bims-ginsta 2023-11-12 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2023–11–12
39 papers selected by
Jinrong Hu, National University of Singapore

Dynamic interplay between human alpha-satellite DNA structure and centromere functions.
Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence.
A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona.
RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size.
Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity.
Transcriptomes and metabolism define mouse and human MAIT cell populations.
Transitional cell states sculpt tissue topology during lung regeneration.
Pioneer factors: roles and their regulation in development.
Perspective: "Current Understanding of NADs Dynamics and Mechanisms of Disease".
Transcriptional elongation control in developmental gene expression, aging, and disease.
Mitopherogenesis, a form of mitochondria-specific ectocytosis, regulates sperm mitochondrial quantity and fertility.
Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus.
Non-canonical MLL1 activity regulates centromeric phase separation and genome stability.
The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.
A cell-based model for size control in the multiple fission alga Chlamydomonas reinhardtii.
NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos.
Exportin-mediated nucleocytoplasmic transport maintains Pch2 homeostasis during meiosis.
Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles.
Disrupting cellular memory to overcome drug resistance.
Solubility phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition.
Structure of the transcribing RNA polymerase II-Elongin complex.
Mechanisms of actin disassembly and turnover.
Transcriptional repression of beige fat innervation via a YAP/TAZ-S100B axis.
RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes.
The power and potential of mitochondria transfer.
Dissecting the human leptomeninges at single-cell resolution.
Context-dependent ciliary regulation of hedgehog pathway repression in tissue morphogenesis.
Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways.
Using biophysical cues and biomaterials to improve genetic models.
PGF2α signaling drives fibrotic remodeling and fibroblast population dynamics in mice.
Macrophage phenotypes and functions: resolving inflammation and restoring homeostasis.
Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.
Comprehensive mapping of cell fates in microsatellite unstable cancer cells supports dual targeting of WRN and ATR.
A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process.
Mitochondrial Permeability Transition Regulator, Cyclophilin D, is Transcriptionally Activated by C/EBP During Adipogenesis.
Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation.
Human follicular fluid elicits select dose- and age-dependent effects on mouse oocytes and cumulus-oocyte-complexes in a heterologous in vitro maturation assay.
Vitamin B5 supports MYC oncogenic metabolism and tumor progression in breast cancer.
Molecular Crowding: Physiologic Sensing and Control.

Semin Cell Dev Biol. 2023 Nov 03. pii: S1084-9521(23)00171-4. [Epub ahead of print]

Dynamic interplay between human alpha-satellite DNA structure and centromere functions.

Elena Di Tommaso, Simona Giunta.

  Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.

Keywords:  Alpha-satellite; Aneuploidy; CENP-A; Cancer; Centromere; Instability

DOI:  https://doi.org/10.1016/j.semcdb.2023.10.002
Cell Rep. 2023 Nov 05. pii: S2211-1247(23)01393-1. [Epub ahead of print]42(11): 113381

Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence.

Aida Rodríguez López, Maria H Jørgensen, Jesper F Havelund, Frederic S Arendrup, Srinivasa Prasad Kolapalli, Thorbjørn M Nielsen, Eva Pais, Carsten Jörn Beese, Ahmad Abdul-Al, Anna Constance Vind, Jiri Bartek, Simon Bekker-Jensen, Marta Montes, Panagiotis Galanos, Nils Faergeman, Lotta Happonen, Lisa B Frankel.

  Oncogene-induced senescence (OIS) is a persistent anti-proliferative response that acts as a barrier against malignant transformation. During OIS, cells undergo dynamic remodeling, which involves alterations in protein and organelle homeostasis through autophagy. Here, we show that ribosomes are selectively targeted for degradation by autophagy during OIS. By characterizing senescence-dependent alterations in the ribosomal interactome, we find that the deubiquitinase USP10 dissociates from the ribosome during the transition to OIS. This release of USP10 leads to an enhanced ribosome ubiquitination, particularly of small subunit proteins, including lysine 275 on RPS2. Both reinforcement of the USP10-ribosome interaction and mutation of RPS2 K275 abrogate ribosomal delivery to lysosomes without affecting bulk autophagy. We show that the selective recruitment of ubiquitinated ribosomes to autophagosomes is mediated by the p62 receptor. While ribophagy is not required for the establishment of senescence per se, it contributes to senescence-related metabolome alterations and facilitates the senescence-associated secretory phenotype.

Keywords:  CP: Cell biology; CP: Molecular biology; USP10; autophagy; oncogene-induced senescence; ribosomes; selective autophagy; ubiquitin

DOI:  https://doi.org/10.1016/j.celrep.2023.113381
J Cell Biol. 2024 Jan 01. pii: e202303007. [Epub ahead of print]223(1):

A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona.

Jingchao Wu, Maximilian W D Raas, Paula Sobrevals Alcaraz, Harmjan R Vos, Eelco C Tromer, Berend Snel, Geert J P L Kops.

Correct chromosome segregation during cell division depends on proper connections between spindle microtubules and kinetochores. During prometaphase, kinetochores are temporarily covered with a dense protein meshwork known as the fibrous corona. Formed by oligomerization of ROD/ZW10/ZWILCH-SPINDLY (RZZ-S) complexes, the fibrous corona promotes spindle assembly, chromosome orientation, and spindle checkpoint signaling. The molecular requirements for formation of the fibrous corona are not fully understood. Here, we show that the fibrous corona depends on the mitotic kinesin CENP-E and that poorly expanded fibrous coronas after CENP-E depletion are functionally compromised. This previously unrecognized role for CENP-E does not require its motor activity but instead is driven by farnesyl modification of its C-terminal kinetochore- and microtubule-binding domain. We show that in cells, CENP-E binds Spindly and recruits RZZ-S complexes to ectopic locations in a farnesyl-dependent manner. CENP-E is recruited to kinetochores following RZZ-S, and-while not required for RZZ-S oligomerization per se-promotes subsequent fibrous corona expansion. Our comparative genomics analyses suggest that the farnesylation motif in CENP-E orthologs emerged alongside the full RZZ-S module in an ancestral lineage close to the fungi-animal split (Obazoa), revealing potential conservation of the mechanisms for fibrous corona formation. Our results show that proper spindle assembly has a potentially conserved non-motor contribution from the kinesin CENP-E through stabilization of the fibrous corona meshwork during its formation.

DOI: https://doi.org/10.1083/jcb.202303007
Cell. 2023 Nov 01. pii: S0092-8674(23)01128-5. [Epub ahead of print]

RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size.

Matthew P Swaffer, Georgi K Marinov, Huan Zheng, Lucas Fuentes Valenzuela, Crystal Yee Tsui, Andrew W Jones, Jessica Greenwood, Anshul Kundaje, William J Greenleaf, Rodrigo Reyes-Lamothe, Jan M Skotheim.

