Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER, bioRxiv, 2018-12-29
AbstractProbing the molecular organization of tissues requires in situ analysis by microscopy. However current limitations in multiplexing, sensitivity, and throughput collectively constitute a major barrier for comprehensive single-cell profiling of proteins. Here, we report Immunostaining with Signal Amplification By Exchange Reaction (Immuno-SABER), a rapid, highly multiplexed signal amplification method that simultaneously tackles these key challenges. Immuno-SABER utilizes DNA-barcoded antibodies and provides a method for highly multiplexed signal amplification via modular orthogonal DNA concatemers generated by Primer Exchange Reaction. This approach offers the capability to preprogram and control the amplification level independently for multiple targets without in situ enzymatic reactions, and the intrinsic scalability to rapidly amplify and image a large number of protein targets. We validated our approach in diverse sample types including cultured cells, cryosections, FFPE sections, and whole mount tissues. We demonstrated independently tunable 5-180-fold amplification for multiple targets, covering the full signal range conventionally achieved by secondary antibodies to tyramide signal amplification, as well as simultaneous signal amplification for 10 different proteins using standard equipment and workflow. We further combined Immuno-SABER with Expansion Microscopy to enable rapid and highly multiplexed super-resolution tissue imaging. Overall, Immuno-SABER presents an effective and accessible platform for rapid, multiplexed imaging of proteins across scales with high sensitivity.
biorxiv cell-biology 200-500-users 2018Self-repair protects microtubules from their destruction by molecular motors, bioRxiv, 2018-12-18
Microtubules are dynamic polymers that are used for intracellular transport and chromosome segregation during cell division. Their instability stems from the low energy of tubulin dimer interactions, which sets the growing polymer close to its disassembly conditions. Microtubules function in coordination with kinesin and dynein molecular motors, which use ATP hydrolysis to produce mechanical work and move on microtubules. This raises the possibility that the forces produced by walking motors can break dimer interactions and trigger microtubule disassembly. We tested this hypothesis by studying the interplay between microtubules and moving molecular motors in vitro. Our results show that the mechanical work of molecular motors can remove tubulin dimers from the lattice and rapidly destroy microtubules. This effect was not observed when free tubulin dimers were present in the assay. Using fluorescently labelled tubulin dimers we found that dimer removal by motors was compensated for by the insertion of free tubulin dimers into the microtubule lattice. This self-repair mechanism allows microtubules to survive the damage induced by molecular motors as they move along their tracks. Our study reveals the existence of coupling between the motion of kinesin and dynein motors and the renewal of the microtubule lattice.
biorxiv cell-biology 100-200-users 2018A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells, bioRxiv, 2018-12-12
AbstractPeriodicity is a fundamental property of biological oscillators such as the mitotic cell cycle. In this context, periodicity refers to the time interval between the same phases of two consecutive cell cycles. The length of this interval, or the cell cycle speed, varies widely depending on cell type and the pathophysiological conditions. The relevance of cell cycle speed in various biological contexts has not been well-studied, partially due to the lack of experimental approaches that capture this parameter. Here, we describe a genetically encoded live-cell reporter of cell cycle speed. This reporter is based on the color-changing Fluorescent Timer (FT) protein, which emits blue fluorescence when newly synthesized before maturing into a red fluorescent protein. Its ability to report cell cycle speed exploits the different half-life of the blue vs. red form of the same molecule, as predicted by mathematical modeling. When a Histone H2B-FT fusion protein is expressed at steady-state in heterogeneously dividing cells, faster-cycling cells can be distinguished from slower-cycling ones by differences in their intracellular ratio between the blue and red fluorescent wavelengths. Cell cycle perturbation experiments demonstrate that the H2B-FT is a bona fide reporter of cell cycle speed in multiple cultured cell lines. In vivo, the bluered profile faithfully tracked with known proliferation kinetics of various hematopoietic stem and progenitor cells, when expressed either from lentiviral vectors or from a targeted knock-in allele. As the H2B-FT is compatible with flow cytometry, it provides a strategy to physically separate subpopulations of live cells cycling at different rates for downstream analysis. We anticipate this system to be useful in diverse cell types and tissue contexts for dissecting the role of cell cycle speed in development and disease.
biorxiv cell-biology 100-200-users 2018Resolving cell cycle speed in one snapshot with a live-cell fluorescent reporter, bioRxiv, 2018-12-12
SummaryCell proliferation changes concomitantly with fate transitions during reprogramming, differentiation, regeneration, and oncogenesis. Methods to resolve cell cycle length heterogeneity in real-time are currently lacking. Here, we describe a genetically encoded fluorescent reporter that captures live cell cycle speed using a single measurement. This reporter is based on the color-changing Fluorescent Timer (FT) protein, which emits blue fluorescence when newly synthesized before maturing into a red fluorescent protein. We generated a mouse strain expressing an H2B-FT fusion reporter from a universally active locus, and demonstrate that faster-cycling cells can be distinguished from slower-cycling ones based on the intracellular fluorescence ratio between the FT’s blue and red states. Using this reporter, we reveal the native cell cycle speed distributions of fresh hematopoietic cells, and demonstrate its utility in analyzing cell proliferation in solid tissues. This system is broadly applicable for dissecting functional heterogeneity associated with cell cycle dynamics in complex tissues.
biorxiv cell-biology 100-200-users 2018A risk-reward tradeoff of high ribosome production in proliferating cells, bioRxiv, 2018-10-31
AbstractTo achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs), which are required to produce thousands of new ribosomes every minute. Although ribosomes are essential in all cells, disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we modeled these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result immediately in acute loss of proteostasis (protein folding homeostasis). Imbalances in the synthesis of r-proteins and rRNAs lead to the rapid aggregation of newly synthesized orphan r-proteins and compromise essential cellular processes. In response, proteostasis genes are activated by an Hsf1-dependent stress response pathway that is required for recovery from r-protein assembly stress. Importantly, we show that exogenously bolstering the proteostasis network increases cellular fitness in the face of challenges to ribosome assembly, demonstrating the direct contribution of orphan r-proteins to cellular phenotypes. Our results highlight ribosome assembly as a linchpin of cellular homeostasis, representing a key proteostasis vulnerability for rapidly proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic conditions that generate orphan r-proteins.
biorxiv cell-biology 0-100-users 2018Atlas of Subcellular RNA Localization Revealed by APEX-seq, bioRxiv, 2018-10-27
SUMMARYWe introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
biorxiv cell-biology 200-500-users 2018