bims-ginsta 2024-09-08 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–09–08
forty-six papers selected by
Jinrong Hu, National University of Singapore

Genome access is transcription factor-specific and defined by nucleosome position.
Disorder-mediated interactions target proteins to specific condensates.
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers.
ERK synchronizes embryonic cleavages in Drosophila.
The valine-arginine dipeptide repeat protein encoded by mammalian telomeric RNA appears highly expressed in mitosis and may repress global translation.
5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming.
Criteria for the standardization of stem-cell-based embryo models.
DNA methylation controls stemness of astrocytes in health and ischaemia.
Ribosomal S6 kinase 1 regulates inflammaging via the senescence secretome.
Virally delivered CMYA5 enhances the assembly of cardiac dyads.
PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance.
Chromosome breakage-replication/fusion enables rapid DNA amplification.
ImAge quantitates aging and rejuvenation.
Mapping cellular interactions from spatially resolved transcriptomics data.
Clinical-transcriptional prioritization of the circulating proteome in human heart failure.
Transient Inhibition of Translation Improves Cardiac Function After Ischemia/Reperfusion by Attenuating the Inflammatory Response.
Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake.
Integrin signaling in pluripotent cells acts as a gatekeeper of mouse germline entry.
A p62-dependent rheostat dictates micronuclei catastrophe and chromosome rearrangements.
Ophthalmic acid is a bloodborne metabolite that contributes to age-induced cardiomyocyte hypertrophy.
CDK5-cyclin B1 regulates mitotic fidelity.
Self-organizing ovarian somatic organoids preserve cellular heterogeneity and reveal cellular contributions to ovarian aging.
Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes.
Excitable Rho dynamics control cell shape and motility by sequentially activating ERM proteins and actomyosin contractility.
Smarcd1 subunit of SWI/SNF chromatin-remodeling complexes collaborates with E2a to promote murine lymphoid specification.
Alveolar regeneration by airway secretory-cell-derived p63+ progenitors.
α-Ketoglutarate promotes cardiomyocyte proliferation and heart regeneration after myocardial infarction.
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease.
Role of protein kinase PLK1 in the epigenetic maintenance of centromeres.
Micronuclear collapse from oxidative damage.
A size filter at the Golgi regulates apical membrane protein sorting.
A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis.
Mechanisms of assembly and remodelling of the extracellular matrix.
Achieving optical transparency in live animals with absorbing molecules.
Noncanonical inheritance of phenotypic information by protein amyloids.
A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate.
Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes.
Spermidine controls autophagy during fasting.
Protocol for generating human cortical organoids enriched in outer radial glia by guided differentiation.
Hematopoietic aging promotes cancer by fueling IL-1⍺-driven emergency myelopoiesis.
Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering.
A molecular brain atlas reveals cellular shifts during the repair phase of stroke.
Long-term engrafting multilineage hematopoietic cells differentiated from human induced pluripotent stem cells.
Extracellular Vesicle-Associated Neutrophil Elastase Activates Hepatic Stellate Cells and Promotes Liver Fibrogenesis via ERK1/2 Pathway.
Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome.
Human genomic DNA is widely interspersed with i-motif structures.

Mol Cell. 2024 Aug 22. pii: S1097-2765(24)00663-4. [Epub ahead of print]

Genome access is transcription factor-specific and defined by nucleosome position.

Ralph Stefan Grand, Marco Pregnolato, Lisa Baumgartner, Leslie Hoerner, Lukas Burger, Dirk Schübeler.

  Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable the binding of TFs with diverse tissue specificities, functions, and DNA-binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly phased nucleosome. The pluripotency factors OCT4-SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome-internal sites, a preference that also guides binding genome wide. By contrast, factors such as BANP, REST, or CTCF engage throughout, causing nucleosomal displacement. This supports that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF specific and influenced by nucleosome position in the cell.

Keywords:  accessibility; chromatin; genome; nucleosome; pioneer factors; transcription factors

DOI:  https://doi.org/10.1016/j.molcel.2024.08.009
Mol Cell. 2024 Aug 27. pii: S1097-2765(24)00671-3. [Epub ahead of print]

Disorder-mediated interactions target proteins to specific condensates.

Nancy De La Cruz, Prashant Pradhan, Reshma T Veettil, Brooke A Conti, Mariano Oppikofer, Benjamin R Sabari.

  Selective compartmentalization of cellular contents is fundamental to the regulation of biochemistry. Although membrane-bound organelles control composition by using a semi-permeable barrier, biomolecular condensates rely on interactions among constituents to determine composition. Condensates are formed by dynamic multivalent interactions, often involving intrinsically disordered regions (IDRs) of proteins, yet whether distinct compositions can arise from these dynamic interactions is not known. Here, by comparative analysis of proteins differentially partitioned by two different condensates, we find that distinct compositions arise through specific IDR-mediated interactions. The IDRs of differentially partitioned proteins are necessary and sufficient for selective partitioning. Distinct sequence features are required for IDRs to partition, and swapping these sequence features changes the specificity of partitioning. Swapping whole IDRs retargets proteins and their biochemical activity to different condensates. Our results demonstrate that IDR-mediated interactions can target proteins to specific condensates, enabling the spatial regulation of biochemistry within the cell.

Keywords:  IDR; biomolecular condensates; condensate composition; condensate function; intrinsically disordered regions; nuclear organization; specificity

DOI:  https://doi.org/10.1016/j.molcel.2024.08.017
Science. 2024 Sep 06. 385(6713): eadk9217

Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers.

Cancer Genome Atlas Analysis Network‡

To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy number alterations that can be used to identify subclones, yet underlying cis-regulatory landscapes retain cancer type-specific features. Using organ-matched healthy tissues, we identified the "nearest healthy" cell types in diverse cancers, demonstrating that the chromatin signature of basal-like-subtype breast cancer is most similar to secretory-type luminal epithelial cells. Neural network models trained to learn regulatory programs in cancer revealed enrichment of model-prioritized somatic noncoding mutations near cancer-associated genes, suggesting that dispersed, nonrecurrent, noncoding mutations in cancer are functional. Overall, these data and interpretable gene regulatory models for cancer and healthy tissue provide a framework for understanding cancer-specific gene regulation.

DOI: https://doi.org/10.1126/science.adk9217
Dev Cell. 2024 Aug 27. pii: S1534-5807(24)00487-8. [Epub ahead of print]

ERK synchronizes embryonic cleavages in Drosophila.

Liu Yang, Audrey Zhu, Javed M Aman, David Denberg, Marcus D Kilwein, Robert A Marmion, Alex N T Johnson, Alexey Veraksa, Mona Singh, Martin Wühr, Stanislav Y Shvartsman.

  Extracellular-signal-regulated kinase (ERK) signaling controls development and homeostasis and is genetically deregulated in human diseases, including neurocognitive disorders and cancers. Although the list of ERK functions is vast and steadily growing, the full spectrum of processes controlled by any specific ERK activation event remains unknown. Here, we show how ERK functions can be systematically identified using targeted perturbations and global readouts of ERK activation. Our experimental model is the Drosophila embryo, where ERK signaling at the embryonic poles has thus far only been associated with the transcriptional patterning of the future larva. Through a combination of live imaging and phosphoproteomics, we demonstrated that ERK activation at the poles is also critical for maintaining the speed and synchrony of embryonic cleavages. The presented approach to interrogating phosphorylation networks identifies a hidden function of a well-studied signaling event and sets the stage for similar studies in other organisms.

Keywords:  Cdc25; Cdk1; ERK; cell cycle; cleavages; embryonic; optogenetics; phosphoproteome; sychrony

DOI:  https://doi.org/10.1016/j.devcel.2024.08.004
bioRxiv. 2024 Jul 29. pii: 2024.07.24.604971. [Epub ahead of print]

The valine-arginine dipeptide repeat protein encoded by mammalian telomeric RNA appears highly expressed in mitosis and may repress global translation.

Taghreed M Al-Turki, Venkata Mantri, Smaranda Willcox, C Allie Mills, Laura E Herring, Su-Ji Cho, Hannah Lee, Cailyn Meyer, E S Anton, Jack D Griffith.