  A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component of this is that global transcription rates increase in larger cells. Here, we identify RNA polymerase II (RNAPII) as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.

Keywords:  RNA; RNA biology; RNA polymerase II; cell biology; cell size; size scaling; systems biology; transcription

DOI:  https://doi.org/10.1016/j.cell.2023.10.012
Nat Commun. 2023 Nov 06. 14(1): 6943

Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity.

Zhi Liu, Dong-Sung Lee, Yuqiong Liang, Ye Zheng, Jesse R Dixon.

Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

DOI: https://doi.org/10.1038/s41467-023-42647-y
Sci Immunol. 2023 Nov 10. 8(89): eabn8531

Transcriptomes and metabolism define mouse and human MAIT cell populations.

Shilpi Chandra, Gabriel Ascui, Thomas Riffelmacher, Ashu Chawla, Ciro Ramírez-Suástegui, Viankail C Castelan, Gregory Seumois, Hayley Simon, Mallory P Murray, Goo-Young Seo, Ashmitaa L R Premlal, Benjamin Schmiedel, Greet Verstichel, Yingcong Li, Chia-Hao Lin, Jason Greenbaum, John Lamberti, Raghav Murthy, John Nigro, Hilde Cheroutre, Christian H Ottensmeier, Stephen M Hedrick, Li-Fan Lu, Pandurangan Vijayanand, Mitchell Kronenberg.

Mucosal-associated invariant T (MAIT) cells are a subset of T lymphocytes that respond to microbial metabolites. We defined MAIT cell populations in different organs and characterized the developmental pathway of mouse and human MAIT cells in the thymus using single-cell RNA sequencing and phenotypic and metabolic analyses. We showed that the predominant mouse subset, which produced IL-17 (MAIT17), and the subset that produced IFN-γ (MAIT1) had not only greatly different transcriptomes but also different metabolic states. MAIT17 cells in different organs exhibited increased lipid uptake, lipid storage, and mitochondrial potential compared with MAIT1 cells. All these properties were similar in the thymus and likely acquired there. Human MAIT cells in lung and blood were more homogeneous but still differed between tissues. Human MAIT cells had increased fatty acid uptake and lipid storage in blood and lung, similar to human CD8 T resident memory cells, but unlike mouse MAIT17 cells, they lacked increased mitochondrial potential. Although mouse and human MAIT cell transcriptomes showed similarities for immature cells in the thymus, they diverged more strikingly in the periphery. Analysis of pet store mice demonstrated decreased lung MAIT17 cells in these so-called "dirty" mice, indicative of an environmental influence on MAIT cell subsets and function.

DOI: https://doi.org/10.1126/sciimmunol.abn8531
Cell Stem Cell. 2023 Nov 02. pii: S1934-5909(23)00363-6. [Epub ahead of print]30(11): 1486-1502.e9

Transitional cell states sculpt tissue topology during lung regeneration.

Arvind Konkimalla, Satoshi Konishi, Lauren Macadlo, Yoshihiko Kobayashi, Zachary J Farino, Naoya Miyashita, Léa El Haddad, Jeremy Morowitz, Christina E Barkauskas, Pankaj Agarwal, Tomokazu Souma, Mai K ElMallah, Aleksandra Tata, Purushothama Rao Tata.

  Organ regeneration requires dynamic cell interactions to reestablish cell numbers and tissue architecture. While we know the identity of progenitor cells that replace lost tissue, the transient states they give rise to and their role in repair remain elusive. Here, using multiple injury models, we find that alveolar fibroblasts acquire distinct states marked by Sfrp1 and Runx1 that influence tissue remodeling and reorganization. Unexpectedly, ablation of alveolar epithelial type-1 (AT1) cells alone is sufficient to induce tissue remodeling and transitional states. Integrated scRNA-seq followed by genetic interrogation reveals RUNX1 is a key driver of fibroblast states. Importantly, the ectopic induction or accumulation of epithelial transitional states induce rapid formation of transient alveolar fibroblasts, leading to organ-wide fibrosis. Conversely, the elimination of epithelial or fibroblast transitional states or RUNX1 loss, leads to tissue simplification resembling emphysema. This work uncovered a key role for transitional states in orchestrating tissue topologies during regeneration.

Keywords:  RUNX1; alveolar epithelial cells; alveolar fibroblasts; emphysema; extracellular matrix organization; fibrosis; lung regeneration; remodeling; tissue topology; transitional states

DOI:  https://doi.org/10.1016/j.stem.2023.10.001
Trends Genet. 2023 Nov 06. pii: S0168-9525(23)00235-4. [Epub ahead of print]

Pioneer factors: roles and their regulation in development.

Amandine Barral, Kenneth S Zaret.

  Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.

Keywords:  development; gene expression; heterochromatin; nucleosome; pioneer factor; zygotic gene activation

DOI:  https://doi.org/10.1016/j.tig.2023.10.007
Gene. 2023 Nov 01. pii: S0378-1119(23)00801-6. [Epub ahead of print] 147960

Perspective: "Current Understanding of NADs Dynamics and Mechanisms of Disease".

Amrita Kumari, Anastassiia Vertii.

  Chromatin architecture is essential for gene regulation, and multiple levels of the 3D chromatin organization exhibit dynamic changes during organismal development and cell differentiation. Heterochromatin, termed compartment B in Hi-C datasets, is a phase-separating gene-silencing form of chromatin, preferentially located at the two nuclear sites, nuclear (lamina-associate chromatin domains, LADs) and nucleoli (nucleoli-associated chromatin domains, NADs) peripheries. LADs and NADs contain both interchangeable and location-specific chromatin domains. Recent studies suggest striking dynamics in LADs and NADs during the differentiation of embryonic stem cells into neural progenitors and neurons. Here we discuss recent advances in understanding NADs changes during neuronal differentiation and future questions on how NADs integrity can contribute to healthy neurodevelopment and neurodevelopment diseases.

Keywords:  chromatin; differentiation; heterochromatin; histone modification; neurodevelopment; nucleolus-associated chromatin domains (NADs)

DOI:  https://doi.org/10.1016/j.gene.2023.147960
Mol Cell. 2023 Oct 26. pii: S1097-2765(23)00807-9. [Epub ahead of print]

Transcriptional elongation control in developmental gene expression, aging, and disease.

Yuki Aoi, Ali Shilatifard.

  The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.

Keywords:  BRD4; CDK9; Integrator; NELF; RNA polymerase II; SEC; SPT5; SPT6; aging; cancer; development; elongation; super elongation complex; transcription

DOI:  https://doi.org/10.1016/j.molcel.2023.10.004
Nat Cell Biol. 2023 Nov;25(11): 1625-1636

Mitopherogenesis, a form of mitochondria-specific ectocytosis, regulates sperm mitochondrial quantity and fertility.

