bims-ginsta 2023-10-01 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2023–10–01
eightteen papers selected by
Jinrong Hu, National University of Singapore

Mild replication stress causes premature centriole disengagement via a sub-critical Plk1 activity under the control of ATR-Chk1.
Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.
An updated view of the kinetochore architecture.
Variation in the CENP-A sequence association landscape across diverse inbred mouse strains.
The CCR4-NOT complex suppresses untimely translational activation of maternal mRNAs.
Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.
Cla4 phosphorylates histone methyltransferase Set1 to prevent its degradation by the APC/CCdh1 complex.
Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential.
Rapid mechanosensitive migration and dispersal of newly divided mesenchymal cells aid their recruitment into dermal condensates.
PLK4 self-phosphorylation drives the selection of a single site for procentriole assembly.
Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells.
Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion.
Three-dimensional nuclear organisation and the DNA replication timing program.
Human microglial state dynamics in Alzheimer's disease progression.
A bioelectrical phase transition patterns the first vertebrate heartbeats.
Structural insights into the activation of ataxia-telangiectasia mutated by oxidative stress.
Microenvironmental stiffness induces metabolic reprogramming in glioblastoma.
Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics.

Nat Commun. 2023 Sep 29. 14(1): 6088

Mild replication stress causes premature centriole disengagement via a sub-critical Plk1 activity under the control of ATR-Chk1.

Devashish Dwivedi, Daniela Harry, Patrick Meraldi.

A tight synchrony between the DNA and centrosome cycle is essential for genomic integrity. Centriole disengagement, which licenses centrosomes for duplication, occurs normally during mitotic exit. We recently demonstrated that mild DNA replication stress typically seen in cancer cells causes premature centriole disengagement in untransformed mitotic human cells, leading to transient multipolar spindles that favour chromosome missegregation. How mild replication stress accelerates the centrosome cycle at the molecular level remained, however, unclear. Using ultrastructure expansion microscopy, we show that mild replication stress induces premature centriole disengagement already in G2 via the ATR-Chk1 axis of the DNA damage repair pathway. This results in a sub-critical Plk1 kinase activity that primes the pericentriolar matrix for Separase-dependent disassembly but is insufficient for rapid mitotic entry, causing premature centriole disengagement in G2. We postulate that the differential requirement of Plk1 activity for the DNA and centrosome cycles explains how mild replication stress disrupts the synchrony between both processes and contributes to genomic instability.

DOI: https://doi.org/10.1038/s41467-023-41753-1
Nat Biotechnol. 2023 Sep 25.

Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.

Kunal Jindal, Mohd Tayyab Adil, Naoto Yamaguchi, Xue Yang, Helen C Wang, Kenji Kamimoto, Guillermo C Rivera-Gonzalez, Samantha A Morris.

Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.

DOI: https://doi.org/10.1038/s41587-023-01931-4
Trends Genet. 2023 Sep 27. pii: S0168-9525(23)00220-2. [Epub ahead of print]

An updated view of the kinetochore architecture.

Mariko Ariyoshi, Tatsuo Fukagawa.

  The kinetochore is a supramolecular complex that facilitates faithful chromosome segregation by bridging the centromere and spindle microtubules. Recent functional and structural studies on the inner kinetochore subcomplex, constitutive centromere-associated network (CCAN) have updated our understanding of kinetochore architecture. While the CCAN core establishes a stable interface with centromeric chromatin, CCAN organization is dynamically altered and coupled with cell cycle progression. Furthermore, the CCAN components, centromere protein (CENP)-C and CENP-T, mediate higher-order assembly of multiple kinetochore units on the regional centromeres of vertebrates. This review highlights new insights into kinetochore rigidity, plasticity, and clustering, which are key to understanding temporal and spatial regulatory mechanisms of chromosome segregation.

Keywords:  CCAN; centromere; chromosome segregation; cluster; kinetochore; oligomerization

DOI:  https://doi.org/10.1016/j.tig.2023.09.003
Cell Rep. 2023 Sep 23. pii: S2211-1247(23)01190-7. [Epub ahead of print]42(10): 113178

Variation in the CENP-A sequence association landscape across diverse inbred mouse strains.

Uma P Arora, Beth A Sullivan, Beth L Dumont.