Translation of mammalian telomeric G-rich RNA via the Repeat Associated non-AUG translation mechanism can produce two dipeptide repeat proteins: repeating valine-arginine (VR) and repeating glycine-leucine (GL). Their potentially toxic nature suggests that one or both must play a needed role in the cell. Using light microscopy combined with antibody staining we discovered that cultured human cells stain brightly for VR during mitosis with VR staining co-localizing with ribosomes. In vitro , VR protein represses translation in a firefly luciferase assay. Affinity purification combined with mass spectrometry identified ribosomal proteins as the major class of VR interacting proteins. Extension to mouse embryonic cerebral cortical development showed strong staining in the ventricular zone where high mitotic index neural progenitor cells proliferate and in the cortical plate where new neurons settle. These observations point to VR playing a key role in mitosis very possibly depressing global translation, a role mediated by the telomere.
Teaser: The telomeric valine-arginine dipeptide repeat protein is highly expressed in mitotic cells in culture and in mouse embryonic neural tissue.

DOI: https://doi.org/10.1101/2024.07.24.604971
Cell. 2024 Aug 28. pii: S0092-8674(24)00902-4. [Epub ahead of print]

5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming.

Eleftheria Parasyraki, Medhavi Mallick, Victoria Hatch, Viviana Vastolo, Michael U Musheev, Emil Karaulanov, Alexandr Gopanenko, Simon Moxon, Maria Méndez-Lago, Dandan Han, Lars Schomacher, Debasish Mukherjee, Christof Niehrs.

  5-Methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.

Keywords:  5-formylcytosine; B-box; RNA Pol III; TDG; TET; Xenopus; ZGA; perinucleolar compartment; tRNA; tRNA-iMet

DOI:  https://doi.org/10.1016/j.cell.2024.08.011
Nat Cell Biol. 2024 Sep 02.

Criteria for the standardization of stem-cell-based embryo models.

Alfonso Martinez Arias, Nicolas Rivron, Naomi Moris, Patrick Tam, Cantas Alev, Jianping Fu, Anna-Katerina Hadjantonakis, Jacob H Hanna, Gabriella Minchiotti, Olivier Pourquie, Guojun Sheng, Liliana Solnica Krezel, Jesse V Veenvliet, Aryeh Warmflash.

DOI: https://doi.org/10.1038/s41556-024-01492-x
Nature. 2024 Sep 04.

DNA methylation controls stemness of astrocytes in health and ischaemia.

Lukas P M Kremer, Santiago Cerrizuela, Hadil El-Sammak, Mohammad Eid Al Shukairi, Tobias Ellinger, Jannes Straub, Aylin Korkmaz, Katrin Volk, Jan Brunken, Susanne Kleber, Simon Anders, Ana Martin-Villalba.

Astrocytes are the most abundant cell type in the mammalian brain and provide structural and metabolic support to neurons, regulate synapses and become reactive after injury and disease. However, a small subset of astrocytes settles in specialized areas of the adult brain where these astrocytes instead actively generate differentiated neuronal and glial progeny and are therefore referred to as neural stem cells1-3. Common parenchymal astrocytes and quiescent neural stem cells share similar transcriptomes despite their very distinct functions4-6. Thus, how stem cell activity is molecularly encoded remains unknown. Here we examine the transcriptome, chromatin accessibility and methylome of neural stem cells and their progeny, and of astrocytes from the striatum and cortex in the healthy and ischaemic adult mouse brain. We identify distinct methylation profiles associated with either astrocyte or stem cell function. Stem cell function is mediated by methylation of astrocyte genes and demethylation of stem cell genes that are expressed later. Ischaemic injury to the brain induces gain of stemness in striatal astrocytes7. We show that this response involves reprogramming the astrocyte methylome to a stem cell methylome and is absent if the de novo methyltransferase DNMT3A is missing. Overall, we unveil DNA methylation as a promising target for regenerative medicine.

DOI: https://doi.org/10.1038/s41586-024-07898-9
Nat Aging. 2024 Aug 29.

Ribosomal S6 kinase 1 regulates inflammaging via the senescence secretome.

Suchira Gallage, Elaine E Irvine, Jose Efren Barragan Avila, Virinder Reen, Silvia M A Pedroni, Imanol Duran, Vikas Ranvir, Sanjay Khadayate, Joaquim Pombo, Sharon Brookes, Danijela Heide, Gopuraja Dharmalingham, Agharul I Choudhury, Indrabahadur Singh, Nicolás Herranz, Santiago Vernia, Mathias Heikenwalder, Jesús Gil, Dominic J Withers.

Inhibition of S6 kinase 1 (S6K1) extends lifespan and improves healthspan in mice, but the underlying mechanisms are unclear. Cellular senescence is a stable growth arrest accompanied by an inflammatory senescence-associated secretory phenotype (SASP). Cellular senescence and SASP-mediated chronic inflammation contribute to age-related pathology, but the specific role of S6K1 has not been determined. Here we show that S6K1 deletion does not reduce senescence but ameliorates inflammation in aged mouse livers. Using human and mouse models of senescence, we demonstrate that reduced inflammation is a liver-intrinsic effect associated with S6K deletion. Specifically, we show that S6K1 deletion results in reduced IRF3 activation; impaired production of cytokines, such as IL1β; and reduced immune infiltration. Using either liver-specific or myeloid-specific S6K knockout mice, we also demonstrate that reduced immune infiltration and clearance of senescent cells is a hepatocyte-intrinsic phenomenon. Overall, deletion of S6K reduces inflammation in the liver, suggesting that suppression of the inflammatory SASP by loss of S6K could underlie the beneficial effects of inhibiting this pathway on healthspan and lifespan.

DOI: https://doi.org/10.1038/s43587-024-00695-z
Nat Biomed Eng. 2024 Sep 05.

Virally delivered CMYA5 enhances the assembly of cardiac dyads.

Fujian Lu, Carter Liou, Qing Ma, Zexuan Wu, Bingqing Xue, Yu Xia, Shutao Xia, Michael A Trembley, Anna Ponek, Wenjun Xie, Kevin Shani, Raul H Bortolin, Maksymilian Prondzynski, Paul Berkson, Xiaoran Zhang, Francisco J Naya, Kenneth C Bedi, Kenneth B Margulies, Donghui Zhang, Kevin K Parker, William T Pu.

Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) lack nanoscale structures essential for efficient excitation-contraction coupling. Such nanostructures, known as dyads, are frequently disrupted in heart failure. Here we show that the reduced expression of cardiomyopathy-associated 5 (CMYA5), a master protein that establishes dyads, contributes to dyad disorganization in heart failure and to impaired dyad assembly in hiPSC-CMs, and that a miniaturized form of CMYA5 suitable for delivery via an adeno-associated virus substantially improved dyad architecture and normalized cardiac function under pressure overload. In hiPSC-CMs, the miniaturized form of CMYA5 increased contractile forces, improved Ca2+ handling and enhanced the alignment of sarcomere Z-lines with ryanodine receptor 2, a protein that mediates the sarcoplasmic release of stored Ca2+. Our findings clarify the mechanisms responsible for impaired dyad structure in diseased cardiomyocytes, and suggest strategies for promoting dyad assembly and stability in heart disease and during the derivation of hiPSC-CMs.

DOI: https://doi.org/10.1038/s41551-024-01253-z
Science. 2024 Sep 06. 385(6713): 1098-1104

PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance.

Pragya Parashara, Bethan Medina-Pritchard, Maria Alba Abad, Paula Sotelo-Parrilla, Reshma Thamkachy, David Grundei, Juan Zou, Christos Spanos, Chandni Natalia Kumar, Claire Basquin, Vimal Das, Zhaoyue Yan, Asma Abdullah Al-Murtadha, David A Kelly, Toni McHugh, Axel Imhof, Juri Rappsilber, A Arockia Jeyaprakash.

Accurate chromosome segregation requires the attachment of microtubules to centromeres, epigenetically defined by the enrichment of CENP-A nucleosomes. During DNA replication, CENP-A nucleosomes undergo dilution. To preserve centromere identity, correct amounts of CENP-A must be restored in a cell cycle-controlled manner orchestrated by the Mis18 complex (Mis18α-Mis18β-Mis18BP1). We demonstrate here that PLK1 interacts with the Mis18 complex by recognizing self-primed phosphorylations of Mis18α (Ser54) and Mis18BP1 (Thr78 and Ser93) through its Polo-box domain. Disrupting these phosphorylations perturbed both centromere recruitment of the CENP-A chaperone HJURP and new CENP-A loading. Biochemical and functional analyses showed that phosphorylation of Mis18α and PLK1 binding were required to activate Mis18α-Mis18β and promote Mis18 complex-HJURP interaction. Thus, our study reveals key molecular events underpinning the licensing role of PLK1 in ensuring accurate centromere inheritance.

