bims-ginsta 2024-08-04 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–08–04
33 papers selected by
Jinrong Hu, National University of Singapore

Cell size regulates human endoderm specification through actomyosin-dependent AMOT-YAP signaling.
Transcriptomic balance and optimal growth are determined by cell size.
The fork protection complex promotes parental histone recycling and epigenetic memory.
An egg-sabotaging mechanism drives non-Mendelian transmission in mice.
mTORC1 activity oscillates throughout the cell cycle, promoting mitotic entry and differentially influencing autophagy induction.
ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition.
HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos.
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.
Zygotic spindle orientation defines cleavage pattern and nuclear status of human embryos.
Spindle assembly checkpoint-dependent mitotic delay is required for cell division in absence of centrosomes.
A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance.
Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.
CLASP-mediated competitive binding in protein condensates directs microtubule growth.
mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer.
Cleavage-independent GSDME activation by UVC.
Declining translational capacity as a potential driver for oocyte meiotic instability.
Local nuclear to cytoplasmic ratio regulates chaperone-dependent H3 variant incorporation during zygotic genome activation.
Myocardial Regeneration: Feasible or Fantasy?
Diffusing protein binders to intrinsically disordered proteins.
Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization.
Primitive macrophages induce sarcomeric maturation and functional enhancement of developing human cardiac microtissues via efferocytic pathways.
Transcriptional insights from the human embryo identify laminin-511 as a suitable matrix for human trophoblast stem cell culture.
Dynamical forces drive organ morphology changes during embryonic development.
Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis.
Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms.
Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry.
Maternal age enhances purifying selection on pathogenic mutations in complex I genes of mammalian mtDNA.
Dietary Branched Chain Amino Acids Modify Post-Infarct Cardiac Remodeling and Function in the Murine Heart.
Human Antigen R, a Myofibroblast-Specific Target in Treating Cardiac Fibrosis.
Intramyocardial Sprouting Tip Cells Specify Coronary Arterialization.
Spatiotemporal transcriptomic profiling and modeling of mouse brain at single-cell resolution reveals cell proximity effects of aging and rejuvenation.
Myocardial Infarction Suppresses Protein Synthesis and Causes Decoupling of Transcription and Translation.

Stem Cell Reports. 2024 Jul 17. pii: S2213-6711(24)00208-X. [Epub ahead of print]

Cell size regulates human endoderm specification through actomyosin-dependent AMOT-YAP signaling.

Lai Jiang, Chenchao Yan, Ying Yi, Lihang Zhu, Zheng Liu, Donghui Zhang, Wei Jiang.

  Cell size is a crucial physical property that significantly impacts cellular physiology and function. However, the influence of cell size on stem cell specification remains largely unknown. Here, we investigated the dynamic changes in cell size during the differentiation of human pluripotent stem cells into definitive endoderm (DE). Interestingly, cell size exhibited a gradual decrease as DE differentiation progressed with higher stiffness. Furthermore, the application of hypertonic pressure or chemical to accelerate the reduction in cell size significantly and specifically enhanced DE differentiation. By functionally intervening in mechanosensitive elements, we have identified actomyosin activity as a crucial mediator of both DE differentiation and cell size reduction. Mechanistically, the reduction in cell size induces actomyosin-dependent angiomotin (AMOT) nuclear translocation, which suppresses Yes-associated protein (YAP) activity and thus facilitates DE differentiation. Together, our study has established a novel connection between cell size diminution and DE differentiation, which is mediated by AMOT nuclear translocation. Additionally, our findings suggest that the application of osmotic pressure can effectively promote human endodermal lineage differentiation.

Keywords:  AMOT; YAP; actomyosin; cell size; human endoderm differentiation; osmotic pressure; pluripotent stem cell

DOI:  https://doi.org/10.1016/j.stemcr.2024.07.001
Mol Cell. 2024 Jul 26. pii: S1097-2765(24)00581-1. [Epub ahead of print]

Transcriptomic balance and optimal growth are determined by cell size.

Pedro J Vidal, Alexis P Pérez, Galal Yahya, Martí Aldea.

  Cell size and growth are intimately related across the evolutionary scale, but whether cell size is important to attain maximal growth or fitness is still an open question. We show that growth rate is a non-monotonic function of cell volume, with maximal values around the critical size of wild-type yeast cells. The transcriptome of yeast and mouse cells undergoes a relative inversion in response to cell size, which we associate theoretically and experimentally with the necessary genome-wide diversity in RNA polymerase II affinity for promoters. Although highly expressed genes impose strong negative effects on fitness when the DNA/mass ratio is reduced, transcriptomic alterations mimicking the relative inversion by cell size strongly restrain cell growth. In all, our data indicate that cells set the critical size to obtain a properly balanced transcriptome and, as a result, maximize growth and fitness during proliferation.

Keywords:  RNA polymerase II; cell size; fitness; growth; transcriptome

DOI:  https://doi.org/10.1016/j.molcel.2024.07.005
Cell. 2024 Jul 26. pii: S0092-8674(24)00777-3. [Epub ahead of print]

The fork protection complex promotes parental histone recycling and epigenetic memory.

Sebastian Jespersen Charlton, Valentin Flury, Yutaka Kanoh, Aitana Victoria Genzor, Leonie Kollenstart, Wantong Ao, Peter Brøgger, Melanie Bianca Weisser, Marek Adamus, Nicolas Alcaraz, Charlotte M Delvaux de Fenffe, Francesca Mattiroli, Guillermo Montoya, Hisao Masai, Anja Groth, Geneviève Thon.

