek Shenoy, Lin Han, Robert L Mauck, Jason A Burdick.

Cell migration is critical for tissue development and regeneration but requires extracellular environments that are conducive to motion. Cells may actively generate migratory routes in vivo by degrading or remodeling their environments or instead utilize existing extracellular matrix microstructures or microtracks as innate pathways for migration. While hydrogels in general are valuable tools for probing the extracellular regulators of 3-dimensional migration, few recapitulate these natural migration paths. Here, we develop a biopolymer-based bicontinuous hydrogel system that comprises a covalent hydrogel of enzymatically crosslinked gelatin and a physical hydrogel of guest and host moieties bonded to hyaluronic acid. Bicontinuous hydrogels form through controlled solution immiscibility, and their continuous subdomains and high micro-interfacial surface area enable rapid 3D migration, particularly when compared to homogeneous hydrogels. Migratory behavior is mesenchymal in nature and regulated by biochemical and biophysical signals from the hydrogel, which is shown across various cell types and physiologically relevant contexts (e.g., cell spheroids, ex vivo tissues, in vivo tissues). Our findings introduce a design that leverages important local interfaces to guide rapid cell migration.

DOI: https://doi.org/10.1038/s41467-024-46774-y
Am J Pathol. 2024 Mar 26. pii: S0002-9440(24)00118-4. [Epub ahead of print]

TGFβ1 Drives Integrin Dependent Pericyte Migration and Microvascular Destabilization In Fibrotic Disease.

Amanda S Pellowe, Michelle J Wu, Tae-Yun Kang, Tracy D Chung, Adrian Ledesma-Mendoza, Erica Herzog, Andre Levchenko, Ian Odell, John Varga, Anjelica L Gonzalez.

Interactions between endothelial cells (EC) and mural pericytes (PC) are critical to maintaining the stability and function of the microvascular wall. Abnormal interactions between these two cell types are a hallmark of progressive fibrotic diseases, such as systemic sclerosis (SSc, scleroderma). However, the role that PCs play in signaling microvascular dysfunction remains underexplored. It is hypothesized that integrin-matrix interactions contribute to PC migration from the vascular wall and conversion into interstitial myofibroblasts. Using pro-inflammatory TNF alpha (TNFα) or fibrotic growth factor TGF beta-1 (TGFβ1), human PC inflammatory and fibrotic phenotypes were evaluated by assessing their migration, matrix deposition, integrin expression, and subsequent effects on endothelial dysfunction. Both TNFα and TGFβ1 treatment altered integrin expression and matrix protein deposition, but only fibrotic TGFβ1 drove PC migration in an integrin-dependent manner. In addition, integrin-dependent PC migration was correlated to changes in EC angiopoietin-2 levels, a marker of vascular instability. Finally, there was evidence of changes in vascular stability corresponding to disease state in human SSc skin. The work presented demonstrates that TNFα and TGFβ1 induce changes in PC integrin expression and matrix deposition that facilitate migration and reduce vascular stability, providing evidence that microvascular destabilization can be an early indicator of tissue fibrosis.

DOI: https://doi.org/10.1016/j.ajpath.2024.02.021
Nature. 2024 Mar 27.

The HEAT repeat protein HPO-27 is a lysosome fission factor.

Letao Li, Xilu Liu, Shanshan Yang, Meijiao Li, Yanwei Wu, Siqi Hu, Wenjuan Wang, Amin Jiang, Qianqian Zhang, Junbing Zhang, Xiaoli Ma, Junyan Hu, Qiaohong Zhao, Yubing Liu, Dong Li, Junjie Hu, Chonglin Yang, Wei Feng, Xiaochen Wang.

Lysosomes are degradation and signalling centres crucial for homeostasis, development and ageing1. To meet diverse cellular demands, lysosomes remodel their morphology and function through constant fusion and fission2,3. Little is known about the molecular basis of fission. Here we identify HPO-27, a conserved HEAT repeat protein, as a lysosome scission factor in Caenorhabditis elegans. Loss of HPO-27 impairs lysosome fission and leads to an excessive tubular network that ultimately collapses. HPO-27 and its human homologue MROH1 are recruited to lysosomes by RAB-7 and enriched at scission sites. Super-resolution imaging, negative-staining electron microscopy and in vitro reconstitution assays reveal that HPO-27 and MROH1 self-assemble to mediate the constriction and scission of lysosomal tubules in worms and mammalian cells, respectively, and assemble to sever supported membrane tubes in vitro. Loss of HPO-27 affects lysosomal morphology, integrity and degradation activity, which impairs animal development and longevity. Thus, HPO-27 and MROH1 act as self-assembling scission factors to maintain lysosomal homeostasis and function.