Peng Liu, Jing Shi, Danli Sheng, Wenqing Lu, Jie Guo, Lei Gao, Xiaoqing Wang, Shaofeng Wu, Yanwen Feng, Dashan Dong, Xiaoshuai Huang, Hongyun Tang.

Mitochondrial export into the extracellular space is emerging as a fundamental cellular process implicated in diverse physiological activities. Although a few studies have shed light on the process of discarding damaged mitochondria, how mitochondria are exported and the functions of mitochondrial release remain largely unclear. Here we describe mitopherogenesis, a formerly unknown process that specifically secretes mitochondria through a unique extracellular vesicle termed a 'mitopher'. We observed that during sperm development in male Caenorhabditis elegans, healthy mitochondria are exported out of the spermatids through mitopherogenesis and each of the generated mitophers harbours only one mitochondrion. In mitopherogenesis, the plasma membrane first forms mitochondrion-embedding outward buds, which then promptly bud off and thereby result in the generation of mitophers. Mechanistically, extracellular protease signalling in the testis triggers mitopher formation from spermatids, which is partially mediated by the tyrosine kinase SPE-8. Moreover, mitopherogenesis requires normal microfilament dynamics, whereas myosin VI antagonizes mitopher generation. Strikingly, our three-dimensional electron microscopy analyses indicate that mitochondrial quantity requires precise modulation during sperm development, which is critically mediated by mitopherogenesis. Inhibition of mitopherogenesis causes accumulation of mitochondria in sperm, which may lead to sperm motility and fertility defects. Our findings identify mitopherogenesis as a previously undescribed process for mitochondria-specific ectocytosis, which may represent a fundamental branch of mechanisms underlying mitochondrial quantity control to regulate cell functions during development.

DOI: https://doi.org/10.1038/s41556-023-01264-z
Commun Biol. 2023 11 07. 6(1): 1129

Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus.

Tetsuya Yamamoto, Tomohiro Yamazaki, Kensuke Ninomiya, Tetsuro Hirose.

Liquid-liquid phase separation (LLPS) has been thought to be the biophysical principle governing the assembly of the multiphase structures of nucleoli, the site of ribosomal biogenesis. Condensates assembled through LLPS increase their sizes to minimize the surface energy as far as their components are available. However, multiple microphases, fibrillar centers (FCs), dispersed in a nucleolus are stable and their sizes do not grow unless the transcription of pre-ribosomal RNA (pre-rRNA) is inhibited. To understand the mechanism of the suppression of the FC growth, we here construct a minimal theoretical model by taking into account nascent pre-rRNAs tethered to FC surfaces by RNA polymerase I. The prediction of this theory was supported by our experiments that quantitatively measure the dependence of the size of FCs on the transcription level. This work sheds light on the role of nascent RNAs in controlling the size of nuclear bodies.

DOI: https://doi.org/10.1038/s42003-023-05519-1
Nat Cell Biol. 2023 Nov;25(11): 1637-1649

Non-canonical MLL1 activity regulates centromeric phase separation and genome stability.

Liang Sha, Zi Yang, Sojin An, Wentao Yang, Sungmin Kim, Hoon Oh, Jing Xu, Jun Yin, He Wang, Heinz-Josef Lenz, Woojin An, Uhn-Soo Cho, Yali Dou.

Epigenetic dysregulation is a prominent feature in cancer, as exemplified by frequent mutations in chromatin regulators, including the MLL/KMT2 family of histone methyltransferases. Although MLL1/KMT2A activity on H3K4 methylation is well documented, their non-canonical activities remain mostly unexplored. Here we show that MLL1/KMT2A methylates Borealin K143 in the intrinsically disordered region essential for liquid-liquid phase separation of the chromosome passenger complex (CPC). The co-crystal structure highlights the distinct binding mode of the MLL1 SET domain with Borealin K143. Inhibiting MLL1 activity or mutating Borealin K143 to arginine perturbs CPC phase separation, reduces Aurora kinase B activity, and impairs the resolution of erroneous kinetochore-microtubule attachments and sister-chromatid cohesion. They significantly increase chromosome instability and aneuploidy in a subset of hepatocellular carcinoma, resulting in growth inhibition. These results demonstrate a non-redundant function of MLL1 in regulating inner centromere liquid condensates and genome stability via a non-canonical enzymatic activity.

DOI: https://doi.org/10.1038/s41556-023-01270-1
Nat Struct Mol Biol. 2023 Nov 09.

The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.

Julian R Braxton, Chad R Altobelli, Maxwell R Tucker, Eric Tse, Aye C Thwin, Michelle R Arkin, Daniel R Southworth.

p97, also known as valosin-containing protein, is an essential cytosolic AAA+ (ATPases associated with diverse cellular activities) hexamer that unfolds substrate polypeptides to support protein homeostasis and macromolecular disassembly. Distinct sets of p97 adaptors guide cellular functions but their roles in direct control of the hexamer are unclear. The UBXD1 adaptor localizes with p97 in critical mitochondria and lysosome clearance pathways and contains multiple p97-interacting domains. Here we identify UBXD1 as a potent p97 ATPase inhibitor and report structures of intact human p97-UBXD1 complexes that reveal extensive UBXD1 contacts across p97 and an asymmetric remodeling of the hexamer. Conserved VIM, UBX and PUB domains tether adjacent protomers while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface. An additional VIM-connecting helix binds along the second (D2) AAA+ domain. Together, these contacts split the hexamer into a ring-open conformation. Structures, mutagenesis and comparisons to other adaptors further reveal how adaptors containing conserved p97-remodeling motifs regulate p97 ATPase activity and structure.

DOI: https://doi.org/10.1038/s41594-023-01126-0
Curr Biol. 2023 Nov 06. pii: S0960-9822(23)01409-4. [Epub ahead of print]

A cell-based model for size control in the multiple fission alga Chlamydomonas reinhardtii.

Dianyi Liu, César Augusto Vargas-García, Abhyudai Singh, James Umen.