  The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

Keywords:  Claspin; DNA replication; H3K9 methylation; chromatin replication; epigenetic inheritance; epigenome maintenance; fission yeast; heterochromatin; histone chaperone; histone recycling; mouse embryonic stem cells

DOI:  https://doi.org/10.1016/j.cell.2024.07.017
Curr Biol. 2024 Jul 24. pii: S0960-9822(24)00901-1. [Epub ahead of print]

An egg-sabotaging mechanism drives non-Mendelian transmission in mice.

Frances E Clark, Naomi L Greenberg, Duilio M Z A Silva, Emily Trimm, Morgan Skinner, R Zaak Walton, Leah F Rosin, Michael A Lampson, Takashi Akera.

  Selfish genetic elements drive in meiosis to distort their transmission ratio and increase their representation in gametes, violating Mendel's law of segregation. The two established paradigms for meiotic drive, gamete killing and biased segregation, are fundamentally different. In gamete killing, typically observed with male meiosis, selfish elements sabotage gametes that do not contain them. By contrast, killing is predetermined in female meiosis, and selfish elements bias their segregation to the single surviving gamete (i.e., the egg in animal meiosis). Here, we show that a selfish element on mouse chromosome 2, Responder to drive 2 (R2d2), drives using a hybrid mechanism in female meiosis, incorporating elements of both killing and biased segregation. We propose that if R2d2 is destined for the polar body, it manipulates segregation to sabotage the egg by causing aneuploidy, which is subsequently lethal in the embryo, ensuring that surviving progeny preferentially contain R2d2. In heterozygous females, R2d2 orients randomly on the metaphase spindle but lags during anaphase and preferentially remains in the egg, regardless of its initial orientation. Thus, the egg genotype is either euploid with R2d2 or aneuploid with both homologs of chromosome 2, with only the former generating viable embryos. Consistent with this model, R2d2 heterozygous females produce eggs with increased aneuploidy for chromosome 2, increased embryonic lethality, and increased transmission of R2d2. In contrast to typical gamete killing of sisters produced as daughter cells in a single meiosis, R2d2 prevents production of any viable gametes from meiotic divisions in which it should have been excluded from the egg.

Keywords:  aneuploidy; chromosome segregation; female meiotic drive; meiosis; mouse oocyte; selfish genetic element

DOI:  https://doi.org/10.1016/j.cub.2024.07.001
Cell Rep. 2024 Jul 26. pii: S2211-1247(24)00872-6. [Epub ahead of print]43(8): 114543

mTORC1 activity oscillates throughout the cell cycle, promoting mitotic entry and differentially influencing autophagy induction.

Jay N Joshi, Ariel D Lerner, Frank Scallo, Alexandra N Grumet, Paul Matteson, James H Millonig, Alexander J Valvezan.

  Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that is active in nearly all proliferating eukaryotic cells; however, it is unclear whether mTORC1 activity changes throughout the cell cycle. We find that mTORC1 activity oscillates from lowest in mitosis/G1 to highest in S/G2. The interphase oscillation is mediated through the TSC complex but is independent of major known regulatory inputs, including Akt and Mek/Erk signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex. mTORC1 has long been known to promote progression through G1. We find that mTORC1 also promotes progression through S and G2 and is important for satisfying the Chk1/Wee1-dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together, these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific consequences for proliferating cells.

Keywords:  CDK1; CP: Cell biology; G2/M checkpoint; TSC complex; TSC2; autophagy; cell cycle; mTOR; mTORC1; mitosis

DOI:  https://doi.org/10.1016/j.celrep.2024.114543
Development. 2024 Jul 15. pii: dev203106. [Epub ahead of print]151(14):

ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition.

Carla Mulas, Melanie Stammers, Siiri I Salomaa, Constanze Heinzen, David M Suter, Austin Smith, Kevin J Chalut.

  Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functional features. Here, we examine the role of mitogen-activated protein kinase (ERK1/2) signalling in pluripotent state transition. We show that a primary consequence of ERK activation in mouse embryonic stem cells is elimination of Nanog, which precipitates breakdown of the naïve state gene regulatory network. Variability in pERK dynamics results in heterogeneous loss of Nanog and metachronous state transition. Knockdown of Nanog allows exit without ERK activation. However, transition to formative pluripotency does not proceed and cells collapse to an indeterminate identity. This outcome is due to failure to maintain expression of the central pluripotency factor Oct4. Thus, during formative transition ERK signalling both dismantles the naïve state and preserves pluripotency. These results illustrate how a single signalling pathway can both initiate and secure transition between cell states.

Keywords:  Differentiation; ERK; Formative; Mouse embryonic stem cells; Naive; Nanog

DOI:  https://doi.org/10.1242/dev.203106
bioRxiv. 2024 Jul 19. pii: 2023.09.04.556218. [Epub ahead of print]

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos.

Estefania Sanchez-Vasquez, Marianne E Bronner, Magdalena Zernicka-Goetz.

  Human fertility is suboptimal, partly due to error-prone divisions in early cleavage-stages that result in aneuploidy. Most human pre-implantation are mosaics of euploid and aneuploid cells, however, mosaic embryos with a low proportion of aneuploid cells have a similar likelihood of developing to term as fully euploid embryos. How embryos manage aneuploidy during development is poorly understood. This knowledge is crucial for improving fertility treatments and reducing developmental defects. To explore these mechanisms, we established a new mouse model of chromosome mosaicism to study the fate of aneuploid cells during pre-implantation development. We previously used the Mps1 inhibitor reversine to generate aneuploidy in embryos. Here, we found that treatment with the more specific Mps1 inhibitor AZ3146 induced chromosome segregation defects in pre-implantation embryos, similar to reversine. However, AZ3146-treated embryos showed a higher developmental potential than reversine-treated embryos. Unlike reversine-treated embryos, AZ3146-treated embryos exhibited transient upregulation of Hypoxia Inducible-Factor-1A (HIF1A) and lacked p53 upregulation. Pre-implantation embryos develop in a hypoxic environment in vivo, and hypoxia exposure in vitro reduced DNA damage in response to Mps1 inhibition and increased the proportion of euploid cells in the mosaic epiblast. Inhibiting HIF1A in mosaic embryos also decreased the proportion of aneuploid cells in mosaic embryos. Our work illuminates potential strategies to improve the developmental potential of mosaic embryos.