DOI: https://doi.org/10.1126/science.ado8270
bioRxiv. 2024 Aug 19. pii: 2024.08.17.608415. [Epub ahead of print]

Chromosome breakage-replication/fusion enables rapid DNA amplification.

Cheng-Zhong Zhang, David Pellman.

DNA rearrangements are thought to arise from two classes of processes. The first class involves DNA breakage and fusion ("cut-and-paste") without net DNA gain or loss. The second class involves aberrant DNA replication ("copy-and-paste") and can produce either net DNA gain or loss. We previously demonstrated that the partitioning of chromosomes into aberrant structures of the nucleus, micronuclei or chromosome bridges, can generate cut-and-paste rearrangements by chromosome fragmentation and ligation. Surprisingly, in the progeny clones of single cells that have undergone chromosome bridge breakage, we identified large segmental duplications and short sequence insertions that are commonly attributed to copy-and-paste processes. Here, we demonstrate that both large duplications and short insertions are inherent outcomes of the replication and fusion of unligated DNA ends, a process we term breakage-replication/fusion (B-R/F). We propose that B-R/F provides a unifying explanation for complex rearrangement patterns including chromothripsis and chromoanasynthesis and enables rapid DNA amplification after chromosome fragmentation.

DOI: https://doi.org/10.1101/2024.08.17.608415
Nat Aging. 2024 Aug 29.

ImAge quantitates aging and rejuvenation.

Martin Alvarez-Kuglen, Kenta Ninomiya, Haodong Qin, Delany Rodriguez, Lorenzo Fiengo, Chen Farhy, Wei-Mien Hsu, Brian Kirk, Aaron Havas, Gen-Sheng Feng, Amanda J Roberts, Rozalyn M Anderson, Manuel Serrano, Peter D Adams, Tatyana O Sharpee, Alexey V Terskikh.

For efficient, cost-effective and personalized healthcare, biomarkers that capture aspects of functional, biological aging, thus predicting disease risk and lifespan more accurately and reliably than chronological age, are essential. We developed an imaging-based chromatin and epigenetic age (ImAge) that captures intrinsic age-related trajectories of the spatial organization of chromatin and epigenetic marks in single nuclei, in mice. We show that such trajectories readily emerge as principal changes in each individual dataset without regression on chronological age, and that ImAge can be computed using several epigenetic marks and DNA labeling. We find that interventions known to affect biological aging induce corresponding effects on ImAge, including increased ImAge upon chemotherapy treatment and decreased ImAge upon caloric restriction and partial reprogramming by transient OSKM expression in liver and skeletal muscle. Further, ImAge readouts from chronologically identical mice inversely correlated with their locomotor activity, suggesting that ImAge may capture elements of biological and functional age. In sum, we developed ImAge, an imaging-based biomarker of aging with single-cell resolution rooted in the analysis of spatial organization of epigenetic marks.

DOI: https://doi.org/10.1038/s43587-024-00685-1
Nat Methods. 2024 Sep 03.

Mapping cellular interactions from spatially resolved transcriptomics data.

James Zhu, Yunguan Wang, Woo Yong Chang, Alicia Malewska, Fabiana Napolitano, Jeffrey C Gahan, Nisha Unni, Min Zhao, Rongqing Yuan, Fangjiang Wu, Lauren Yue, Lei Guo, Zhuo Zhao, Danny Z Chen, Raquibul Hannan, Siyuan Zhang, Guanghua Xiao, Ping Mu, Ariella B Hanker, Douglas Strand, Carlos L Arteaga, Neil Desai, Xinlei Wang, Yang Xie, Tao Wang.

Cell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently through the introduction of spatially resolved transcriptomics (SRT) technologies, especially those that achieve single-cell resolution. Nevertheless, substantial challenges remain to analyze such highly complex data properly. Here, we introduce a multiple-instance learning framework, Spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight Spacia's power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates and, most importantly, the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of Spacia for three commercialized single-cell resolution SRT technologies: MERSCOPE/Vizgen, CosMx/NanoString and Xenium/10x. Overall, Spacia represents a notable step in advancing quantitative theories of cellular communications.

DOI: https://doi.org/10.1038/s41592-024-02408-1
Cell Rep Med. 2024 Aug 30. pii: S2666-3791(24)00425-7. [Epub ahead of print] 101704

Clinical-transcriptional prioritization of the circulating proteome in human heart failure.

Andrew S Perry, Kaushik Amancherla, Xiaoning Huang, Michelle L Lance, Eric Farber-Eger, Priya Gajjar, Junedh Amrute, Lindsey Stolze, Shilin Zhao, Quanhu Sheng, Cassandra M Joynes, Zhongsheng Peng, Toshiko Tanaka, Stavros G Drakos, Kory J Lavine, Craig Selzman, Joseph R Visker, Thirupura S Shankar, Luigi Ferrucci, Saumya Das, Jane Wilcox, Ravi B Patel, Ravi Kalhan, Sanjiv J Shah, Keenan A Walker, Quinn Wells, Nathan Tucker, Matthew Nayor, Ravi V Shah, Sadiya S Khan.

  Given expanding studies in epidemiology and disease-oriented human studies offering hundreds of associations between the human "ome" and disease, prioritizing molecules relevant to disease mechanisms among this growing breadth is important. Here, we link the circulating proteome to human heart failure (HF) propensity (via echocardiographic phenotyping and clinical outcomes) across the lifespan, demonstrating key pathways of fibrosis, inflammation, metabolism, and hypertrophy. We observe a broad array of genes encoding proteins linked to HF phenotypes and outcomes in clinical populations dynamically expressed at a transcriptional level in human myocardium during HF and cardiac recovery (several in a cell-specific fashion). Many identified targets do not have wide precedent in large-scale genomic discovery or human studies, highlighting the complementary roles for proteomic and tissue transcriptomic discovery to focus epidemiological targets to those relevant in human myocardium for further interrogation.

Keywords:  heart failure; multiomics; proteomics; snRNA-seq; transcriptomics

DOI:  https://doi.org/10.1016/j.xcrm.2024.101704
Circulation. 2024 Aug 29.

Transient Inhibition of Translation Improves Cardiac Function After Ischemia/Reperfusion by Attenuating the Inflammatory Response.

Christoph Hofmann, Adrian Serafin, Ole M Schwerdt, Johannes Fischer, Florian Sicklinger, Fereshteh S Younesi, Nikole J Byrne, Ingmar S Meyer, Ellen Malovrh, Clara Sandmann, Lonny Jürgensen, Verena Kamuf-Schenk, Claudia Stroh, Zoe Löwenthal, Daniel Finke, Etienne Boileau, Arica Beisaw, Heiko Bugger, Mandy Rettel, Frank Stein, Hugo A Katus, Tobias Jakobi, Norbert Frey, Florian Leuschner, Mirko Völkers.

   BACKGROUND: The myocardium adapts to ischemia/reperfusion (I/R) by changes in gene expression, determining the cardiac response to reperfusion. mRNA translation is a key component of gene expression. It is largely unknown how regulation of mRNA translation contributes to cardiac gene expression and inflammation in response to reperfusion and whether it can be targeted to mitigate I/R injury.
METHODS: To examine translation and its impact on gene expression in response to I/R, we measured protein synthesis after reperfusion in vitro and in vivo. Underlying mechanisms of translational control were examined by pharmacological and genetic targeting of translation initiation in mice. Cell type-specific ribosome profiling was performed in mice that had been subjected to I/R to determine the impact of mRNA translation on the regulation of gene expression in cardiomyocytes. Translational regulation of inflammation was studied by quantification of immune cell infiltration, inflammatory gene expression, and cardiac function after short-term inhibition of translation initiation.
RESULTS: Reperfusion induced a rapid recovery of translational activity that exceeds baseline levels in the infarct and border zone and is mediated by translation initiation through the mTORC1 (mechanistic target of rapamycin complex 1)-4EBP1 (eIF4E-binding protein 1)-eIF (eukaryotic initiation factor) 4F axis. Cardiomyocyte-specific ribosome profiling identified that I/R increased translation of mRNA networks associated with cardiac inflammation and cell infiltration. Short-term inhibition of the mTORC1-4EBP1-eIF4F axis decreased the expression of proinflammatory cytokines such as Ccl2 (C-C motif chemokine ligand 2) of border zone cardiomyocytes, thereby attenuating Ly6Chi monocyte infiltration and myocardial inflammation. In addition, we identified a systemic immunosuppressive effect of eIF4F translation inhibitors on circulating monocytes, directly inhibiting monocyte infiltration. Short-term pharmacological inhibition of eIF4F complex formation by 4EGI-1 or rapamycin attenuated translation, reduced infarct size, and improved cardiac function after myocardial infarction.
CONCLUSIONS: Global protein synthesis is inhibited during ischemia and shortly after reperfusion, followed by a recovery of protein synthesis that exceeds baseline levels in the border and infarct zones. Activation of mRNA translation after reperfusion is driven by mTORC1/eIF4F-mediated regulation of initiation and mediates an mRNA network that controls inflammation and monocyte infiltration to the myocardium. Transient inhibition of the mTORC1-/eIF4F axis inhibits translation and attenuates Ly6Chi monocyte infiltration by inhibiting a proinflammatory response at the site of injury and of circulating monocytes.