  Understanding how population-size homeostasis emerges from stochastic individual cell behaviors remains a challenge in biology.1,2,3,4,5,6,7 The unicellular green alga Chlamydomonas reinhardtii (Chlamydomonas) proliferates using a multiple fission cell cycle, where a prolonged G1 phase is followed by n rounds of alternating division cycles (S/M) to produce 2n daughters. A "Commitment" sizer in mid-G1 phase ensures sufficient cell growth before completing the cell cycle. A mitotic sizer couples mother-cell size to division number (n) such that daughter size distributions are uniform regardless of mother size distributions. Although daughter size distributions were highly robust to altered growth conditions, ∼40% of daughter cells fell outside of the 2-fold range expected from a "perfect" multiple fission sizer.7,8 A simple intuitive power law model with stochastic noise failed to reproduce individual division behaviors of tracked single cells. Through additional iterative modeling, we identified an alternative modified threshold (MT) model, where cells need to cross a threshold greater than 2-fold their median starting size to become division-competent (i.e., Committed), after which their behaviors followed a power law model. The Commitment versus mitotic size threshold uncoupling in the MT model was likely a key pre-adaptation in the evolution of volvocine algal multicellularity. A similar experimental approach was used in size mutants mat3/rbr and dp1 that are, respectively, missing repressor or activator subunits of the retinoblastoma tumor suppressor complex (RBC). Both mutants showed altered relationships between Commitment and mitotic sizer, suggesting that RBC functions to decouple the two sizers.

Keywords:  cell cycle; cell imaging; quantitative modeling; retinoblastoma; stochastic behavior; volvocine algae

DOI:  https://doi.org/10.1016/j.cub.2023.10.023
Cell Res. 2023 Nov 07.

NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos.

Fangnong Lai, Lijia Li, Xiaoyu Hu, Bofeng Liu, Ziqi Zhu, Ling Liu, Qiang Fan, Huabin Tian, Kai Xu, Xukun Lu, Qing Li, Kong Feng, Lijuan Wang, Zili Lin, Hongyu Deng, Jinsong Li, Wei Xie.

Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to the inner cell mass (ICM) where pluripotent epiblast arises, and extraembryonic trophectoderm. However, how ZGA is connected to the first lineage segregation in mammalian embryos remains elusive. Here, we investigated the role of nuclear receptor (NR) transcription factors (TFs), whose motifs are highly enriched and accessible from the 2-cell (2C) to 8-cell (8C) stages in mouse embryos. We found that NR5A2, an NR TF strongly induced upon ZGA, was required for this connection. Upon Nr5a2 knockdown or knockout, embryos developed beyond 2C normally with the zygotic genome largely activated. However, 4-8C-specific gene activation was substantially impaired and Nr5a2-deficient embryos subsequently arrested at the morula stage. Genome-wide chromatin binding analysis showed that NR5A2-bound cis-regulatory elements in both 2C and 8C embryos are strongly enriched for B1 elements where its binding motif is embedded. NR5A2 was not required for the global opening of its binding sites in 2C embryos but was essential to the opening of its 8C-specific binding sites. These 8C-specific, but not 2C-specific, binding sites are enriched near genes involved in blastocyst and stem cell regulation, and are often bound by master pluripotency TFs in blastocysts and embryonic stem cells (ESCs). Importantly, NR5A2 regulated key pluripotency genes Nanog and Pou5f1/Oct4, and primitive endoderm regulatory genes including Gata6 among many early ICM genes, as well as key trophectoderm regulatory genes including Tead4 and Gata3 at the 8C stage. By contrast, master pluripotency TFs NANOG, SOX2, and OCT4 targeted both early and late ICM genes in mouse ESCs. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that bridges ZGA to the first lineage segregation during mouse early development.

DOI: https://doi.org/10.1038/s41422-023-00887-z
PLoS Genet. 2023 Nov 10. 19(11): e1011026

Exportin-mediated nucleocytoplasmic transport maintains Pch2 homeostasis during meiosis.

Esther Herruzo, Estefanía Sánchez-Díaz, Sara González-Arranz, Beatriz Santos, Jesús A Carballo, Pedro A San-Segundo.

The meiotic recombination checkpoint reinforces the order of events during meiotic prophase I, ensuring the accurate distribution of chromosomes to the gametes. The AAA+ ATPase Pch2 remodels the Hop1 axial protein enabling adequate levels of Hop1-T318 phosphorylation to support the ensuing checkpoint response. While these events are localized at chromosome axes, the checkpoint activating function of Pch2 relies on its cytoplasmic population. In contrast, forced nuclear accumulation of Pch2 leads to checkpoint inactivation. Here, we reveal the mechanism by which Pch2 travels from the cell nucleus to the cytoplasm to maintain Pch2 cellular homeostasis. Leptomycin B treatment provokes the nuclear accumulation of Pch2, indicating that its nucleocytoplasmic transport is mediated by the Crm1 exportin recognizing proteins containing Nuclear Export Signals (NESs). Consistently, leptomycin B leads to checkpoint inactivation and impaired Hop1 axial localization. Pch2 nucleocytoplasmic traffic is independent of its association with Zip1 and Orc1. We also identify a functional NES in the non-catalytic N-terminal domain of Pch2 that is required for its nucleocytoplasmic trafficking and proper checkpoint activity. In sum, we unveil another layer of control of Pch2 function during meiosis involving nuclear export via the exportin pathway that is crucial to maintain the critical balance of Pch2 distribution among different cellular compartments.

DOI: https://doi.org/10.1371/journal.pgen.1011026
Nat Cell Biol. 2023 Nov;25(11): 1664-1675

Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles.

Hiro Takakuwa, Tomohiro Yamazaki, Sylvie Souquere, Shungo Adachi, Hyura Yoshino, Naoko Fujiwara, Tetsuya Yamamoto, Tohru Natsume, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose.

Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 long noncoding RNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 long noncoding RNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.

DOI: https://doi.org/10.1038/s41556-023-01254-1
Nat Commun. 2023 Nov 06. 14(1): 7130

Disrupting cellular memory to overcome drug resistance.

Guillaume Harmange, Raúl A Reyes Hueros, Dylan L Schaff, Benjamin Emert, Michael Saint-Antoine, Laura C Kim, Zijian Niu, Shivani Nellore, Mitchell E Fane, Gretchen M Alicea, Ashani T Weeraratna, M Celeste Simon, Abhyudai Singh, Sydney M Shaffer.

Gene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching. Here, we develop a lineage tracing-based technique to quantify memory and identify cells that switch states. Applied to melanoma cells without therapy, we quantify long-lived fluctuations in gene expression that are predictive of later resistance to targeted therapy. We also identify the PI3K and TGF-β pathways as state switching modulators. We propose a pretreatment model, first applying a PI3K inhibitor to modulate gene expression states, then applying targeted therapy, which leads to less resistance than targeted therapy alone. Together, we present a method for finding modulators of gene expression memory and their associated cell fates.

DOI: https://doi.org/10.1038/s41467-023-41811-8
Dev Cell. 2023 Oct 28. pii: S1534-5807(23)00524-5. [Epub ahead of print]

Solubility phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition.