Keywords:  Aneuploidy; DNA repair; Embryogenesis; Hypoxia; Mosaic embryos

DOI:  https://doi.org/10.1101/2023.09.04.556218
bioRxiv. 2024 Jul 23. pii: 2024.07.23.604718. [Epub ahead of print]

Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.

Yelena Y Bernadskaya, Ariel Kuan, Andreas Tjärnberg, Jonas Brandenburg, Ping Zheng, Keira Wiechecki, Nicole Kaplan, Margaux Failla, Maria Bikou, Oliver Madilian, Wei Wang, Lionel Christiaen.

During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process "transcriptome maturation", and identified candidate "mature genes", including the Rho GAP-coding gene Depdc1 , which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.

DOI: https://doi.org/10.1101/2024.07.23.604718
Nat Commun. 2024 Jul 29. 15(1): 6369

Zygotic spindle orientation defines cleavage pattern and nuclear status of human embryos.

Volodymyr Porokh, Drahomíra Kyjovská, Martina Martonová, Tereza Klenková, Pavel Otevřel, Soňa Kloudová, Zuzana Holubcová.

The first embryonic division represents a starting point for the development of a new individual. In many species, tight control over the first embryonic division ensures its accuracy. However, the first division in humans is often erroneous and can impair embryo development. To delineate the spatiotemporal organization of the first mitotic division typical for normal human embryo development, we systematically analyzed a unique timelapse dataset of 300 IVF embryos that developed into healthy newborns. The zygotic division pattern of these best-quality embryos was compared to their siblings that failed to implant or arrested during cleavage stage. We show that division at the right angle to the juxtaposed pronuclei is preferential and supports faithful zygotic division. Alternative configurations of the first mitosis are associated with reduced clustering of nucleoli and multinucleation at the 2-cell stage, which are more common in women of advanced age. Collectively, these data imply that orientation of the first division predisposes human embryos to genetic (in)stability and may contribute to aneuploidy and age-related infertility.

DOI: https://doi.org/10.1038/s41467-024-50732-z
Elife. 2024 Aug 02. pii: RP84875. [Epub ahead of print]12

Spindle assembly checkpoint-dependent mitotic delay is required for cell division in absence of centrosomes.

K C Farrell, Jennifer T Wang, Tim Stearns.

  The spindle assembly checkpoint (SAC) temporally regulates mitosis by preventing progression from metaphase to anaphase until all chromosomes are correctly attached to the mitotic spindle. Centrosomes refine the spatial organization of the mitotic spindle at the spindle poles. However, centrosome loss leads to elongated mitosis, suggesting that centrosomes also inform the temporal organization of mitosis in mammalian cells. Here, we find that the mitotic delay in acentrosomal cells is enforced by the SAC in a MPS1-dependent manner, and that a SAC-dependent mitotic delay is required for bipolar cell division to occur in acentrosomal cells. Although acentrosomal cells become polyploid, polyploidy is not sufficient to cause dependency on a SAC-mediated delay to complete cell division. Rather, the division failure in absence of MPS1 activity results from mitotic exit occurring before acentrosomal spindles can become bipolar. Furthermore, prevention of centrosome separation suffices to make cell division reliant on a SAC-dependent mitotic delay. Thus, centrosomes and their definition of two spindle poles early in mitosis provide a 'timely two-ness' that allows cell division to occur in absence of a SAC-dependent mitotic delay.

Keywords:  cell biology; centrosome; human; mitosis; spindle; spindle assembly checkpoint

DOI:  https://doi.org/10.7554/eLife.84875
Cell. 2024 Jul 25. pii: S0092-8674(24)00766-9. [Epub ahead of print]

A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance.

Juntao Yu, Yujie Zhang, Yimeng Fang, Joao A Paulo, Dadmehr Yaghoubi, Xu Hua, Gergana Shipkovenska, Takenori Toda, Zhiguo Zhang, Steven P Gygi, Songtao Jia, Qing Li, Danesh Moazed.

  Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.

Keywords:  CLASPIN; FACT; chromatin replication; epigenetics; fork protection complex; heterochromatin; histone inheritance; parental histone transfer; replisome, Mrc1

DOI:  https://doi.org/10.1016/j.cell.2024.07.006
bioRxiv. 2024 Jul 19. pii: 2024.07.17.604013. [Epub ahead of print]

Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.

Ya-Ting Chang, Benjamin A Barad, Hamidreza Rahmani, Brian M Zid, Danielle A Grotjahn.

Most of the mitochondria proteome is nuclear-encoded, synthesized by cytoplasmic ribosomes, and targeted to mitochondria post-translationally. However, a subset of mitochondrial-targeted proteins is imported co-translationally, although the molecular mechanisms governing this process remain unclear. We employ cellular cryo-electron tomography to visualize interactions between cytoplasmic ribosomes and mitochondria in Saccharomyces cerevisiae. We use surface morphometrics tools to identify a subset of ribosomes optimally oriented on mitochondrial membranes for protein import. This allows us to establish the first subtomogram average structure of a cytoplasmic ribosome on the surface of the mitochondria in the native cellular context, which showed three distinct connections with the outer mitochondrial membrane surrounding the peptide exit tunnel. Further, this analysis demonstrated that cytoplasmic ribosomes primed for mitochondrial protein import cluster on the outer mitochondrial membrane at sites of local constrictions of the outer and inner mitochondrial membrane. Overall, our study reveals the architecture and the spatial organization of cytoplasmic ribosomes at the mitochondrial surface, providing a native cellular context to define the mechanisms that mediate efficient mitochondrial co-translational protein import.