  Centromeres are crucial for chromosome segregation, but their underlying sequences evolve rapidly, imposing strong selection for compensatory changes in centromere-associated kinetochore proteins to assure the stability of genome transmission. While this co-evolution is well documented between species, it remains unknown whether population-level centromere diversity leads to functional differences in kinetochore protein association. Mice (Mus musculus) exhibit remarkable variation in centromere size and sequence, but the amino acid sequence of the kinetochore protein CENP-A is conserved. Here, we apply k-mer-based analyses to CENP-A chromatin profiling data from diverse inbred mouse strains to investigate the interplay between centromere variation and kinetochore protein sequence association. We show that centromere sequence diversity is associated with strain-level differences in both CENP-A positioning and sequence preference along the mouse core centromere satellite. Our findings reveal intraspecies sequence-dependent differences in CENP-A/centromere association and open additional perspectives for understanding centromere-mediated variation in genome stability.

Keywords:  CENP-A association; CENP-A positioning; CP: Genomics; Mus musculus; centromere evolution; centromere transcription; centromere variation; genome instability; kinetochore; meiotic drive

DOI:  https://doi.org/10.1016/j.celrep.2023.113178
Development. 2023 Sep 28. pii: dev.201773. [Epub ahead of print]

The CCR4-NOT complex suppresses untimely translational activation of maternal mRNAs.

Shou Soeda, Masaaki Oyama, Hiroko Kozuka-Hata, Tadashi Yamamoto.

  Control of mRNA poly(A) tails is essential for regulation of mRNA metabolism, specifically translation efficiency and mRNA stability. Gene expression in maturing oocytes relies largely on post-transcriptional regulation, as genes are transcriptionally silent during oocyte maturation. The CCR4-NOT complex is a major mammalian deadenylase, which regulates poly(A) tails of maternal mRNAs; however, the function of the CCR4-NOT complex in translational regulation has not been well understood. Here we show that this complex suppresses translational activity of maternal mRNAs during oocyte maturation. Oocytes that lack all CCR4-NOT deadenylase activity due to genetic deletion of its catalytic subunits, Cnot7 and Cnot8, showed a large-scale gene expression change caused by increased translational activity during oocyte maturation. Developmental arrest during meiosis I in these oocytes results in sterility of oocyte-specific Cnot7- and Cnot8-knockout female mice. We further showed that recruitment of CCR4-NOT to maternal mRNAs is mediated by the 3'UTR element, CPE, which suppresses translational activation of maternal mRNAs. We propose that suppression of untimely translational activation of maternal mRNAs via deadenylation by CCR4-NOT is essential for proper oocyte maturation.

Keywords:  CCR4-NOT complex; MRNA deadenylation; Mouse oocyte; Translation

DOI:  https://doi.org/10.1242/dev.201773
Nat Cell Biol. 2023 Sep 28.

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.

Nicholas J Kramer, Gyan Prakash, R Stefan Isaac, Karine Choquet, Iliana Soto, Boryana Petrova, Hope E Merens, Naama Kanarek, L Stirling Churchman.

Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

DOI: https://doi.org/10.1038/s41556-023-01244-3
Sci Adv. 2023 Sep 29. 9(39): eadi7238

Cla4 phosphorylates histone methyltransferase Set1 to prevent its degradation by the APC/CCdh1 complex.

Xuanyunjing Gong, Shanshan Wang, Qi Yu, Min Wang, Feng Ge, Shanshan Li, Xilan Yu.

H3K4 trimethylation (H3K4me3) is a conserved histone modification catalyzed by histone methyltransferase Set1, and its dysregulation is associated with pathologies. Here, we show that Set1 is intrinsically unstable and elucidate how its protein levels are controlled within cell cycle and during gene transcription. Specifically, Set1 contains a destruction box (D-box) that is recognized by E3 ligase APC/CCdh1 and degraded by the ubiquitin-proteasome pathway. Cla4 phosphorylates serine 228 (S228) within Set1 D-box, which inhibits APC/CCdh1-mediated Set1 proteolysis. During gene transcription, PAF complex facilitates Cla4 to phosphorylate Set1-S228 and protect chromatin-bound Set1 from degradation. By modulating Set1 stability and its binding to chromatin, Cla4 and APC/CCdh1 control H3K4me3 levels, which then regulate gene transcription, cell cycle progression, and chronological aging. In addition, there are 141 proteins containing the D-box that can be potentially phosphorylated by Cla4 to prevent their degradation by APC/CCdh1. We addressed the long-standing question about how Set1 stability is controlled and uncovered a new mechanism to regulate protein stability.

DOI: https://doi.org/10.1126/sciadv.adi7238
Nat Commun. 2023 09 23. 14(1): 5941

Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential.

Ceren Pajanoja, Jenny Hsin, Bradley Olinger, Andrew Schiffmacher, Rita Yazejian, Shaun Abrams, Arvydas Dapkunas, Zarin Zainul, Andrew D Doyle, Daniel Martin, Laura Kerosuo.