Keywords:  Ccl2; inflammation; mTOR; myocardial infarction; reperfusion injury; translation

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.067479
Cell. 2024 Aug 27. pii: S0092-8674(24)00895-X. [Epub ahead of print]

Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake.

Tao Long, Dongyu Li, Goncalo Vale, Yaoyukun Jiang, Philip Schmiege, Zhongyue J Yang, Jeffrey G McDonald, Xiaochun Li.

  In mammalian cells, two phosphatidylserine (PS) synthases drive PS synthesis. Gain-of-function mutations in the Ptdss1 gene lead to heightened PS production, causing Lenz-Majewski syndrome (LMS). Recently, pharmacological inhibition of PSS1 has been shown to suppress tumorigenesis. Here, we report the cryo-EM structures of wild-type human PSS1 (PSS1WT), the LMS-causing Pro269Ser mutant (PSS1P269S), and PSS1WT in complex with its inhibitor DS55980254. PSS1 contains 10 transmembrane helices (TMs), with TMs 4-8 forming a catalytic core in the luminal leaflet. These structures revealed a working mechanism of PSS1 akin to the postulated mechanisms of the membrane-bound O-acyltransferase family. Additionally, we showed that both PS and DS55980254 can allosterically inhibit PSS1 and that inhibition by DS55980254 activates the SREBP pathways, thus enhancing the expression of LDL receptors and increasing cellular LDL uptake. This work uncovers a mechanism of mammalian PS synthesis and suggests that selective PSS1 inhibitors have the potential to lower blood cholesterol levels.

Keywords:  DS55980254; LDL; LDL receptors; MBOAT; PSS1; cholesterol trafficking; phosphatidylserine

DOI:  https://doi.org/10.1016/j.cell.2024.08.004
Sci Adv. 2024 Sep 06. 10(36): eadk2252

Integrin signaling in pluripotent cells acts as a gatekeeper of mouse germline entry.

Aly Makhlouf, Anfu Wang, Nanami Sato, Viviane S Rosa, Marta N Shahbazi.

Primordial germ cells (PGCs) are the precursors of gametes and the sole mechanism by which animals transmit genetic information across generations. In the mouse embryo, the transcriptional and epigenetic regulation of PGC specification has been extensively characterized. However, the initial event that triggers the soma-germline segregation remains poorly understood. Here, we uncover a critical role for the basement membrane in regulating germline entry. We show that PGCs arise in a region of the mouse embryo that lacks contact with the basement membrane, and the addition of exogenous extracellular matrix (ECM) inhibits both PGC and PGC-like cell (PGCLC) specification in mouse embryos and stem cell models, respectively. Mechanistically, we demonstrate that the engagement of β1 integrin with laminin blocks PGCLC specification by preventing the Wnt signaling-dependent down-regulation of the PGC transcriptional repressor, Otx2. In this way, the physical segregation of cells away from the basement membrane acts as a morphogenetic fate switch that controls the soma-germline bifurcation.

DOI: https://doi.org/10.1126/sciadv.adk2252
Science. 2024 Aug 30. 385(6712): eadj7446

A p62-dependent rheostat dictates micronuclei catastrophe and chromosome rearrangements.

Sara Martin, Simone Scorzoni, Sara Cordone, Alice Mazzagatti, Galina V Beznoussenko, Amanda L Gunn, Melody Di Bona, Yonatan Eliezer, Gil Leor, Tal Ben-Yishay, Alessia Loffreda, Valeria Cancila, Maria Chiara Rainone, Marica Rosaria Ippolito, Valentino Martis, Fabio Bedin, Massimiliano Garrè, Laura Pontano Vaites, Paolo Vasapolli, Simona Polo, Dario Parazzoli, Claudio Tripodo, Alexander A Mironov, Alessandro Cuomo, Uri Ben-David, Samuel F Bakhoum, Emily M Hatch, Peter Ly, Stefano Santaguida.

Chromosomal instability (CIN) generates micronuclei-aberrant extranuclear structures that catalyze the acquisition of complex chromosomal rearrangements present in cancer. Micronuclei are characterized by persistent DNA damage and catastrophic nuclear envelope collapse, which exposes DNA to the cytoplasm. We found that the autophagic receptor p62/SQSTM1 modulates micronuclear stability, influencing chromosome fragmentation and rearrangements. Mechanistically, proximity of micronuclei to mitochondria led to oxidation-driven homo-oligomerization of p62, limiting endosomal sorting complex required for transport (ESCRT)-dependent micronuclear envelope repair by triggering autophagic degradation. We also found that p62 levels correlate with increased chromothripsis across human cancer cell lines and with increased CIN in colorectal tumors. Thus, p62 acts as a regulator of micronuclei and may serve as a prognostic marker for tumors with high CIN.

DOI: https://doi.org/10.1126/science.adj7446
bioRxiv. 2024 Aug 09. pii: 2024.08.08.607218. [Epub ahead of print]

Ophthalmic acid is a bloodborne metabolite that contributes to age-induced cardiomyocyte hypertrophy.

Melod Mehdipour, Sangsoon Park, Wei Wei, Jonathan Z Long, Guo N Huang.

Cardiac aging involves the development of left ventricular hypertrophy alongside a decline in functional capacity. Here, we use neutral blood exchange to demonstrate that the acute removal of age-accumulated blood factors significantly regresses cardiac hypertrophy in aged mice. The reversal of hypertrophy was not attributed to age-associated hemodynamic effects, implicating a role of blood-derived factors. In addition, the overarching paradigm of systemic aging maintains that the age-related overabundance of plasma proteins are largely responsible for causing pathological phenotypes in tissues. Our results suggest that blood metabolites, not proteins, drive cardiac hypertrophy instead. Upon analyzing serum metabolomics data sets, we identified ophthalmic acid as a circulating metabolite whose levels increase with advanced age. Treatment of adult mouse and neonatal rat cardiomyocytes in culture with ophthalmic acid increased their relative surface areas. This study uncovers a non-protein metabolite that may contribute to cardiomyocyte hypertrophy during aging. Identifying a method to counteract ophthalmic acid's hypertrophic effects may reveal novel therapeutic opportunities for cardiac rejuvenation.

DOI: https://doi.org/10.1101/2024.08.08.607218
Nature. 2024 Sep 04.

CDK5-cyclin B1 regulates mitotic fidelity.

Xiao-Feng Zheng, Aniruddha Sarkar, Humphrey Lotana, Aleem Syed, Huy Nguyen, Richard G Ivey, Jacob J Kennedy, Jeffrey R Whiteaker, Bartłomiej Tomasik, Kaimeng Huang, Feng Li, Alan D D'Andrea, Amanda G Paulovich, Kavita Shah, Alexander Spektor, Dipanjan Chowdhury.

CDK1 has been known to be the sole cyclin-dependent kinase (CDK) partner of cyclin B1 to drive mitotic progression1. Here we demonstrate that CDK5 is active during mitosis and is necessary for maintaining mitotic fidelity. CDK5 is an atypical CDK owing to its high expression in post-mitotic neurons and activation by non-cyclin proteins p35 and p392. Here, using independent chemical genetic approaches, we specifically abrogated CDK5 activity during mitosis, and observed mitotic defects, nuclear atypia and substantial alterations in the mitotic phosphoproteome. Notably, cyclin B1 is a mitotic co-factor of CDK5. Computational modelling, comparison with experimentally derived structures of CDK-cyclin complexes and validation with mutational analysis indicate that CDK5-cyclin B1 can form a functional complex. Disruption of the CDK5-cyclin B1 complex phenocopies CDK5 abrogation in mitosis. Together, our results demonstrate that cyclin B1 partners with both CDK5 and CDK1, and CDK5-cyclin B1 functions as a canonical CDK-cyclin complex to ensure mitotic fidelity.