Hyojeong Hwang, Sijie Chen, Meng Ma, Divyanshi, Hao-Chun Fan, Elizabeth Borwick, Elvan Böke, Wenyan Mei, Jing Yang.

  The oocyte-to-embryo transition (OET) is regulated by maternal products stored in the oocyte cytoplasm, independent of transcription. How maternal products are precisely remodeled to dictate the OET remains largely unclear. In this work, we discover the dynamic solubility phase transition of maternal RNAs during Xenopus OET. We have identified 863 maternal transcripts that transition from a soluble state to a detergent-insoluble one after oocyte maturation. These RNAs are enriched in the animal hemisphere, and many of them encode key cell cycle regulators. In contrast, 165 transcripts, including nearly all Xenopus germline RNAs and some vegetally localized somatic RNAs, undergo an insoluble-to-soluble phase transition. This phenomenon is conserved in zebrafish. Our results demonstrate that the phase transition of germline RNAs influences their susceptibility to RNA degradation machinery and is mediated by the remodeling of germ plasm. This work thus identifies important remodeling mechanisms that act on RNAs to control vertebrate OET.

Keywords:  Bucky ball; RNA phase transition; Xenopus; Xvelo1; germ plasm; oocyte-to-embryo transition; zebrafish

DOI:  https://doi.org/10.1016/j.devcel.2023.10.005
Nat Struct Mol Biol. 2023 Nov 06.

Structure of the transcribing RNA polymerase II-Elongin complex.

Ying Chen, Goran Kokic, Christian Dienemann, Olexandr Dybkov, Henning Urlaub, Patrick Cramer.

Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.

DOI: https://doi.org/10.1038/s41594-023-01138-w
J Cell Biol. 2023 Dec 04. pii: e202309021. [Epub ahead of print]222(12):

Mechanisms of actin disassembly and turnover.

Bruce L Goode, Julian Eskin, Shashank Shekhar.

Cellular actin networks exhibit a wide range of sizes, shapes, and architectures tailored to their biological roles. Once assembled, these filamentous networks are either maintained in a state of polarized turnover or induced to undergo net disassembly. Further, the rates at which the networks are turned over and/or dismantled can vary greatly, from seconds to minutes to hours or even days. Here, we review the molecular machinery and mechanisms employed in cells to drive the disassembly and turnover of actin networks. In particular, we highlight recent discoveries showing that specific combinations of conserved actin disassembly-promoting proteins (cofilin, GMF, twinfilin, Srv2/CAP, coronin, AIP1, capping protein, and profilin) work in concert to debranch, sever, cap, and depolymerize actin filaments, and to recharge actin monomers for new rounds of assembly.

DOI: https://doi.org/10.1083/jcb.202309021
Nat Commun. 2023 Nov 04. 14(1): 7102

Transcriptional repression of beige fat innervation via a YAP/TAZ-S100B axis.

Xun Huang, Xinmeng Li, Hongyu Shen, Yiheng Zhao, Zhao Zhou, Yushuang Wang, Jingfei Yao, Kaili Xue, Dongmei Wu, Yifu Qiu.

Sympathetic innervation is essential for the development of functional beige fat that maintains body temperature and metabolic homeostasis, yet the molecular mechanisms controlling this innervation remain largely unknown. Here, we show that adipocyte YAP/TAZ inhibit sympathetic innervation of beige fat by transcriptional repression of neurotropic factor S100B. Adipocyte-specific loss of Yap/Taz induces S100b expression to stimulate sympathetic innervation and biogenesis of functional beige fat both in subcutaneous white adipose tissue (WAT) and browning-resistant visceral WAT. Mechanistically, YAP/TAZ compete with C/EBPβ for binding to the zinc finger-2 domain of PRDM16 to suppress S100b transcription, which is released by adrenergic-stimulated YAP/TAZ phosphorylation and inactivation. Importantly, Yap/Taz loss in adipocytes or AAV-S100B overexpression in visceral WAT restricts both age-associated and diet-induced obesity, and improves metabolic homeostasis by enhancing energy expenditure of mice. Together, our data reveal that YAP/TAZ act as a brake on the beige fat innervation by blocking PRDM16-C/EBPβ-mediated S100b expression.

DOI: https://doi.org/10.1038/s41467-023-43021-8
Mol Cell Biol. 2023 Nov 08. 1-15

RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes.

Preeti Khan, Priyabrata Singha, Ronita Nag Chaudhuri.

  Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.

Keywords:  H3K56; H4K16; RNA polymerase II; gene expression; histone acetylation; transcription regulation

DOI:  https://doi.org/10.1080/10985549.2023.2270912
Nature. 2023 Nov;623(7986): 283-291

The power and potential of mitochondria transfer.

Nicholas Borcherding, Jonathan R Brestoff.

Mitochondria are believed to have originated through an ancient endosymbiotic process in which proteobacteria were captured and co-opted for energy production and cellular metabolism. Mitochondria segregate during cell division and differentiation, with vertical inheritance of mitochondria and the mitochondrial DNA genome from parent to daughter cells. However, an emerging body of literature indicates that some cell types export their mitochondria for delivery to developmentally unrelated cell types, a process called intercellular mitochondria transfer. In this Review, we describe the mechanisms by which mitochondria are transferred between cells and discuss how intercellular mitochondria transfer regulates the physiology and function of various organ systems in health and disease. In particular, we discuss the role of mitochondria transfer in regulating cellular metabolism, cancer, the immune system, maintenance of tissue homeostasis, mitochondrial quality control, wound healing and adipose tissue function. We also highlight the potential of targeting intercellular mitochondria transfer as a therapeutic strategy to treat human diseases and augment cellular therapies.

DOI: https://doi.org/10.1038/s41586-023-06537-z
Nat Commun. 2023 Nov 03. 14(1): 7036

Dissecting the human leptomeninges at single-cell resolution.

Nicola A Kearns, Artemis Iatrou, Daniel J Flood, Sashini De Tissera, Zachary M Mullaney, Jishu Xu, Chris Gaiteri, David A Bennett, Yanling Wang.

Emerging evidence shows that the meninges conduct essential immune surveillance and immune defense at the brain border, and the dysfunction of meningeal immunity contributes to aging and neurodegeneration. However, no study exists on the molecular properties of cell types within human leptomeninges. Here, we provide single nuclei profiling of dissected postmortem leptomeninges from aged individuals. We detect diverse cell types, including unique meningeal endothelial, mural, and fibroblast subtypes. For immune cells, we show that most T cells express CD8 and bear characteristics of tissue-resident memory T cells. We also identify distinct subtypes of border-associated macrophages (BAMs) that display differential gene expressions from microglia and express risk genes for Alzheimer's Disease (AD), as nominated by genome-wide association studies (GWAS). We discover cell-type-specific differentially expressed genes in individuals with Alzheimer's dementia, particularly in fibroblasts and BAMs. Indeed, when cultured, leptomeningeal cells display the signature of ex vivo AD fibroblasts upon amyloid-β treatment. We further explore ligand-receptor interactions within the leptomeningeal niche and computationally infer intercellular communications in AD. Thus, our study establishes a molecular map of human leptomeningeal cell types, providing significant insight into the border immune and fibrotic responses in AD.