The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like derivatives is obtained. Here, we monitor transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. We show maintenance of pluripotency-like signature (Nanog, Oct4/PouV, Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-like signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-like signature is found at multiple axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond "ectodermal-capacity" in chick and mouse embryos.

DOI: https://doi.org/10.1038/s41467-023-41384-6
PLoS Biol. 2023 Sep 25. 21(9): e3002316

Rapid mechanosensitive migration and dispersal of newly divided mesenchymal cells aid their recruitment into dermal condensates.

Jon Riddell, Shahzeb Raja Noureen, Luigi Sedda, James D Glover, William K W Ho, Connor A Bain, Arianna Berbeglia, Helen Brown, Calum Anderson, Yuhang Chen, Michael L Crichton, Christian A Yates, Richard L Mort, Denis J Headon.

Embryonic mesenchymal cells are dispersed within an extracellular matrix but can coalesce to form condensates with key developmental roles. Cells within condensates undergo fate and morphological changes and induce cell fate changes in nearby epithelia to produce structures including hair follicles, feathers, or intestinal villi. Here, by imaging mouse and chicken embryonic skin, we find that mesenchymal cells undergo much of their dispersal in early interphase, in a stereotyped process of displacement driven by 3 h of rapid and persistent migration followed by a long period of low motility. The cell division plane and the elevated migration speed and persistence of newly born mesenchymal cells are mechanosensitive, aligning with tissue tension, and are reliant on active WNT secretion. This behaviour disperses mesenchymal cells and allows daughters of recent divisions to travel long distances to enter dermal condensates, demonstrating an unanticipated effect of cell cycle subphase on core mesenchymal behaviour.

DOI: https://doi.org/10.1371/journal.pbio.3002316
J Cell Biol. 2023 Dec 04. pii: e202301069. [Epub ahead of print]222(12):

PLK4 self-phosphorylation drives the selection of a single site for procentriole assembly.

Phillip Scott, Ana Curinha, Colin Gliech, Andrew J Holland.

Polo-like kinase 4 (PLK4) is a key regulator of centriole biogenesis, but how PLK4 selects a single site for procentriole assembly remains unclear. Using ultrastructure expansion microscopy, we show that PLK4 localizes to discrete sites along the wall of parent centrioles. While there is variation in the number of sites PLK4 occupies on the parent centriole, most PLK4 localize at a dominant site that directs procentriole assembly. Inhibition of PLK4 activity leads to stable binding of PLK4 to the centriole and increases occupancy to a maximum of nine sites. We show that self-phosphorylation of an unstructured linker promotes the release of active PLK4 from the centriole to drive the selection of a single site for procentriole assembly. Preventing linker phosphorylation blocks PLK4 turnover, leading to supernumerary sites of PLK4 localization and centriole amplification. Therefore, self-phosphorylation is a major driver of the spatial patterning of PLK4 at the centriole and plays a critical role in selecting a single centriole duplication site.

DOI: https://doi.org/10.1083/jcb.202301069
Dev Cell. 2023 Sep 25. pii: S1534-5807(23)00438-0. [Epub ahead of print]58(18): 1701-1715.e8

Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells.

Liangru Fei, Kaiyang Zhang, Nikita Poddar, Sampsa Hautaniemi, Biswajyoti Sahu.

  Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TFs). However, the exact cell state transitions during transdifferentiation are still poorly understood. Here, we have generated pancreatic exocrine cells of ductal epithelial identity from human fibroblasts using a set of six TFs. We mapped the molecular determinants of lineage dynamics using a factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: an endodermal progenitor state defined by activation of HHEX with FOXA2 and SOX17 and a temporal GATA4 activation essential for the maintenance of pancreatic cell fate program. Collectively, our data suggest that transdifferentiation-although being considered a direct cell fate conversion method-occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs.

Keywords:  cell fate; direct reprogramming; epigenetics; exocrine pancreas; gene regulation; single-cell multiome sequencing; transcription factor

DOI:  https://doi.org/10.1016/j.devcel.2023.08.023
Cell. 2023 Sep 28. pii: S0092-8674(23)00974-1. [Epub ahead of print]186(20): 4422-4437.e21

Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion.

Xushen Xiong, Benjamin T James, Carles A Boix, Yongjin P Park, Kyriaki Galani, Matheus B Victor, Na Sun, Lei Hou, Li-Lun Ho, Julio Mantero, Aine Ni Scannail, Vishnu Dileep, Weixiu Dong, Hansruedi Mathys, David A Bennett, Li-Huei Tsai, Manolis Kellis.