DOI: https://doi.org/10.1038/s41586-024-07888-x
bioRxiv. 2024 Aug 10. pii: 2024.08.10.607456. [Epub ahead of print]

Self-organizing ovarian somatic organoids preserve cellular heterogeneity and reveal cellular contributions to ovarian aging.

Shweta S Dipali, Madison Q Gowett, Pratik Kamat, Aubrey Converse, Emily J Zaniker, Abigail Fennell, Teresa Chou, Michele T Pritchard, Mary Zelinski, Jude M Phillip, Francesca E Duncan.

Ovarian somatic cells are essential for reproductive function, but no existing ex vivo models recapitulate the cellular heterogeneity or interactions within this compartment. We engineered a novel ovarian somatic organoid model by culturing a stroma-enriched fraction of mouse ovaries in scaffold-free agarose micromolds. Ovarian somatic organoids self-organized, maintained diverse cell populations, produced extracellular matrix, and secreted hormones. Organoids generated from reproductively old mice exhibited reduced aggregation and growth compared to young counterparts, as well as differences in cellular composition. Interestingly, matrix fibroblasts from old mice demonstrated upregulation of pathways associated with the actin cytoskeleton and downregulation of cell adhesion pathways, indicative of increased cellular stiffness which may impair organoid aggregation. Cellular morphology, which is regulated by the cytoskeleton, significantly changed with age and in response to actin depolymerization. Moreover, actin depolymerization rescued age-associated organoid aggregation deficiency. Overall, ovarian somatic organoids have advanced fundamental knowledge of cellular contributions to ovarian aging.

DOI: https://doi.org/10.1101/2024.08.10.607456
Mol Cell. 2024 Aug 28. pii: S1097-2765(24)00658-0. [Epub ahead of print]

Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes.

Rose Westhorpe, Johann J Roske, Joseph T P Yeeles.

  Topoisomerase 1 cleavage complexes (Top1-ccs) comprise a DNA-protein crosslink and a single-stranded DNA break that can significantly impact the DNA replication machinery (replisome). Consequently, inhibitors that trap Top1-ccs are used extensively in research and clinical settings to generate DNA replication stress, yet how the replisome responds upon collision with a Top1-cc remains obscure. By reconstituting collisions between budding yeast replisomes, assembled from purified proteins, and site-specific Top1-ccs, we have uncovered mechanisms underlying replication fork stalling and collapse. We find that stalled replication forks are surprisingly stable and that their stability is influenced by the template strand that Top1 is crosslinked to, the fork protection complex proteins Tof1-Csm3 (human TIMELESS-TIPIN), and the convergence of replication forks. Moreover, nascent-strand mapping and cryoelectron microscopy (cryo-EM) of stalled forks establishes replisome remodeling as a key factor in the initial response to Top1-ccs. These findings have important implications for the use of Top1 inhibitors in research and in the clinic.

Keywords:  CMG helicase; Top1; Top1 cleavage complex; fork protection complex; replication stress; replisome; topoisomerase

DOI:  https://doi.org/10.1016/j.molcel.2024.08.004
Sci Adv. 2024 Sep 06. 10(36): eadn6858

Excitable Rho dynamics control cell shape and motility by sequentially activating ERM proteins and actomyosin contractility.

Seph Marshall-Burghardt, Rodrigo A Migueles-Ramírez, Qiyao Lin, Nada El Baba, Rayan Saada, Mustakim Umar, Kian Mavalwala, Arnold Hayer.

Migration of endothelial and many other cells requires spatiotemporal regulation of protrusive and contractile cytoskeletal rearrangements that drive local cell shape changes. Unexpectedly, the small GTPase Rho, a crucial regulator of cell movement, has been reported to be active in both local cell protrusions and retractions, raising the question of how Rho activity can coordinate cell migration. Here, we show that Rho activity is absent in local protrusions and active during retractions. During retractions, Rho rapidly activated ezrin-radixin-moesin proteins (ERMs) to increase actin-membrane attachment, and, with a delay, nonmuscle myosin 2 (NM2). Rho activity was excitable, with NM2 acting as a slow negative feedback regulator. Strikingly, inhibition of SLK/LOK kinases, through which Rho activates ERMs, caused elongated cell morphologies, impaired Rho-induced cell contractions, and reverted Rho-induced blebbing. Together, our study demonstrates that Rho activity drives retractions by sequentially enhancing ERM-mediated actin-membrane attachment for force transmission and NM2-dependent contractility.

DOI: https://doi.org/10.1126/sciadv.adn6858
Dev Cell. 2024 Aug 30. pii: S1534-5807(24)00490-8. [Epub ahead of print]

Smarcd1 subunit of SWI/SNF chromatin-remodeling complexes collaborates with E2a to promote murine lymphoid specification.

Pierre Priam, Veneta Krasteva, Philippe Rousseau, Alexandre Polsinelli, Laurence Côté, Ines Desanlis, Azer Farah, Vincent-Philippe Lavallée, Marie Kmita, Julie A Lessard.

  Lymphocyte development from murine hematopoietic stem cells (HSCs) entails a loss of self-renewal capacity and a progressive restriction of developmental potential. Previous research from our laboratory suggests that specialized assemblies of ATP-dependent SWI/SNF chromatin-remodeling complexes play lineage-specific roles during murine hematopoiesis. Here, we demonstrate that the Smarcd1 subunit is essential for specification of lymphoid cell fate from multipotent progenitors. Acute deletion of Smarcd1 in murine adult hematopoiesis leads to lymphopenia, characterized by a near-complete absence of early lymphoid progenitors and mature B and T cells, while the myeloid and erythroid lineages remain unaffected. Mechanistically, we demonstrate that Smarcd1 is essential for the coordinated activation of a lymphoid gene signature in murine multipotent progenitors. This is achieved by interacting with the E2a transcription factor at proximal promoters and by regulating the activity of distal enhancers. Globally, these findings identify Smarcd1 as an essential chromatin remodeler that governs lymphoid cell fate.

Keywords:  E2a/Tcf3; SWI/SNF complexes; Smarcd1/BAF60a; active enhancers; chromatin remodeling; lymphoid priming; lymphopenia

DOI:  https://doi.org/10.1016/j.devcel.2024.08.007
Cell Stem Cell. 2024 Aug 30. pii: S1934-5909(24)00291-1. [Epub ahead of print]

Alveolar regeneration by airway secretory-cell-derived p63+ progenitors.

Zan Lv, Zixin Liu, Kuo Liu, Xiuyu Lin, Wenjuan Pu, Yan Li, Huan Zhao, Ying Xi, Pengfei Sui, Andrew E Vaughan, Astrid Gillich, Bin Zhou.

  Lung injury activates epithelial stem or progenitor cells for alveolar repair and regeneration. Unraveling the origin and fate of injury-induced progenitors is crucial for elucidating lung repair mechanisms. Here, we report that p63-expressing progenitors emerge upon bleomycin-induced mouse lung injury. Single-cell RNA sequencing and clonal analysis reveal that these p63+ progenitors proliferate rapidly and differentiate into alveolar type 1 and type 2 cells through different trajectories. Dual recombinase-mediated sequential genetic-lineage tracing demonstrates that p63+ progenitors originate from airway secretory cells and subsequently generate alveolar cells. Functionally, p63 activation is essential for efficient alveolar regeneration from secretory cells post injury. Our study identifies secretory-cell-derived p63+ progenitors as contributors to alveolar repair, suggesting a potential therapeutic avenue for lung regeneration following injury.

Keywords:  dual lineage tracing; lineage differentiation; lung stem cells; p63(+) progenitor; regeneration

DOI:  https://doi.org/10.1016/j.stem.2024.08.005
Nat Cardiovasc Res. 2024 Sep 02.

α-Ketoglutarate promotes cardiomyocyte proliferation and heart regeneration after myocardial infarction.

Yu Shi, Miao Tian, Xiaofang Zhao, Luxun Tang, Feng Wang, Hao Wu, Qiao Liao, Hongmei Ren, Wenbin Fu, Shuo Zheng, Pedro A Jose, Liangpeng Li, Chunyu Zeng.