DOI: https://doi.org/10.1101/2024.07.17.604013
Nature. 2024 Jul 31.

FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.

Pablo Alcón, Artur P Kaczmarczyk, Korak Kumar Ray, Themistoklis Liolios, Guillaume Guilbaud, Tamara Sijacki, Yichao Shen, Stephen H McLaughlin, Julian E Sale, Puck Knipscheer, David S Rueda, Lori A Passmore.

DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion1. However, D2-I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation2-4. At present, it is unclear how DNA crosslinks are recognized and how D2-I functions in replication fork protection. Here, using single-molecule imaging, we show that D2-I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2-I stalls on encountering single-stranded-double-stranded (ss-ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions5. Using cryogenic electron microscopy, we determined structures of D2-I on DNA that show that stalled D2-I makes specific interactions with the ss-dsDNA junction that are distinct from those made by sliding D2-I. Thus, D2-I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss-dsDNA junctions. Because ss-dsDNA junctions are found at stalled replication forks, D2-I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2-I in the recognition and protection of stalled replication forks in several DNA repair pathways.

DOI: https://doi.org/10.1038/s41586-024-07770-w
Nat Commun. 2024 Aug 02. 15(1): 6509

CLASP-mediated competitive binding in protein condensates directs microtubule growth.

Xuanyan Jia, Leishu Lin, Siqi Guo, Lulu Zhou, Gaowei Jin, Jiayuan Dong, Jinman Xiao, Xingqiao Xie, Yiming Li, Sicong He, Zhiyi Wei, Cong Yu.

Microtubule organization in cells relies on targeting mechanisms. Cytoplasmic linker proteins (CLIPs) and CLIP-associated proteins (CLASPs) are key regulators of microtubule organization, yet the underlying mechanisms remain elusive. Here, we reveal that the C-terminal domain of CLASP2 interacts with a common motif found in several CLASP-binding proteins. This interaction drives the dynamic localization of CLASP2 to distinct cellular compartments, where CLASP2 accumulates in protein condensates at the cell cortex or the microtubule plus end. These condensates physically contact each other via CLASP2-mediated competitive binding, determining cortical microtubule targeting. The phosphorylation of CLASP2 modulates the dynamics of the condensate-condensate interaction and spatiotemporally navigates microtubule growth. Moreover, we identify additional CLASP-interacting proteins that are involved in condensate contacts in a CLASP2-dependent manner, uncovering a general mechanism governing microtubule targeting. Our findings not only unveil a tunable multiphase system regulating microtubule organization, but also offer general mechanistic insights into intricate protein-protein interactions at the mesoscale level.

DOI: https://doi.org/10.1038/s41467-024-50863-3
Nat Cell Biol. 2024 Jul 30.

mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer.

Guoqing Lv, Qian Wang, Lin Lin, Qiao Ye, Xi Li, Qian Zhou, Xiangzhen Kong, Hongxia Deng, Fuping You, Hebing Chen, Song Wu, Lin Yuan.

Cyclic GMP-AMP synthase (cGAS), a cytosolic DNA sensor that initiates a STING-dependent innate immune response, binds tightly to chromatin, where its catalytic activity is inhibited; however, mechanisms underlying cGAS recruitment to chromatin and functions of chromatin-bound cGAS (ccGAS) remain unclear. Here we show that mTORC2-mediated phosphorylation of human cGAS serine 37 promotes its chromatin localization in colorectal cancer cells, regulating cell growth and drug resistance independently of STING. We discovered that ccGAS recruits the SWI/SNF complex at specific chromatin regions, modifying expression of genes linked to glutaminolysis and DNA replication. Although ccGAS depletion inhibited cell growth, it induced chemoresistance to fluorouracil treatment in vitro and in vivo. Moreover, blocking kidney-type glutaminase, a downstream ccGAS target, overcame chemoresistance caused by ccGAS loss. Thus, ccGAS coordinates colorectal cancer plasticity and acquired chemoresistance through epigenetic patterning. Targeting both mTORC2-ccGAS and glutaminase provides a promising strategy to eliminate quiescent resistant cancer cells.

DOI: https://doi.org/10.1038/s41556-024-01473-0
Nat Cell Biol. 2024 Jul 31.

Cleavage-independent GSDME activation by UVC.

Ellie Zhang, Liam Healy, Gang Du, Hao Wu.

DOI: https://doi.org/10.1038/s41556-024-01470-3
Reproduction. 2024 Jul 01. pii: REP-24-0198. [Epub ahead of print]

Declining translational capacity as a potential driver for oocyte meiotic instability.

Katie Jordanna Danielson, Kayla Lee Judson, Ethan Joseph Greenblatt.

Errors during female meiosis lead to embryonic aneuploidy and miscarriage and occur with increasing frequency during aging. The underlying molecular changes that drive female meiotic instability remain a subject of debate. Developing oocytes undergo a tremendous increase in cytoplasmic volume during follicle development and rely on long-lived mRNAs and ribosomes accumulated during this growth phase for subsequent meiotic maturation. In this perspective article, we discuss how the unique reliance on stores of long-lived mRNAs and ribosomes may represent an Achilles' heel for oocyte function, and that alterations that reduce the translational capacity of oocytes could be a factor significantly contributing to meiotic instability. Understanding these mechanisms could lead to new diagnostic and therapeutic strategies to improve fertility outcomes.