DOI: https://doi.org/10.1038/s41467-023-42825-y
PLoS Genet. 2023 Nov 09. 19(11): e1011028

Context-dependent ciliary regulation of hedgehog pathway repression in tissue morphogenesis.

Sun-Hee Hwang, Kevin Andrew White, Bandarigoda Nipunika Somatilaka, Baolin Wang, Saikat Mukhopadhyay.

A fundamental problem in tissue morphogenesis is identifying how subcellular signaling regulates mesoscale organization of tissues. The primary cilium is a paradigmatic organelle for compartmentalized subcellular signaling. How signaling emanating from cilia orchestrates tissue organization-especially, the role of cilia-generated effectors in mediating diverse morpho-phenotypic outcomes-is not well understood. In the hedgehog pathway, bifunctional GLI transcription factors generate both GLI-activators (GLI-A) and GLI-repressors (GLI-R). The formation of GLI-A/GLI-R requires cilia. However, how these counterregulatory effectors coordinate cilia-regulated morphogenetic pathways is unclear. Here we determined GLI-A/GLI-R requirements in phenotypes arising from lack of hedgehog pathway repression (derepression) during mouse neural tube and skeletal development. We studied hedgehog pathway repression by the GPCR GPR161, and the ankyrin repeat protein ANKMY2 that direct cAMP/protein kinase-A signaling by cilia in GLI-R generation. We performed genetic epistasis between Gpr161 or Ankmy2 mutants, and Gli2/Gli3 knockouts, Gli3R knock-in and knockout of Smoothened, the hedgehog pathway transducer. We also tested the role of cilia-generated signaling using a Gpr161 ciliary localization knock-in mutant that is cAMP signaling competent. We found that the cilia-dependent derepression phenotypes arose in three modes: lack of GLI-R only, excess GLI-A formation only, or dual regulation of either lack of GLI-R or excess GLI-A formation. These modes were mostly independent of Smoothened. The cAMP signaling-competent non-ciliary Gpr161 knock-in recapitulated Gpr161 loss-of-function tissue phenotypes solely from lack of GLI-R only. Our results show complex tissue-specific GLI-effector requirements in morphogenesis and point to tissue-specific GLI-R thresholds generated by cilia in hedgehog pathway repression. Broadly, our study sets up a conceptual framework for rationalization of different modes of signaling generated by the primary cilium in mediating morphogenesis in diverse tissues.

DOI: https://doi.org/10.1371/journal.pgen.1011028
Am J Hematol. 2023 Nov 06.

Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways.

Julien Papoin, Hongxia Yan, Marjorie Leduc, Morgane Le Gall, Anupama Narla, James Palis, Laurie A Steiner, Patrick G Gallagher, Christopher D Hillyer, Emilie-Fleur Gautier, Narla Mohandas, Lionel Blanc.

Human erythropoiesis is a complex process leading to the production of 2.5 million red blood cells per second. Following commitment of hematopoietic stem cells to the erythroid lineage, this process can be divided into three distinct stages: erythroid progenitor differentiation, terminal erythropoiesis, and reticulocyte maturation. We recently resolved the heterogeneity of erythroid progenitors into four different subpopulations termed EP1-EP4. Here, we characterized the growth factor(s) responsiveness of these four progenitor populations in terms of proliferation and differentiation. Using mass spectrometry-based proteomics on sorted erythroid progenitors, we quantified the absolute expression of ~5500 proteins from EP1 to EP4. Further functional analyses highlighted dynamic changes in cell cycle in these populations with an acceleration of the cell cycle during erythroid progenitor differentiation. The finding that E2F4 expression was increased from EP1 to EP4 is consistent with the noted changes in cell cycle. Finally, our proteomic data suggest that the protein machinery necessary for both oxidative phosphorylation and glycolysis is present in these progenitor cells. Together, our data provide comprehensive insights into growth factor-dependence of erythroid progenitor proliferation and the proteome of four distinct populations of human erythroid progenitors which will be a useful framework for the study of erythroid disorders.

DOI: https://doi.org/10.1002/ajh.27145
Curr Opin Biomed Eng. 2023 Dec;pii: 100502. [Epub ahead of print]28

Using biophysical cues and biomaterials to improve genetic models.

Thomas G Molley, Adam J Engler.

  With the advent of induced pluripotent stem cells and modern differentiation protocols, many advances in our understanding of disease have been made possible by in vitro disease modeling; in some cases, their use may have supplanted animal models. Yet in vitro models often rely on rigid cell culture substrates that could limit our ability to completely reproduce human disease in a dish. Nascent work, however, suggests that the combination of biomaterials and/or advanced microphysiological systems-which better recapitulate tissue properties-with stem cells expressing disease mimicking genetics, could substantially improve current disease modeling efforts where genetics alone is insufficient. This review will highlight such recent advances as well as review current challenges that the fields must overcome to create more personalized therapeutics in the future.

Keywords:  Disease modeling; Extracellular matrix; Genome editing; Organoids; Stem cells

DOI:  https://doi.org/10.1016/j.cobme.2023.100502
JCI Insight. 2023 Nov 07. pii: e172977. [Epub ahead of print]

PGF2α signaling drives fibrotic remodeling and fibroblast population dynamics in mice.

Luis R Rodriguez, Soon Yew Tang, Willy Roque Barboza, Aditi Murthy, Yaniv Tomer, Tian-Quan Cai, Swati Iyer, Katrina Chavez, Ujjalkumar Subhash Das, Soumita Ghosh, Charlotte Cooper, Thalia T Dimopoulos, Apoorva Babu, Caitlin F Connelly, Garret A FitzGerald, Michael F Beers.