The neonatal mammalian heart can regenerate following injury through cardiomyocyte proliferation but loses this potential by postnatal day 7. Stimulating adult cardiomyocytes to reenter the cell cycle remains unclear. Here we show that cardiomyocyte proliferation depends on its metabolic state. Given the connection between the tricarboxylic acid cycle and cell proliferation, we analyzed these metabolites in mouse hearts from postnatal day 0.5 to day 7 and found that α-ketoglutarate ranked highest among the decreased metabolites. Injection of α-ketoglutarate extended the window of cardiomyocyte proliferation during heart development and promoted heart regeneration after myocardial infarction by inducing adult cardiomyocyte proliferation. This was confirmed in Ogdh-siRNA-treated mice with increased α-ketoglutarate levels. Mechanistically, α-ketoglutarate decreases H3K27me3 deposition at the promoters of cell cycle genes in cardiomyocytes. Thus, α-ketoglutarate promotes cardiomyocyte proliferation through JMJD3-dependent demethylation, offering a potential approach for treating myocardial infarction.

DOI: https://doi.org/10.1038/s44161-024-00531-y
Nat Commun. 2024 Sep 05. 15(1): 7010

Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease.

Michal Polonsky, Louisa M S Gerhardt, Jina Yun, Kari Koppitch, Katsuya Lex Colón, Henry Amrhein, Barbara Wold, Shiwei Zheng, Guo-Cheng Yuan, Matt Thomson, Long Cai, Andrew P McMahon.

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, together with injury-invoked inflammation and fibrosis. Deciphering the molecular pathways and cellular interactions driving these processes is challenging due to the complex tissue structure. Here, we apply single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics reveals injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicts Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and their neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis identifies cellular microenvironments resembling early tertiary lymphoid structures and associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

DOI: https://doi.org/10.1038/s41467-024-51186-z
Science. 2024 Sep 06. 385(6713): 1091-1097

Role of protein kinase PLK1 in the epigenetic maintenance of centromeres.

Duccio Conti, Arianna Esposito Verza, Marion E Pesenti, Verena Cmentowski, Ingrid R Vetter, Dongqing Pan, Andrea Musacchio.

The centromere, a chromosome locus defined by the histone H3-like protein centromeric protein A (CENP-A), promotes assembly of the kinetochore to bind microtubules during cell division. Centromere maintenance requires CENP-A to be actively replenished by dedicated protein machinery in the early G1 phase of the cell cycle to compensate for its dilution after DNA replication. Cyclin-dependent kinases (CDKs) limit CENP-A deposition to once per cell cycle and function as negative regulators outside of early G1. Antithetically, Polo-like kinase 1 (PLK1) promotes CENP-A deposition in early G1, but the molecular details of this process are still unknown. We reveal here a phosphorylation network that recruits PLK1 to the deposition machinery to control a conformational switch required for licensing the CENP-A deposition reaction. Our findings clarify how PLK1 contributes to the epigenetic maintenance of centromeres.

DOI: https://doi.org/10.1126/science.ado5178
Science. 2024 Aug 30. 385(6712): eadj8691

Micronuclear collapse from oxidative damage.

Melody Di Bona, Yanyang Chen, Albert S Agustinus, Alice Mazzagatti, Mercedes A Duran, Matthew Deyell, Daniel Bronder, James Hickling, Christy Hong, Lorenzo Scipioni, Giulia Tedeschi, Sara Martin, Jun Li, Aušrinė Ruzgaitė, Nadeem Riaz, Parin Shah, Edridge K D'Souza, D Zack Brodtman, Simone Sidoli, Bill Diplas, Manisha Jalan, Nancy Y Lee, Alban Ordureau, Benjamin Izar, Ashley M Laughney, Simon Powell, Enrico Gratton, Stefano Santaguida, John Maciejowski, Peter Ly, Thomas M Jeitner, Samuel F Bakhoum.

Chromosome-containing micronuclei are a hallmark of aggressive cancers. Micronuclei frequently undergo irreversible collapse, exposing their enclosed chromatin to the cytosol. Micronuclear rupture catalyzes chromosomal rearrangements, epigenetic abnormalities, and inflammation, yet mechanisms safeguarding micronuclear integrity are poorly understood. In this study, we found that mitochondria-derived reactive oxygen species (ROS) disrupt micronuclei by promoting a noncanonical function of charged multivesicular body protein 7 (CHMP7), a scaffolding protein for the membrane repair complex known as endosomal sorting complex required for transport III (ESCRT-III). ROS retained CHMP7 in micronuclei while disrupting its interaction with other ESCRT-III components. ROS-induced cysteine oxidation stimulated CHMP7 oligomerization and binding to the nuclear membrane protein LEMD2, disrupting micronuclear envelopes. Furthermore, this ROS-CHMP7 pathological axis engendered chromosome shattering known to result from micronuclear rupture. It also mediated micronuclear disintegrity under hypoxic conditions, linking tumor hypoxia with downstream processes driving cancer progression.

DOI: https://doi.org/10.1126/science.adj8691
Nat Cell Biol. 2024 Sep 05.

A size filter at the Golgi regulates apical membrane protein sorting.

Christian de Caestecker, Ian G Macara.

Despite decades of research, apical sorting of epithelial membrane proteins remains incompletely understood. We noted that apical cytoplasmic domains are smaller than those of basolateral proteins; however, the reason for this discrepancy is unknown. Here we used a synthetic biology approach to investigate whether a size barrier at the Golgi apparatus might hinder apical sorting of proteins with large cytoplasmic tails. We focused on Crb3, Ace2 and Muc1 as representative apical proteins with short cytoplasmic tails. By incorporating a streptavidin-binding peptide, these proteins can be trapped in the endoplasmic reticulum until addition of biotin, which triggers synchronous release to the Golgi and subsequent transport to the apical cortex. Strikingly, increasing the size of their cytoplasmic domains caused partial mislocalization to the basolateral cortex and significantly delayed Golgi departure. Moreover, N-glycosylation of 'large' Crb3 was delayed, and 'small' Crb3 segregated into spatially distinct Golgi regions. Biologically, Crb3 forms a complex through its cytoplasmic tail with the Pals1 protein, which could also delay departure, but although associated at the endoplasmic reticulum and Golgi, Pals1 disassociated before Crb3 departure. Notably, a non-dissociable mutant Pals1 hampered the exit of Crb3. We conclude that, unexpectedly, a size filter at the Golgi facilitates apical sorting of proteins with small cytoplasmic domains and that timely release of Pals1, to reduce cytoplasmic domain size, is essential for normal Crb3 sorting.

DOI: https://doi.org/10.1038/s41556-024-01500-0
Development. 2024 Sep 02. pii: dev.202834. [Epub ahead of print]

A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis.

Shin-Ichi Tomizawa, Rachel Fellows, Michio Ono, Kazushige Kuroha, Ivana Dočkal, Yuki Kobayashi, Keisuke Minamizawa, Koji Natsume, Kuniko Nakajima, Ikue Hoshi, Shion Matsuda, Masahide Seki, Yutaka Suzuki, Kazushi Aoto, Hirotomo Saitsu, Kazuyuki Ohbo.

  Male infertility can be caused by chromosomal abnormalities, mutations, and epigenetic defects. Epigenetic modifiers pre-program hundreds of spermatogenic genes in spermatogonial stem cells (SSCs) for expression later in spermatids, but it remains mostly unclear whether and how those genes are involved in fertility. Here, we report that Wfdc15a, a WFDC family protease inhibitor pre-programmed by KMT2B, is essential for spermatogenesis. We found that Wfdc15a is a non-canonical bivalent gene carrying both H3K4me3 and facultative H3K9me3 in SSCs but is later activated along with the loss of H3K9me3 and acquisition of H3K27ac during meiosis. We show that Wfdc15a deficiency causes defective spermiogenesis at the beginning of spermatid elongation. Notably, depletion of Wfdc15a causes substantial disturbance of the testicular protease-antiprotease network and leads to an orchitis-like inflammatory response associated with TNFa expression in round spermatids. Together, our results reveal a unique epigenetic program regulating innate immunity crucial for fertility.

Keywords:  Epigenetics; Kmt2b; Protease; Spermatid; Spermatogenesis; Wfdc15a

DOI:  https://doi.org/10.1242/dev.202834
Nat Rev Mol Cell Biol. 2024 Sep 02.

Mechanisms of assembly and remodelling of the extracellular matrix.

Alexandra Naba.

The extracellular matrix (ECM) is the complex meshwork of proteins and glycans that forms the scaffold that surrounds and supports cells. It exerts key roles in all aspects of metazoan physiology, from conferring physical and mechanical properties on tissues and organs to modulating cellular processes such as proliferation, differentiation and migration. Understanding the mechanisms that orchestrate the assembly of the ECM scaffold is thus crucial to understand ECM functions in health and disease. This Review discusses novel insights into the compositional diversity of matrisome components and the mechanisms that lead to tissue-specific assemblies and architectures tailored to support specific functions. The Review then highlights recently discovered mechanisms, including post-translational modifications and metabolic pathways such as amino acid availability and the circadian clock, that modulate ECM secretion, assembly and remodelling in homeostasis and human diseases. Last, the Review explores the potential of 'matritherapies', that is, strategies to normalize ECM composition and architecture to achieve a therapeutic benefit.