  Recent work has identified dozens of non-coding loci for Alzheimer's disease (AD) risk, but their mechanisms and AD transcriptional regulatory circuitry are poorly understood. Here, we profile epigenomic and transcriptomic landscapes of 850,000 nuclei from prefrontal cortexes of 92 individuals with and without AD to build a map of the brain regulome, including epigenomic profiles, transcriptional regulators, co-accessibility modules, and peak-to-gene links in a cell-type-specific manner. We develop methods for multimodal integration and detecting regulatory modules using peak-to-gene linking. We show AD risk loci are enriched in microglial enhancers and for specific TFs including SPI1, ELF2, and RUNX1. We detect 9,628 cell-type-specific ATAC-QTL loci, which we integrate alongside peak-to-gene links to prioritize AD variant regulatory circuits. We report differential accessibility of regulatory modules in late AD in glia and in early AD in neurons. Strikingly, late-stage AD brains show global epigenome dysregulation indicative of epigenome erosion and cell identity loss.

Keywords:  ATAC-QTL; Alzheimer’s disease; GWAS; epigenome; epigenome erosion; fine-mapping; multimodal integration; peak-to-gene linking

DOI:  https://doi.org/10.1016/j.cell.2023.08.040
Curr Opin Struct Biol. 2023 Sep 21. pii: S0959-440X(23)00178-1. [Epub ahead of print]83 102704

Three-dimensional nuclear organisation and the DNA replication timing program.

Naiming Chen, Sara C B Buonomo.

In eukaryotic cells, genome duplication is temporally organised according to a program referred to as the replication-timing (RT) program. The RT of individual genomic domains strikingly parallels the three-dimensional architecture of their chromatin contacts and subnuclear distribution. However, it is unclear whether this correspondence is coincidental or whether it indicates a causal and regulatory relationship. In either case, the nature of the molecular mechanisms ensuring this spatio-temporal coordination is still unknown. Here, we review recent evidence that begins to uncover the existence of a shared molecular machinery at the core of the spatio-temporal co-regulation of DNA replication and genome architecture. Finally, we discuss the outstanding, key question of the biological role of their coordination.

DOI: https://doi.org/10.1016/j.sbi.2023.102704
Cell. 2023 Sep 28. pii: S0092-8674(23)00971-6. [Epub ahead of print]186(20): 4386-4403.e29

Human microglial state dynamics in Alzheimer's disease progression.

Na Sun, Matheus B Victor, Yongjin P Park, Xushen Xiong, Aine Ni Scannail, Noelle Leary, Shaniah Prosper, Soujanya Viswanathan, Xochitl Luna, Carles A Boix, Benjamin T James, Yosuke Tanigawa, Kyriaki Galani, Hansruedi Mathys, Xueqiao Jiang, Ayesha P Ng, David A Bennett, Li-Huei Tsai, Manolis Kellis.

  Altered microglial states affect neuroinflammation, neurodegeneration, and disease but remain poorly understood. Here, we report 194,000 single-nucleus microglial transcriptomes and epigenomes across 443 human subjects and diverse Alzheimer's disease (AD) pathological phenotypes. We annotate 12 microglial transcriptional states, including AD-dysregulated homeostatic, inflammatory, and lipid-processing states. We identify 1,542 AD-differentially-expressed genes, including both microglia-state-specific and disease-stage-specific alterations. By integrating epigenomic, transcriptomic, and motif information, we infer upstream regulators of microglial cell states, gene-regulatory networks, enhancer-gene links, and transcription-factor-driven microglial state transitions. We demonstrate that ectopic expression of our predicted homeostatic-state activators induces homeostatic features in human iPSC-derived microglia-like cells, while inhibiting activators of inflammation can block inflammatory progression. Lastly, we pinpoint the expression of AD-risk genes in microglial states and differential expression of AD-risk genes and their regulators during AD progression. Overall, we provide insights underlying microglial states, including state-specific and AD-stage-specific microglial alterations at unprecedented resolution.

Keywords:  Alzheimer's; cell states; disease-stage response; iPSCs; inflammation; microglia; single-cell; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2023.08.037
Nature. 2023 Sep 27.

A bioelectrical phase transition patterns the first vertebrate heartbeats.

Bill Z Jia, Yitong Qi, J David Wong-Campos, Sean G Megason, Adam E Cohen.