DOI: https://doi.org/10.1038/s41586-024-07249-8
Dev Cell. 2024 Mar 25. pii: S1534-5807(24)00108-4. [Epub ahead of print]59(6): 693-694

Trophoblast organoid systems to study human placentation.

Qian Li, Margherita Yayoi Turco, Ashley Moffett.

Human trophoblast organoids provide a valuable in vitro system to investigate human placental development and function. In this issue of Developmental Cell, Shannon et al. benchmark two organoid models against primary trophoblast at single-cell resolution, identifying their strengths and limitations.

DOI: https://doi.org/10.1016/j.devcel.2024.02.009
Science. 2024 Mar 29. 383(6690): eadk8544

Molecular mechanism of dynein-dynactin complex assembly by LIS1.

Kashish Singh, Clinton K Lau, Giulia Manigrasso, José B Gama, Reto Gassmann, Andrew P Carter.

Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.

DOI: https://doi.org/10.1126/science.adk8544
Sci Adv. 2024 Mar 29. 10(13): eadk0564

Extra centrosomes delay DNA damage-driven tumorigenesis.

Vincent Z Braun, Gerlinde Karbon, Fabian Schuler, Marina A Schapfl, Johannes G Weiss, Paul Y Petermann, Diana C J Spierings, Andrea E Tijhuis, Floris Foijer, Verena Labi, Andreas Villunger.

Deregulated centrosome numbers are frequently found in human cancer and can promote malignancies in model organisms. Current research aims to clarify if extra centrosomes are cause or consequence of malignant transformation, and if their biogenesis can be targeted for therapy. Here, we show that oncogene-driven blood cancer is inert to genetic manipulation of centrosome numbers, whereas the formation of DNA damage-induced malignancies is delayed. We provide first evidence that this unexpected phenomenon is connected to extra centrosomes eliciting a pro-death signal engaging the apoptotic machinery. Apoptosis induction requires the PIDDosome multi-protein complex, as it can be abrogated by loss of any of its three components, Caspase-2, Raidd/Cradd, or Pidd1. BCL2 overexpression equally blocks cell death, documenting for the first time induction of mitochondrial apoptosis downstream of extra centrosomes. Our findings demonstrate context-dependent effects of centrosome amplification during transformation and ask to adjust current belief that extra centrosomes are intrinsically pro-tumorigenic.

DOI: https://doi.org/10.1126/sciadv.adk0564
bioRxiv. 2023 Sep 08. pii: 2023.09.06.556593. [Epub ahead of print]

Hippo-deficient cardiac fibroblasts differentiate into osteochondroprogenitors.

Chang-Ru Tsai, Jong Kim, Xiao Li, Paulo Czarnewski, Rich Li, Fansen Meng, Mingjie Zheng, Xiaolei Zhao, Jeffrey Steimle, Francisco Grisanti, Jun Wang, Md Abul Hassan Samee, James Martin.

Cardiac fibrosis, a common pathophysiology associated with various heart diseases, occurs from the excess deposition of extracellular matrix (ECM) 1 . Cardiac fibroblasts (CFs) are the primary cells that produce, degrade, and remodel ECM during homeostasis and tissue repair 2 . Upon injury, CFs gain plasticity to differentiate into myofibroblasts 3 and adipocyte-like 4,5 and osteoblast-like 6 cells, promoting fibrosis and impairing heart function 7 . How CFs maintain their cell state during homeostasis and adapt plasticity upon injury are not well defined. Recent studies have shown that Hippo signalling in CFs regulates cardiac fibrosis and inflammation 8-11 . Here, we used single-nucleus RNA sequencing (snRNA-seq) and spatially resolved transcriptomic profiling (ST) to investigate how the cell state was altered in the absence of Hippo signaling and how Hippo-deficient CFs interact with macrophages during cardiac fibrosis. We found that Hippo-deficient CFs differentiate into osteochondroprogenitors (OCPs), suggesting that Hippo restricts CF plasticity. Furthermore, Hippo-deficient CFs colocalized with macrophages, suggesting their intercellular communications. Indeed, we identified several ligand-receptor pairs between the Hippo-deficient CFs and macrophages. Blocking the Hippo-deficient CF-induced CSF1 signaling abolished macrophage expansion. Interestingly, blocking macrophage expansion also reduced OCP differentiation of Hippo-deficient CFs, indicating that macrophages promote CF plasticity.

DOI: https://doi.org/10.1101/2023.09.06.556593