DOI: https://doi.org/10.1038/s41580-024-00767-3
Science. 2024 Sep 06. 385(6713): eadm6869

Achieving optical transparency in live animals with absorbing molecules.

Zihao Ou, Yi-Shiou Duh, Nicholas J Rommelfanger, Carl H C Keck, Shan Jiang, Kenneth Brinson, Su Zhao, Elizabeth L Schmidt, Xiang Wu, Fan Yang, Betty Cai, Han Cui, Wei Qi, Shifu Wu, Adarsh Tantry, Richard Roth, Jun Ding, Xiaoke Chen, Julia A Kaltschmidt, Mark L Brongersma, Guosong Hong.

Optical imaging plays a central role in biology and medicine but is hindered by light scattering in live tissue. We report the counterintuitive observation that strongly absorbing molecules can achieve optical transparency in live animals. We explored the physics behind this observation and found that when strongly absorbing molecules dissolve in water, they can modify the refractive index of the aqueous medium through the Kramers-Kronig relations to match that of high-index tissue components such as lipids. We have demonstrated that our straightforward approach can reversibly render a live mouse body transparent to allow visualization of a wide range of deep-seated structures and activities. This work suggests that the search for high-performance optical clearing agents should focus on strongly absorbing molecules.

DOI: https://doi.org/10.1126/science.adm6869
Nat Cell Biol. 2024 Sep 02.

Noncanonical inheritance of phenotypic information by protein amyloids.

Matthew Eroglu, Tanner Zocher, Jacob McAuley, Rachel Webster, Maggie Z X Xiao, Bin Yu, Calvin Mok, W Brent Derry.

All known heritable phenotypic information in animals is transmitted by direct inheritance of nucleic acids, their covalent modifications or histone modifications that modulate expression of associated genomic regions. Nonetheless, numerous familial traits and disorders cannot be attributed to known heritable molecular factors. Here we identify amyloid-like protein structures that are stably inherited in wild-type animals and influence traits. Their perturbation by genetic, environmental or pharmacological treatments leads to developmental phenotypes that can be epigenetically passed onto progeny. Injection of amyloids isolated from different phenotypic backgrounds into naive animals recapitulates the associated phenotype in offspring. Genetic and proteomic analyses reveal that the 26S proteasome and its conserved regulators maintain heritable amyloids across generations, which enables proper germ cell sex differentiation. We propose that inheritance of a proteinaceous epigenetic memory coordinates developmental timing and patterning with the environment to confer adaptive fitness.

DOI: https://doi.org/10.1038/s41556-024-01494-9
bioRxiv. 2024 Aug 25. pii: 2024.08.25.609458. [Epub ahead of print]

A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate.

Eric R Brooks, Andrew R Moorman, Bhaswati Bhattacharya, Ian Prudhomme, Max Land, Heather L Alcorn, Roshan Sharma, Dana Pe'er, Jennifer A Zallen.

The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.

DOI: https://doi.org/10.1101/2024.08.25.609458
J Mol Cell Cardiol. 2024 Aug 31. pii: S0022-2828(24)00142-1. [Epub ahead of print]

Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes.

Aaron D Simmons, Claudia Baumann, Xiangyu Zhang, Timothy J Kamp, Rabindranath De La Fuente, Sean P Palecek.

  Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are advancing cardiovascular development and disease modeling, drug testing, and regenerative therapies. However, hPSC-CM production is hindered by significant variability in the differentiation process. Establishment of early quality markers to monitor lineage progression and predict terminal differentiation outcomes would address this robustness and reproducibility roadblock in hPSC-CM production. An integrated transcriptomic and epigenomic analysis assesses how attributes of the cardiac progenitor cell (CPC) affect CM differentiation outcome. Resulting analysis identifies predictive markers of CPCs that give rise to high purity CM batches, including TTN, TRIM55, DGKI, MEF2C, MAB21L2, MYL7, LDB3, SLC7A11, MAB21L2, and CALD1. Predictive models developed from these genes provide high accuracy in determining terminal CM purities at the CPC stage. Further, insights into mechanisms of batch failure and dominant non-CM cell types generated in failed batches are elucidated. Namely EMT, MAPK, and WNT signaling emerge as significant drivers of batch divergence, giving rise to off-target populations of fibroblasts/mural cells, skeletal myocytes, epicardial cells, and a non-CPC SLC7A11+ subpopulation. This study demonstrates how integrated multi-omic analysis of progenitor cells can identify quality attributes of that progenitor and predict differentiation outcomes, thereby improving differentiation protocols and increasing process robustness.

Keywords:  Cardiac progenitor cells; Cardiomyocytes; Differentiation; Epigenomics; Human pluripotent stem cells; Multi-omics; Transcriptomics

DOI:  https://doi.org/10.1016/j.yjmcc.2024.08.007
Nat Aging. 2024 Sep 04.

Spermidine controls autophagy during fasting.

Anna Kriebs.

DOI: https://doi.org/10.1038/s43587-024-00710-3
STAR Protoc. 2024 Aug 29. pii: S2666-1667(24)00445-3. [Epub ahead of print]5(3): 103280

Protocol for generating human cortical organoids enriched in outer radial glia by guided differentiation.

Raffaele Luongo, Ryan M Walsh, Antonietta Verrillo, Lorenz Studer, Arianna Baggiolini.

  The generation of human pluripotent stem cell (hPSC)-derived brain organoids is continuously refined, enhancing their reproducibility and complexity. Here, we present a guided differentiation protocol for generating cortical forebrain organoids and cortico-pericyte (CP)assembloids composed of a robust outer radial glia (oRG) population and an expanded outer subventricular zone (oSVZ). We describe the steps to generate hPSC-derived cortical organoids (COs), cortical pericytes, and CP assembloids. Moreover, we outline the procedures to characterize the organoids by immunostaining and to perform single-cell dissociation. For complete details on the use and execution of this protocol, please refer to Walsh et al.1.

Keywords:  Cell Biology; Cell Differentiation; Cell culture; Cell isolation; Developmental biology; Flow Cytometry; Neuroscience; Organoids; Stem Cells

DOI:  https://doi.org/10.1016/j.xpro.2024.103280
Science. 2024 Sep 05. eadn0327

Hematopoietic aging promotes cancer by fueling IL-1⍺-driven emergency myelopoiesis.

Matthew D Park, Jessica Le Berichel, Pauline Hamon, C Matthias Wilk, Meriem Belabed, Nader Yatim, Alexis Saffon, Jesse Boumelha, Chiara Falcomatà, Alexander Tepper, Samarth Hegde, Raphaël Mattiuz, Brian Y Soong, Nelson M LaMarche, Frederika Rentzeperis, Leanna Troncoso, Laszlo Halasz, Clotilde Hennequin, Theodore Chin, Earnest P Chen, Amanda M Reid, Matthew Su, Ashley Reid Cahn, Laura L Koekkoek, Nicholas Venturini, Shira Wood-Isenberg, Darwin D'souza, Rachel Chen, Travis Dawson, Kai Nie, Zhihong Chen, Seunghee Kim-Schulze, Maria Casanova-Acebes, Filip K Swirski, Julian Downward, Nicolas Vabret, Brian D Brown, Thomas U Marron, Miriam Merad.

Age is a major risk factor for cancer, but how aging impacts tumor control remains unclear. Here, we establish that aging of the immune system, regardless of the age of the stroma and tumor, drives lung cancer progression. Hematopoietic aging enhances emergency myelopoiesis, resulting in the local accumulation of myeloid progenitor-like cells in lung tumors. These cells are a major source of IL-1⍺ that drives the enhanced myeloid response. The age-associated decline of DNMT3A enhances IL-1⍺ production, and disrupting IL-1R1 signaling early during tumor development normalized myelopoiesis and slowed the growth of lung, colonic, and pancreatic tumors. In human tumors, we identified an enrichment for IL-1⍺-expressing monocyte-derived macrophages linked to age, poorer survival, and recurrence, unraveling how aging promotes cancer and offering actionable therapeutic strategies.

DOI: https://doi.org/10.1126/science.adn0327
EMBO J. 2024 Sep 04.

Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering.