A regular heartbeat is essential to vertebrate life. In the mature heart, this function is driven by an anatomically localized pacemaker. By contrast, pacemaking capability is broadly distributed in the early embryonic heart1-3, raising the question of how tissue-scale activity is first established and then maintained during embryonic development. The initial transition of the heart from silent to beating has never been characterized at the timescale of individual electrical events, and the structure in space and time of the early heartbeats remains poorly understood. Using all-optical electrophysiology, we captured the very first heartbeat of a zebrafish and analysed the development of cardiac excitability and conduction around this singular event. The first few beats appeared suddenly, had irregular interbeat intervals, propagated coherently across the primordial heart and emanated from loci that varied between animals and over time. The bioelectrical dynamics were well described by a noisy saddle-node on invariant circle bifurcation with action potential upstroke driven by CaV1.2. Our work shows how gradual and largely asynchronous development of single-cell bioelectrical properties produces a stereotyped and robust tissue-scale transition from quiescence to coordinated beating.

DOI: https://doi.org/10.1038/s41586-023-06561-z
Sci Adv. 2023 Sep 29. 9(39): eadi8291

Structural insights into the activation of ataxia-telangiectasia mutated by oxidative stress.

Anna C Howes, Olga Perisic, Roger L Williams.

Ataxia-telangiectasia mutated (ATM) is a master kinase regulating DNA damage response that is activated by DNA double-strand breaks. However, ATM is also directly activated by reactive oxygen species, but how oxidative activation is achieved remains unknown. We determined the cryo-EM structure of an H2O2-activated ATM and showed that under oxidizing conditions, ATM formed an intramolecular disulfide bridge between two protomers that are rotated relative to each other when compared to the basal state. This rotation is accompanied by release of the substrate-blocking PRD region and twisting of the N-lobe relative to the C-lobe, which greatly optimizes catalysis. This active site remodeling enabled us to capture a substrate (p53) bound to the enzyme. This provides the first structural insights into how ATM is activated during oxidative stress.

DOI: https://doi.org/10.1126/sciadv.adi8291
Cell Rep. 2023 Sep 26. pii: S2211-1247(23)01187-7. [Epub ahead of print]42(10): 113175

Microenvironmental stiffness induces metabolic reprogramming in glioblastoma.

Alireza Sohrabi, Austin E Y T Lefebvre, Mollie J Harrison, Michael C Condro, Talia M Sanazzaro, Gevick Safarians, Itay Solomon, Soniya Bastola, Shadi Kordbacheh, Nadia Toh, Harley I Kornblum, Michelle A Digman, Stephanie K Seidlits.

  The mechanical properties of solid tumors influence tumor cell phenotype and the ability to invade surrounding tissues. Using bioengineered scaffolds to provide a matrix microenvironment for patient-derived glioblastoma (GBM) spheroids, this study demonstrates that a soft, brain-like matrix induces GBM cells to shift to a glycolysis-weighted metabolic state, which supports invasive behavior. We first show that orthotopic murine GBM tumors are stiffer than peritumoral brain tissues, but tumor stiffness is heterogeneous where tumor edges are softer than the tumor core. We then developed 3D scaffolds with μ-compressive moduli resembling either stiffer tumor core or softer peritumoral brain tissue. We demonstrate that the softer matrix microenvironment induces a shift in GBM cell metabolism toward glycolysis, which manifests in lower proliferation rate and increased migration activities. Finally, we show that these mechanical cues are transduced from the matrix via CD44 and integrin receptors to induce metabolic and phenotypic changes in cancer cells.

Keywords:  CP: Cancer; CP: Metabolism; extracellular matrix; tissue mechanics

DOI:  https://doi.org/10.1016/j.celrep.2023.113175
Nat Commun. 2023 Sep 27. 14(1): 6016

Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics.

Feng Lin, Xia Li, Shiyu Sun, Zhongyi Li, Chenglin Lv, Jianbo Bai, Lin Song, Yizhao Han, Bo Li, Jianping Fu, Yue Shao.

Region-specific gut spheroids are precursors for gastrointestinal and pulmonary organoids that hold great promise for fundamental studies and translations. However, efficient production of gut spheroids remains challenging due to a lack of control and mechanistic understanding of gut spheroid morphogenesis. Here, we report an efficient biomaterial system, termed micropatterned gut spheroid generator (μGSG), to generate gut spheroids from human pluripotent stem cells through mechanically enhanced tissue morphogenesis. We show that μGSG enhances the biogenesis of gut spheroids independent of micropattern shape and size; instead, mechanically enforced cell multilayering and crowding is demonstrated as a general, geometry-insensitive mechanism that is necessary and sufficient for promoting spheroid formation. Combining experimental findings and an active-phase-field morphomechanics theory, our study further reveals an instability-driven mechanism and a mechanosensitive phase diagram governing spheroid pearling and fission in μGSG. This work unveils mechanobiological paradigms based on tissue architecture and surface tension for controlling tissue morphogenesis and advancing organoid technology.

DOI: https://doi.org/10.1038/s41467-023-41760-2