DOI: https://doi.org/10.1530/REP-24-0198
bioRxiv. 2024 Jul 16. pii: 2024.07.15.603602. [Epub ahead of print]

Local nuclear to cytoplasmic ratio regulates chaperone-dependent H3 variant incorporation during zygotic genome activation.

Anusha D Bhatt, Madeleine G Brown, Aurora B Wackford, Yuki Shindo, Amanda A Amodeo.

  Early embryos often have relatively unstructured chromatin that lacks active and inactive domains typical of differentiated cells. In many species, these regulatory domains are established during zygotic genome activation (ZGA). In Drosophila, ZGA occurs after 13 fast, reductive, syncytial nuclear divisions during which the nuclear to cytoplasmic (N/C) ratio grows exponentially. These divisions incorporate maternally-loaded, cytoplasmic pools of histones into chromatin. Previous work found that chromatin incorporation of replication-coupled histone H3 decreases while its variant H3.3 increases in the cell cycles leading up to ZGA. In other cell types, H3.3 is associated with sites of active transcription as well as heterochromatin, suggesting a link between H3.3 incorporation and ZGA. Here, we examine the factors that contribute to H3.3 incorporation at ZGA. We identify a more rapid decrease in the nuclear availability of H3 than H3.3 over the final pre-ZGA cycles. We also observe an N/C ratio-dependent increase in H3.3 incorporation in mutant embryos with non-uniform local N/C ratios. We find that chaperone binding, not gene expression, controls incorporation patterns using H3/H3.3 chimeric proteins at the endogenous H3.3A locus. We test the specificity of the H3.3 chaperone pathways for H3.3 incorporation using Hira (H3.3 chaperone) mutant embryos. Overall, we propose a model in which local N/C ratios and specific chaperone binding regulate differential incorporation of H3.3 during ZGA.

Keywords:  Zygotic genome activation; chromatin; heterochromatin; histones; nuclear to cytoplasmic ratio; transcription

DOI:  https://doi.org/10.1101/2024.07.15.603602
Circulation. 2024 Jul 30. 150(5): 347-349

Myocardial Regeneration: Feasible or Fantasy?

Eric N Olson.



Keywords:  genetic therapy; heart diseases; regeneration

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.124.070136
bioRxiv. 2024 Jul 16. pii: 2024.07.16.603789. [Epub ahead of print]

Diffusing protein binders to intrinsically disordered proteins.

Caixuan Liu, Kejia Wu, Hojun Choi, Hannah Han, Xulie Zhang, Joseph L Watson, Sara Shijo, Asim K Bera, Alex Kang, Evans Brackenbrough, Brian Coventry, Derrick R Hick, Andrew N Hoofnagle, Ping Zhu, Xingting Li, Justin Decarreau, Stacey R Gerben, Wei Yang, Xinru Wang, Mila Lamp, Analisa Murray, Magnus Bauer, David Baker.

  Proteins which bind intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could have considerable utility for therapeutic and diagnostic applications. However, a general methodology for targeting IDPs/IDRs has yet to be developed. Here, we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformation, RFdiffusion can generate binders to IDPs and IDRs in a wide range of conformations. We use this approach to generate binders to the IDPs Amylin, C-peptide and VP48 in a range of conformations with Kds in the 3 -100nM range. The Amylin binder inhibits amyloid fibril formation and dissociates existing fibers, and enables enrichment of amylin for mass spectrometry-based detection. For the IDRs G3bp1, common gamma chain (IL2RG) and prion, we diffused binders to beta strand conformations of the targets, obtaining 10 to 100 nM affinity. The IL2RG binder colocalizes with the receptor in cells, enabling new approaches to modulating IL2 signaling. Our approach should be widely useful for creating binders to flexible IDPs/IDRs spanning a wide range of intrinsic conformational preferences.

Keywords:  Amyloid fibril dissociation; Intrinsically disordered protein; RFdiffusion; Rosetta; deep learning; diagnostics; intrinsically disordered region; protein design

DOI:  https://doi.org/10.1101/2024.07.16.603789
Nat Cardiovasc Res. 2022 Nov;1(11): 1039-1055

Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization.

D M Calcagno, N Taghdiri, V K Ninh, J M Mesfin, A Toomu, R Sehgal, J Lee, Y Liang, J M Duran, E Adler, K L Christman, K Zhang, F Sheikh, Z Fu, K R King.

The border zone (BZ) of the infarcted heart is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZs) from remote zones (RZs). The cellular and molecular mechanisms of myocardial BZs are not well understood because microdissection inevitably combines them with uncontrolled amounts of RZs and IZs. Here, we use single-cell/nucleus RNA sequencing, spatial transcriptomics and multiplexed RNA fluorescence in situ hybridization to redefine the BZ based on cardiomyocyte transcriptomes. BZ1 (Nppa + Xirp2 -) forms a hundreds-of-micrometer-thick layer of morphologically intact cells adjacent to RZs that are detectable within an hour of injury. Meanwhile, BZ2 (Nppa + Xirp2 +) forms a near-single-cell-thick layer of morphologically distorted cardiomyocytes at the IZ edge that colocalize with matricellular protein-expressing myofibroblasts and express predominantly mechanotransduction genes. Surprisingly, mechanical injury alone is sufficient to induce BZ genes. We propose a 'loss of neighbor' hypothesis to explain how ischemic cell death mechanically destabilizes the BZ to induce its transcriptional response.