Paulina Kettel, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, Irmgard Fischer, Gijs A Versteeg, Martin Loose, Roberto Covino, G Elif Karagöz.

  Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.

Keywords:  Biomolecular Condensates; IRE1; Supported Lipid Bilayers; Unfolded Protein Response

DOI:  https://doi.org/10.1038/s44318-024-00207-0
bioRxiv. 2024 Aug 22. pii: 2024.08.21.608971. [Epub ahead of print]

A molecular brain atlas reveals cellular shifts during the repair phase of stroke.

Rebecca Z Weber, Beatriz Achon Buil, Nora H Rentsch, Allison Bosworth, Mingzi Zhang, Kassandra Kisler, Christian Tackenberg, Berislav V Zlokovic, Ruslan Rust.

Ischemic stroke triggers a cascade of pathological events that affect multiple cell types and often lead to incomplete functional recovery. Despite advances in single-cell technologies, the molecular and cellular responses that contribute to long-term post-stroke impairment remain poorly understood. To gain better insight into the underlying mechanisms, we generated a single-cell transcriptomic atlas from distinct brain regions using a mouse model of permanent focal ischemia at one month post-injury. Our findings reveal cell- and region-specific changes within the stroke-injured and peri-infarct brain tissue. For instance, GABAergic and glutamatergic neurons exhibited upregulated genes in signaling pathways involved in axon guidance and synaptic plasticity, and downregulated pathways associated with aerobic metabolism. Using cell-cell communication analysis, we identified increased strength in predicted interactions within stroke tissue among both neural and non-neural cells via signaling pathways such as those involving collagen, protein tyrosine phosphatase receptor, neuronal growth regulator, laminin, and several cell adhesion molecules. Furthermore, we found a strong correlation between mouse transcriptome responses after stroke and those observed in human nonfatal brain stroke lesions. Common molecular features were linked to inflammatory responses, extracellular matrix organization, and angiogenesis. Our findings provide a detailed resource for advancing our molecular understanding of stroke pathology and for discovering therapeutic targets in the repair phase of stroke recovery.

DOI: https://doi.org/10.1101/2024.08.21.608971
Nat Biotechnol. 2024 Sep 02.

Long-term engrafting multilineage hematopoietic cells differentiated from human induced pluripotent stem cells.

Elizabeth S Ng, Gulcan Sarila, Jacky Y Li, Hasindu S Edirisinghe, Ritika Saxena, Shicheng Sun, Freya F Bruveris, Tanya Labonne, Nerida Sleebs, Alexander Maytum, Raymond Y Yow, Chantelle Inguanti, Ali Motazedian, Vincenzo Calvanese, Sandra Capellera-Garcia, Feiyang Ma, Hieu T Nim, Mirana Ramialison, Constanze Bonifer, Hanna K A Mikkola, Edouard G Stanley, Andrew G Elefanty.

Hematopoietic stem cells (HSCs) derived from human induced pluripotent stem cells (iPS cells) have important biomedical applications. We identified differentiation conditions that generate HSCs defined by robust long-term multilineage engraftment in immune-deficient NOD,B6.Prkdcscid Il2rgtm1Wjl/SzJ KitW41/W41 mice. We guided differentiating iPS cells, as embryoid bodies in a defined culture medium supplemented with retinyl acetate, through HOXA-patterned mesoderm to hemogenic endothelium specified by bone morphogenetic protein 4 and vascular endothelial growth factor (VEGF). Removal of VEGF facilitated an efficient endothelial-to-hematopoietic transition, evidenced by release into the culture medium of CD34+ blood cells, which were cryopreserved. Intravenous transplantation of two million thawed CD34+ cells differentiated from four independent iPS cell lines produced multilineage bone marrow engraftment in 25-50% of immune-deficient recipient mice. These functionally defined, multipotent CD34+ hematopoietic cells, designated iPS cell-derived HSCs (iHSCs), produced levels of engraftment similar to those achieved following umbilical cord blood transplantation. Our study provides a step toward the goal of generating HSCs for clinical translation.

DOI: https://doi.org/10.1038/s41587-024-02360-7
bioRxiv. 2024 Aug 21. pii: 2024.08.20.608832. [Epub ahead of print]

Extracellular Vesicle-Associated Neutrophil Elastase Activates Hepatic Stellate Cells and Promotes Liver Fibrogenesis via ERK1/2 Pathway.

Regina Oshins, Zachary Greenberg, Yun-Ling Tai, Derrick Zhao, Xuan Wang, Borna Mehrad, Mei He, Ishan Patel, Laith Khartabil, Huiping Zhou, Mark Brantly, Nazli Khodayari.

Liver fibrosis associated with increased mortality is caused by activation of hepatic stellate cells and excessive production and accumulation of extracellular matrix in response to fibrotic insults. It has been shown that in addition to liver inflammation, systemic inflammation also contributes to liver fibrogenesis. A deeper understanding of mechanisms that control liver fibrotic response to intra- and extra-hepatic inflammation is essential to develop novel clinical strategies against this disease. Extracellular vesicles (EV) have been recognized as immune mediators that facilitate activation of hepatic stellate cells. In inflammatory diseases, activated neutrophils release neutrophil elastase (NE) bound to EV, which has been identified as a significant contributor to inflammation by promoting immune cell activation. Here, we aimed to explore the role of inflammation derived plasma EV-associated NE in liver fibrogenesis and its potential mechanisms. We show EV-associated NE induces activation, proliferation and migration of hepatic stellate cells by promoting activation of the ERK1/2 signaling pathway. This effect did not occur through EV without surface NE, and Sivelestat, a NE inhibitor, inhibited activation of the ERK1/2 signaling pathway mediated by EV-associated NE. Moreover, we found plasma EV-associated NE increases deposition of collagen1 and α-smooth muscle actin in the liver of a mouse model of liver fibrosis (Mdr2 -/- ). Notably, this effect does not occur in control mice without preexisting liver disease. These data suggest that EV-associated NE is a pro-fibrogenic factor for hepatic stellate cell activation via the ERK1/2 signaling pathway in pre-existing liver injuries. Inhibition of the plasma EV-associated NE in inflammatory conditions may be a therapeutic target for liver fibrosis in patients with inflammatory diseases.

DOI: https://doi.org/10.1101/2024.08.20.608832
Nat Commun. 2024 Sep 03. 15(1): 7681

Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome.

Marius Klein, Klemens Wild, Irmgard Sinning.

Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common combination of subsequent modifications carried out on the 80S ribosome. How these enzymatic processes are coordinated in the context of a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures of multi-enzyme complexes assembled on vacant human 80S ribosomes, indicating two routes for NME-NTA. Both assemblies form on the 80S independent of nascent chain substrates. Irrespective of the route, NatA occupies a non-intrusive 'distal' binding site on the ribosome which does not interfere with MAP1 or MAP2 binding nor with most other ribosome-associated factors (RAFs). NatA can partake in a coordinated, dynamic assembly with MAP1 through the hydra-like chaperoning function of the abundant Nascent Polypeptide-Associated Complex (NAC). In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Together, our data provide the structural framework for the coordinated orchestration of NME and NTA in protein biogenesis.

DOI: https://doi.org/10.1038/s41467-024-51964-9
EMBO J. 2024 Aug 29.

Human genomic DNA is widely interspersed with i-motif structures.

Cristian David Peña Martinez, Mahdi Zeraati, Romain Rouet, Ohan Mazigi, Jake Y Henry, Brian Gloss, Jessica A Kretzmann, Cameron W Evans, Emanuela Ruggiero, Irene Zanin, Maja Marušič, Janez Plavec, Sara N Richter, Tracy M Bryan, Nicole M Smith, Marcel E Dinger, Sarah Kummerfeld, Daniel Christ.

  DNA i-motif structures are formed in the nuclei of human cells and are believed to provide critical genomic regulation. While the existence, abundance, and distribution of i-motif structures in human cells has been demonstrated and studied by immunofluorescent staining, and more recently NMR and CUT&Tag, the abundance and distribution of such structures in human genomic DNA have remained unclear. Here we utilise high-affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in the purified genomic DNA of human MCF7, U2OS and HEK293T cells. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach aimed to identify DNA sequences capable of i-motif formation on a genome-wide scale, revealing that such sequences are widely distributed throughout the human genome and are common in genes upregulated in G0/G1 cell cycle phases. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA and a foundational resource for future studies of their genomic, structural, and molecular roles.

Keywords:  Antibody; DNA Quadruplex Structures; Immunoprecipitation; i-motif; iMab

DOI:  https://doi.org/10.1038/s44318-024-00210-5