  Idiopathic Pulmonary Fibrosis (IPF) is a chronic parenchymal lung disease characterized by repetitive alveolar cell injury, myofibroblast proliferation, and excessive extracellular matrix deposition for which unmet need persists for effective therapeutics. The bioactive eicosanoid, prostaglandin F2a, and its cognate receptor FPr (Ptfgr) are implicated as a TGFβ1 independent signaling hub for IPF. To assess this, we leveraged our published murine PF model (IER-SftpcI73T) expressing a disease-associated missense mutation in the surfactant protein C (Sftpc) gene. Tamoxifen treated IER-SftpcI73T mice develop an early multiphasic alveolitis and transition to spontaneous fibrotic remodeling by 28 days. IER-SftpcI73T mice crossed to a Ptgfr null (FPr-/-) line showed attenuated weight loss and gene dosage dependent rescue of mortality compared to FPr+/+ cohorts. IER-SftpcI73T/FPr-/- mice also showed reductions in multiple fibrotic endpoints for which administration of nintedanib was not additive. Single cell RNA sequencing, pseudotime analysis, and in vitro assays demonstrated Ptgfr expression predominantly within adventitial fibroblasts which were reprogrammed to an "inflammatory/transitional" cell state in a PGF2a/ FPr dependent manner. Collectively, the findings provide evidence for a role for PGF2a signaling in IPF, mechanistically identify a susceptible fibroblast subpopulation, and establish a benchmark effect size for disruption of this pathway in mitigating fibrotic lung remodeling.

Keywords:  Eicosanoids; Fibrosis; Molecular biology; Pulmonology

DOI:  https://doi.org/10.1172/jci.insight.172977
Trends Immunol. 2023 Nov 06. pii: S1471-4906(23)00211-9. [Epub ahead of print]

Macrophage phenotypes and functions: resolving inflammation and restoring homeostasis.

Patricia Rodríguez-Morales, Ruth A Franklin.

  Inflammation must be tightly regulated to both defend against pathogens and restore tissue homeostasis. The resolution of inflammatory responses is a dynamic process orchestrated by cells of the immune system. Macrophages, tissue-resident innate immune cells, are key players in modulating inflammation. Here, we review recent work highlighting the importance of macrophages in tissue resolution and the return to homeostasis. We propose that enhancing macrophage pro-resolution functions represents a novel and widely applicable therapeutic strategy to dampen inflammation, promote repair, and restore tissue integrity and function.

Keywords:  SARS-CoV-2; efferocytosis; fibrosis; inflammation; macrophages; tissue repair

DOI:  https://doi.org/10.1016/j.it.2023.10.004
Nat Rev Genet. 2023 Nov 08.

Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.

Ksenia Krupina, Alexander Goginashvili, Don W Cleveland.

Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.

DOI: https://doi.org/10.1038/s41576-023-00663-0
Genes Dev. 2023 Nov 06.

Comprehensive mapping of cell fates in microsatellite unstable cancer cells supports dual targeting of WRN and ATR.

Dali Zong, Natasha C Koussa, James A Cornwell, Ajith V Pankajam, Michael J Kruhlak, Nancy Wong, Raj Chari, Steven D Cappell, André Nussenzweig.

  Addiction to the WRN helicase is a unique vulnerability of human cancers with high levels of microsatellite instability (MSI-H). However, while prolonged loss of WRN ultimately leads to cell death, little is known about how MSI-H cancers initially respond to acute loss of WRN-knowledge that would be helpful for informing clinical development of WRN targeting therapy, predicting possible resistance mechanisms, and identifying useful biomarkers of successful WRN inhibition. Here, we report the construction of an inducible ligand-mediated degradation system in which the stability of endogenous WRN protein can be rapidly and specifically tuned, enabling us to track the complete sequence of cellular events elicited by acute loss of WRN function. We found that WRN degradation leads to immediate accrual of DNA damage in a replication-dependent manner that curiously did not robustly engage checkpoint mechanisms to halt DNA synthesis. As a result, WRN-degraded MSI-H cancer cells accumulate DNA damage across multiple replicative cycles and undergo successive rounds of increasingly aberrant mitoses, ultimately triggering cell death. Of potential therapeutic importance, we found no evidence of any generalized mechanism by which MSI-H cancers could adapt to near-complete loss of WRN. However, under conditions of partial WRN degradation, addition of low-dose ATR inhibitor significantly increased their combined efficacy to levels approaching full inactivation of WRN. Overall, our results provide the first comprehensive view of molecular events linking upstream inhibition of WRN to subsequent cell death and suggest that dual targeting of WRN and ATR might be a useful strategy for treating MSI-H cancers.

Keywords:  ATR; WRN; microsatellite instability; synthetic lethality

DOI:  https://doi.org/10.1101/gad.351085.123
Nat Commun. 2023 Nov 09. 14(1): 7262

A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process.

Ruiqi Liao, Abiola Babatunde, Stephanie Qiu, Hamsini Harikumar, Joshua J Coon, Katherine A Overmyer, Yusuf A Hannun, Chiara Luberto, Emery H Bresnick.

Transcriptional mechanisms controlling developmental processes establish and maintain proteomic networks, which can govern the levels of intracellular small molecules. Although dynamic changes in bioactive small molecules can link transcription factor and genome activity with cell state transitions, many mechanistic questions are unresolved. Using quantitative lipidomics and multiomics, we discover that the hematopoietic transcription factor GATA1 establishes ceramide homeostasis during erythroid differentiation by regulating genes encoding sphingolipid metabolic enzymes. Inhibiting a GATA1-induced sphingolipid biosynthetic enzyme, delta(4)-desaturase, or disrupting ceramide homeostasis with cell-permeable dihydroceramide or ceramide is detrimental to erythroid, but not myeloid, progenitor activity. Coupled with genetic editing-based rewiring of the regulatory circuitry, we demonstrate that ceramide homeostasis commissions vital stem cell factor and erythropoietin signaling by opposing an inhibitory protein phosphatase 2A-dependent, dual-component mechanism. Integrating bioactive lipids as essential components of GATA factor mechanisms to control cell state transitions has implications for diverse cell and tissue types.

DOI: https://doi.org/10.1038/s41467-023-42978-w
J Biol Chem. 2023 Nov 08. pii: S0021-9258(23)02486-9. [Epub ahead of print] 105458

Mitochondrial Permeability Transition Regulator, Cyclophilin D, is Transcriptionally Activated by C/EBP During Adipogenesis.

Chen Yu, Rubens Sautchuk, John Martinez, Roman A Eliseev.

  Age-related bone loss is associated with decreased bone formation, increased bone resorption and accumulation of bone marrow fat. During aging, differentiation potential of bone marrow stromal (a.k.a. mesenchymal stem) cells (BMSCs) is shifted towards an adipogenic lineage and away from an osteogenic lineage. In aged bone tissue, we previously observed pathological opening of the mitochondrial permeability transition pore (MPTP) which leads to mitochondrial dysfunction, oxidative phosphorylation uncoupling, and cell death. Cyclophilin D (CypD) is a mitochondrial protein that facilitates opening of the MPTP. We found earlier that CypD is downregulated during osteogenesis of BMSCs leading to lower MPTP activity and, thus, protecting mitochondria from dysfunction. However, during adipogenesis, a fate alternative to osteogenesis, the regulation of mitochondrial function and CypD expression is still unclear. In this study, we observed that BMSCs have increased CypD expression and MPTP activity, activated glycolysis, and fragmented mitochondrial network during adipogenesis. Adipogenic C/EBPα acts as a transcriptional activator of expression of the CypD gene, Ppif, during this process. Inflammation-associated transcription factor NF-κB shows a synergistic effect with C/EBPα inducing Ppif expression. Overall, we demonstrated changes in mitochondrial morphology and function during adipogenesis. We also identified C/EBPα as a transcriptional activator of CypD. The synergistic activation of CypD by C/EBPα and the NF-κB p65 subunit during this process suggests a potential link between adipogenic signaling, inflammation, and MPTP gain-of-function, thus altering BMSC fate during aging.