DOI: https://doi.org/10.1038/s44161-022-00160-3
Nat Cardiovasc Res. 2024 May;3(5): 567-593

Primitive macrophages induce sarcomeric maturation and functional enhancement of developing human cardiac microtissues via efferocytic pathways.

Homaira Hamidzada, Simon Pascual-Gil, Qinghua Wu, Gregory M Kent, Stéphane Massé, Crystal Kantores, Uros Kuzmanov, M Juliana Gomez-Garcia, Naimeh Rafatian, Renée A Gorman, Marianne Wauchop, Wenliang Chen, Shira Landau, Tasnia Subha, Michael H Atkins, Yimu Zhao, Erika Beroncal, Ian Fernandes, Jared Nanthakumar, Shabana Vohra, Erika Y Wang, Tamilla Valdman Sadikov, Babak Razani, Tracy L McGaha, Ana C Andreazza, Anthony Gramolini, Peter H Backx, Kumaraswamy Nanthakumar, Michael A Laflamme, Gordon Keller, Milica Radisic, Slava Epelman.

Yolk sac macrophages are the first to seed the developing heart, however we have no understanding of their roles in human heart development and function due to a lack of accessible tissue. Here, we bridge this gap by differentiating human embryonic stem cells (hESCs) into primitive LYVE1+ macrophages (hESC-macrophages) that stably engraft within contractile cardiac microtissues composed of hESC-cardiomyocytes and fibroblasts. Engraftment induces a human fetal cardiac macrophage gene program enriched in efferocytic pathways. Functionally, hESC-macrophages trigger cardiomyocyte sarcomeric protein maturation, enhance contractile force and improve relaxation kinetics. Mechanistically, hESC-macrophages engage in phosphatidylserine dependent ingestion of apoptotic cardiomyocyte cargo, which reduces microtissue stress, leading hESC-cardiomyocytes to more closely resemble early human fetal ventricular cardiomyocytes, both transcriptionally and metabolically. Inhibiting hESC-macrophage efferocytosis impairs sarcomeric protein maturation and reduces cardiac microtissue function. Taken together, macrophage-engineered human cardiac microtissues represent a considerably improved model for human heart development, and reveal a major beneficial role for human primitive macrophages in enhancing early cardiac tissue function.

DOI: https://doi.org/10.1038/s44161-024-00471-7
Placenta. 2024 Jul 26. pii: S0143-4004(24)00602-7. [Epub ahead of print]

Transcriptional insights from the human embryo identify laminin-511 as a suitable matrix for human trophoblast stem cell culture.

Nathaly Hernández-Díaz, Sofia Tzouganatou, Praditi R Mulik, Paula A Balestrini, Norah M E Fogarty.

  The establishment of culture conditions to propagate self-renewing human trophoblast stem cells in long-term culture provides a paradigm for in vitro modelling of trophoblast. The extracellular matrix (ECM) is a critical determinant of cell identity and behaviour. Therefore, models aiming to reproduce cells in vitro should recapitulate the native cell-ECM microenvironment. Here, we mine human embryo transcriptional datasets to identify ECM components and cognate receptors expressed in the trophectoderm. Following, we identify laminin-511-E8 protein fragment as a physiologically relevant ECM capable of maintaining hTSCs in the stem cell state and retaining differentiation ability.

Keywords:  Embryo development; Stem cells; Trophoblast

DOI:  https://doi.org/10.1016/j.placenta.2024.07.308
bioRxiv. 2024 Jul 17. pii: 2024.07.13.603371. [Epub ahead of print]

Dynamical forces drive organ morphology changes during embryonic development.

Raj Kumar Manna, Emma M Retzlaff, Anna Maria Hinman, Yiling Lan, Osama Abdel-Razek, Mike Bates, Heidi Hehnly, Jeffrey D Amack, M Lisa Manning.

Organs and tissues must change shape in precise ways during embryonic development to execute their functions. Multiple mechanisms including biochemical signaling pathways and biophysical forces help drive these morphology changes, but it has been difficult to tease apart their contributions, especially from tissue-scale dynamic forces that are typically ignored. We use a combination of mathematical models and in vivo experiments to study a simple organ in the zebrafish embryo called Kupffer's vesicle. Modeling indicates that dynamic forces generated by tissue movements in the embryo produce shape changes in Kupffer's vesicle that are observed during development. Laser ablations in the zebrafish embryo that alter these forces result in altered organ shapes matching model predictions. These results demonstrate that dynamic forces sculpt organ shape during embryo development.

DOI: https://doi.org/10.1101/2024.07.13.603371
Science. 2024 Aug 02. 385(6708): eadk5901

Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis.

Zuanning Yuan, Roxana Georgescu, Nina Y Yao, Olga Yurieva, Michael E O'Donnell, Huilin Li.

The proliferating cell nuclear antigen (PCNA) clamp encircles DNA to hold DNA polymerases (Pols) to DNA for processivity. The Ctf18-RFC PCNA loader, a replication factor C (RFC) variant, is specific to the leading-strand Pol (Polε). We reveal here the underlying mechanism of Ctf18-RFC specificity to Polε using cryo-electron microscopy and biochemical studies. We found that both Ctf18-RFC and Polε contain specific structural features that direct PCNA loading onto DNA. Unlike other clamp loaders, Ctf18-RFC has a disordered ATPase associated with a diverse cellular activities (AAA+) motor that requires Polε to bind and stabilize it for efficient PCNA loading. In addition, Ctf18-RFC can pry prebound Polε off of DNA, then load PCNA onto DNA and transfer the PCNA-DNA back to Polε. These elements in both Ctf18-RFC and Polε provide specificity in loading PCNA onto DNA for Polε.

DOI: https://doi.org/10.1126/science.adk5901
Nat Chem Biol. 2024 Aug 01.

Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms.

Chunte Sam Peng, Yunxiang Zhang, Qian Liu, G Edward Marti, Yu-Wen Alvin Huang, Thomas C Südhof, Bianxiao Cui, Steven Chu.

Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.

DOI: https://doi.org/10.1038/s41589-024-01694-2
Nat Biotechnol. 2024 Jul 29.

Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry.

Xiao-Kang Lun, Kuanwei Sheng, Xueyang Yu, Ching Yeung Lam, Gokul Gowri, Matthew Serrata, Yunhao Zhai, Hanquan Su, Jingyi Luan, Youngeun Kim, Donald E Ingber, Hartland W Jackson, Michael B Yaffe, Peng Yin.

Mass cytometry uses metal-isotope-tagged antibodies to label targets of interest, which enables simultaneous measurements of ~50 proteins or protein modifications in millions of single cells, but its sensitivity is limited. Here, we present a signal amplification technology, termed Amplification by Cyclic Extension (ACE), implementing thermal-cycling-based DNA in situ concatenation in combination with 3-cyanovinylcarbazole phosphoramidite-based DNA crosslinking to enable signal amplification simultaneously on >30 protein epitopes. We demonstrate the utility of ACE in low-abundance protein quantification with suspension mass cytometry to characterize molecular reprogramming during the epithelial-to-mesenchymal transition as well as the mesenchymal-to-epithelial transition. We show the capability of ACE to quantify the dynamics of signaling network responses in human T lymphocytes. We further present the application of ACE in imaging mass cytometry-based multiparametric tissue imaging to identify tissue compartments and profile spatial aspects related to pathological states in polycystic kidney tissues.

DOI: https://doi.org/10.1038/s41587-024-02316-x
Nat Aging. 2024 Jul 29.

Maternal age enhances purifying selection on pathogenic mutations in complex I genes of mammalian mtDNA.

Yanfei Ru, Xiaoling Deng, Jiatong Chen, Leping Zhang, Zhe Xu, Qunyu Lv, Shiyun Long, Zijian Huang, Minghua Kong, Jing Guo, Min Jiang.

Mitochondrial diseases, caused mainly by pathogenic mitochondrial DNA (mtDNA) mutations, pose major challenges due to the lack of effective treatments. Investigating the patterns of maternal transmission of mitochondrial diseases could pave the way for preventive approaches. In this study, we used DddA-derived cytosine base editors (DdCBEs) to generate two mouse models, each haboring a single pathogenic mutation in complex I genes (ND1 and ND5), replicating those found in human patients. Our findings revealed that both mutations are under strong purifying selection during maternal transmission and occur predominantly during postnatal oocyte maturation, with increased protein synthesis playing a vital role. Interestingly, we discovered that maternal age intensifies the purifying selection, suggesting that older maternal age may offer a protective effect against the transmission of deleterious mtDNA mutations, contradicting the conventional notion that maternal age correlates with increased transmitted mtDNA mutations. As collecting comprehensive clinical data is needed to understand the relationship between maternal age and transmission patterns in humans, our findings may have profound implications for reproductive counseling of mitochondrial diseases, especially those involving complex I gene mutations.

DOI: https://doi.org/10.1038/s43587-024-00672-6
bioRxiv. 2024 Jul 16. pii: 2024.07.12.603348. [Epub ahead of print]

Dietary Branched Chain Amino Acids Modify Post-Infarct Cardiac Remodeling and Function in the Murine Heart.

Daniel C Nguyen, Collin K Wells, Madison S Taylor, Yania Martinez-Ondaro, Kenneth R Brittian, Robert E Brainard, Joseph B Moore Iv, Bradford G Hill.

   Introduction: Branch-chain amino acids (BCAA) are markedly elevated in the heart following myocardial infarction (MI) in both humans and animal models. Nevertheless, it remains unclear whether dietary BCAA levels influence post-MI remodeling. We hypothesize that lowering dietary BCAA levels prevents adverse cardiac remodeling after MI.
Methods and Results: To assess whether altering dietary BCAA levels would impact circulating BCAA concentrations, mice were fed a low (1/3×), normal (1×), or high (2×) BCAA diet over a 7-day period. We found that mice fed the low BCAA diet had >2-fold lower circulating BCAA concentrations when compared with normal and high BCAA diet feeding strategies; notably, the high BCAA diet did not further increase BCAA levels over the normal chow diet. To investigate the impact of dietary BCAAs on cardiac remodeling and function after MI, male and female mice were fed either the low or high BCAA diet for 2 wk prior to MI and for 4 wk after MI. Although body weights or heart masses were not different in female mice fed the custom diets, male mice fed the high BCAA diet had significantly higher body and heart masses than those on the low BCAA diet. Echocardiographic assessments revealed that the low BCAA diet preserved stroke volume and cardiac output for the duration of the study, while the high BCAA diet led to progressive decreases in cardiac function. Although no discernible differences in cardiac fibrosis, scar collagen topography, or cardiomyocyte cross-sectional area were found between the dietary groups, male mice fed the high BCAA diet showed longer cardiomyocytes and higher capillary density compared with the low BCAA group.
Conclusions: Provision of a diet low in BCAAs to mice mitigates eccentric cardiomyocyte remodeling and loss of cardiac function after MI, with dietary effects more prominent in males.

Keywords:  branched chain amino acids; fibrosis; heart failure; hypertrophy; myocardial infarction

DOI:  https://doi.org/10.1101/2024.07.12.603348
JACC Basic Transl Sci. 2024 Jun;9(6): 771-773

Human Antigen R, a Myofibroblast-Specific Target in Treating Cardiac Fibrosis.

Abhay Srivastava, Sanjiv Dhingra.