Keywords:  Adipogenesis; C/EBP; Cyclophilin D; Mitochondrial permeability transition

DOI:  https://doi.org/10.1016/j.jbc.2023.105458
Mol Cell. 2023 Nov 02. pii: S1097-2765(23)00806-7. [Epub ahead of print]83(21): 3801-3817.e8

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation.

Corina Pascal, Jonathan Zonszain, Ofir Hameiri, Chen Gargi-Levi, Galit Lev-Maor, Luna Tammer, Tamar Levy, Anan Tarabeih, Vanessa Rachel Roy, Stav Ben-Salmon, Liraz Elbaz, Mireille Eid, Tamar Hakim, Salima Abu Rabe'a, Nana Shalev, Albert Jordan, Eran Meshorer, Gil Ast.

  Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.

Keywords:  ChIP-seq; GC content; H1 histones; PRO-seq; RNA polymerase II elongation; RNA-seq; alternative splicing; exon skipping; intron retention

DOI:  https://doi.org/10.1016/j.molcel.2023.10.003
Mol Hum Reprod. 2023 Nov 09. pii: gaad039. [Epub ahead of print]

Human follicular fluid elicits select dose- and age-dependent effects on mouse oocytes and cumulus-oocyte-complexes in a heterologous in vitro maturation assay.

Shweta S Dipali, Chanakarn Suebthawinkul, Joanna E Burdette, Mary Ellen Pavone, Francesca E Duncan.

  Follicular fluid (FF) is a primary microenvironment of the oocyte within an antral follicle. Although several studies have defined the composition of human FF in normal physiology and determined how it is altered in disease states, the direct impacts of human FF on the oocyte are not well understood. The difficulty of obtaining suitable numbers of human oocytes for research makes addressing such a question challenging. Therefore, we used a heterologous model in which we cultured mouse oocytes in human FF. To determine whether FF has dose-dependent effects on gamete quality, we performed in vitro maturation of denuded oocytes from reproductively young mice (6-12 weeks) in 10%, 50% or 100% FF from participants of mid-reproductive age (32-36 years). FF impacted meiotic competence in a dose-dependent manner, with concentrations >10% inhibiting meiotic progression and resulting in spindle and chromosome alignment defects. We previously demonstrated that human FF acquires a fibro-inflammatory cytokine signature with age. Thus, to determine whether exposure to an aging FF microenvironment contributes to the age-dependent decrease in gamete quality, we matured denuded oocytes and cumulus-oocyte-complexes (COCs) in FF from reproductively young (28-30 years) and old (40-42 years) participants. FF decreased meiotic progression of COCs, but not oocytes, from reproductively young and old (9-12 months) mice in an age-dependent manner. Moreover, FF had modest age-dependent impacts on mitochondrial aggregation in denuded oocytes and cumulus layer expansion dynamics in COCs, which may influence fertilization or early embryo development. Overall, these findings demonstrate that acute human FF exposure can impact select markers of mouse oocyte quality in both dose- and age-dependent manners.

Keywords:  chromosome; cumulus expansion; cumulus-oocyte-complex; follicular fluid; meiosis; mitochondria; oocyte; reproductive aging; spindle

DOI:  https://doi.org/10.1093/molehr/gaad039
Nat Metab. 2023 Nov 09.

Vitamin B5 supports MYC oncogenic metabolism and tumor progression in breast cancer.

CRUK Rosetta Grand Challenge Consortium

Tumors are intrinsically heterogeneous and it is well established that this directs their evolution, hinders their classification and frustrates therapy1-3. Consequently, spatially resolved omics-level analyses are gaining traction4-9. Despite considerable therapeutic interest, tumor metabolism has been lagging behind this development and there is a paucity of data regarding its spatial organization. To address this shortcoming, we set out to study the local metabolic effects of the oncogene c-MYC, a pleiotropic transcription factor that accumulates with tumor progression and influences metabolism10,11. Through correlative mass spectrometry imaging, we show that pantothenic acid (vitamin B5) associates with MYC-high areas within both human and murine mammary tumors, where its conversion to coenzyme A fuels Krebs cycle activity. Mechanistically, we show that this is accomplished by MYC-mediated upregulation of its multivitamin transporter SLC5A6. Notably, we show that SLC5A6 over-expression alone can induce increased cell growth and a shift toward biosynthesis, whereas conversely, dietary restriction of pantothenic acid leads to a reversal of many MYC-mediated metabolic changes and results in hampered tumor growth. Our work thus establishes the availability of vitamins and cofactors as a potential bottleneck in tumor progression, which can be exploited therapeutically. Overall, we show that a spatial understanding of local metabolism facilitates the identification of clinically relevant, tractable metabolic targets.

DOI: https://doi.org/10.1038/s42255-023-00915-7
Annu Rev Physiol. 2023 Nov 06.

Molecular Crowding: Physiologic Sensing and Control.

Arohan R Subramanya, Cary R Boyd-Shiwarski.

The cytoplasm is densely packed with molecules that contribute to its nonideal behavior. Cytosolic crowding influences chemical reaction rates, intracellular water mobility, and macromolecular complex formation. Overcrowding is potentially catastrophic; to counteract this problem, cells have evolved acute and chronic homeostatic mechanisms that optimize cellular crowdedness. Here, we provide a physiology-focused overview of molecular crowding, highlighting contemporary advances in our understanding of its sensing and control. Long hypothesized as a form of crowding-induced microcompartmentation, phase separation allows cells to detect and respond to intracellular crowding through the action of biomolecular condensates, as indicated by recent studies. Growing evidence indicates that crowding is closely tied to cell size and fluid volume, homeostatic responses to physical compression and desiccation, tissue architecture, circadian rhythm, aging, transepithelial transport, and total body electrolyte and water balance. Thus, molecular crowding is a fundamental physiologic parameter that impacts diverse functions extending from molecule to organism. Expected final online publication date for the Annual Review of Physiology, Volume 86 is February 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-042222-025920