Keywords:  cardiac fibrosis; heart failure; human antigen R; left ventricular remodeling; myofibroblasts

DOI:  https://doi.org/10.1016/j.jacbts.2024.05.001
Circ Res. 2024 Aug 02.

Intramyocardial Sprouting Tip Cells Specify Coronary Arterialization.

Elena Cano, Jennifer Schwarzkopf, Masatoshi Kanda, Eric L Lindberg, Irene Hollfinger, Cristina Pogontke, Caroline Braeuning, Cornelius Fischer, Norbert Hübner, Holger Gerhardt.

   BACKGROUND: The elaborate patterning of coronary arteries critically supports the high metabolic activity of the beating heart. How coronary endothelial cells coordinate hierarchical vascular remodeling and achieve arteriovenous specification remains largely unknown. Understanding the molecular and cellular cues that pattern coronary arteries is crucial to develop innovative therapeutic strategies that restore functional perfusion within the ischemic heart.
METHODS: Single-cell transcriptomics and histological validation were used to delineate heterogeneous transcriptional states of the developing and mature coronary endothelium with a focus on sprouting endothelium and arterial cell specification. Genetic lineage tracing and high-resolution 3-dimensional imaging were used to characterize the origin and mechanisms of coronary angiogenic sprouting, as well as to fate-map selective endothelial lineages. Integration of single-cell transcriptomic data from ischemic adult mouse hearts and human embryonic data served to assess the conservation of transcriptional states across development, disease, and species.
RESULTS: We discover that coronary arteries originate from cells that have previously transitioned through a specific tip cell phenotype. We identify nonoverlapping intramyocardial and subepicardial tip cell populations with differential gene expression profiles and regulatory pathways. Esm1-lineage tracing confirmed that intramyocardial tip cells selectively contribute to coronary arteries and endocardial tunnels, but not veins. Notably, prearterial cells are detected from development stages to adulthood, increasingly in response to ischemic injury, and in human embryos, suggesting that tip cell-to-artery specification is a conserved mechanism.
CONCLUSIONS: A tip cell-to-artery specification mechanism drives arterialization of the intramyocardial plexus and endocardial tunnels throughout life and is reactivated upon ischemic injury. Differential sprouting programs govern the formation and specification of the venous and arterial coronary plexus.s.

Keywords:  arterialization; coronary artery; endocardial tunnels; endocardium; sprouting; tip cell

DOI:  https://doi.org/10.1161/CIRCRESAHA.124.324868
bioRxiv. 2024 Jul 19. pii: 2024.07.16.603809. [Epub ahead of print]

Spatiotemporal transcriptomic profiling and modeling of mouse brain at single-cell resolution reveals cell proximity effects of aging and rejuvenation.

Eric D Sun, Olivia Y Zhou, Max Hauptschein, Nimrod Rappoport, Lucy Xu, Paloma Navarro Negredo, Ling Liu, Thomas A Rando, James Zou, Anne Brunet.

Old age is associated with a decline in cognitive function and an increase in neurodegenerative disease risk 1 . Brain aging is complex and accompanied by many cellular changes 2-20 . However, the influence that aged cells have on neighboring cells and how this contributes to tissue decline is unknown. More generally, the tools to systematically address this question in aging tissues have not yet been developed. Here, we generate spatiotemporal data at single-cell resolution for the mouse brain across lifespan, and we develop the first machine learning models based on spatial transcriptomics ('spatial aging clocks') to reveal cell proximity effects during brain aging and rejuvenation. We collect a single-cell spatial transcriptomics brain atlas of 4.2 million cells from 20 distinct ages and across two rejuvenating interventions-exercise and partial reprogramming. We identify spatial and cell type-specific transcriptomic fingerprints of aging, rejuvenation, and disease, including for rare cell types. Using spatial aging clocks and deep learning models, we find that T cells, which infiltrate the brain with age, have a striking pro-aging proximity effect on neighboring cells. Surprisingly, neural stem cells have a strong pro-rejuvenating effect on neighboring cells. By developing computational tools to identify mediators of these proximity effects, we find that pro-aging T cells trigger a local inflammatory response likely via interferon-γ whereas pro-rejuvenating neural stem cells impact the metabolism of neighboring cells possibly via growth factors (e.g. vascular endothelial growth factor) and extracellular vesicles, and we experimentally validate some of these predictions. These results suggest that rare cells can have a drastic influence on their neighbors and could be targeted to counter tissue aging. We anticipate that these spatial aging clocks will not only allow scalable assessment of the efficacy of interventions for aging and disease but also represent a new tool for studying cell-cell interactions in many spatial contexts.

DOI: https://doi.org/10.1101/2024.07.16.603809
JACC Basic Transl Sci. 2024 Jun;9(6): 792-807

Myocardial Infarction Suppresses Protein Synthesis and Causes Decoupling of Transcription and Translation.

Shijie Liu, Vaibhav Deshmukh, Fangfei Wang, Jie Liang, Jenna Cusick, Xiao Li, James F Martin.

  Gene expression involves transcription, translation, and mRNA and protein degradation. Advanced RNA sequencing measures mRNA levels for cell state assessment, but mRNA level does not fully reflect protein level. Identifying heart cell proteomes and their stress response is crucial. Using a cardiomyocyte-specific mouse model, we tracked protein synthesis after myocardial infarction. Our results showed that myocardial infarction suppresses protein synthesis and unveils a decoupling of translation and transcription regulation in cardiomyocytes.

Keywords:  azidonorleucine (ANL); mass spectrometry; methionyl-tRNA synthetase (MetRS); myocardial infarction; newly synthesized protein

DOI:  https://doi.org/10.1016/j.jacbts.2024.02.014