A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation.

The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled ∼1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures.

Morphological diversity of single neurons in molecularly defined cell types.

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.

In Situ Measurement of Intra-tumoral Tissue Rigidity.

Local tissue scale mechanical properties are essential for understanding cell fate and function; however, few methods to measure stiffness at this length scale exist, and applications in 3D tissues can present further challenges. To address this need, microgel-based sensors fabricated out of the thermally responsive hydrogel poly(N-isopropylacrylamide) were developed allowing internal architectures of tissues to be mapped by optically measuring microgel response when actuated in a matrix. These robust probes are widely applicable for in vitro and in vivo studies of tissue mechanics providing tissues can be fluorescently imaged. Here we describe the fabrication of these thermally responsive hydrogel sensors, calibration of the microgels using phantom tissues, and image processing techniques used to make the measurements.

Compressive molding of engineered tissues via thermoresponsive hydrogel devices.

Biofabrication of tissues requires sourcing appropriate combinations of cells, and then arranging those cells into a functionally-useful construct. Recently, organoids with diverse cell populations have shown great promise as building blocks from which to assemble more complex structures. However, organoids typically adopt spherical or uncontrolled morphologies, which intrinsically limit the tissue structures that can be produced using this bioassembly technique. Here, we develop microfabricated smart hydrogel platforms in thermoresponsive poly(N-isopropylacrylamide) to compressively mold microtissues such as spheroids or organoids into customized forms, on demand. These Compressive Hydrogel Molders (CHyMs) compact at cell culture temperatures to force loaded tissues into a new shape, and then expand to release the tissues for downstream applications. As a first demonstration, breast cancer spheroids were biaxially compacted in cylindrical cavities, and uniaxially compacted in rectangular ones. Spheroid shape changes persisted after the tissues were released from the CHyMs. We then demonstrate long-term molding of spherical brain organoids in ring-shaped CHyMs over one week. Fused bridges formed only when brain organoids were encased in Matrigel, and the resulting ring-shaped organoids expressed tissue markers that correspond with expected differentiation profiles. These results demonstrate that tissues differentiate appropriately even during long-term molding in a CHyM. This platform hence provides a new tool to shape pre-made tissues as desired, via temporary compression and release, allowing an exploration of alternative organoid geometries as building blocks for bioassembly applications.

Revisiting tissue tensegrity: Biomaterial-based approaches to measure forces across length scales.

Cell-generated forces play a foundational role in tissue dynamics and homeostasis and are critically important in several biological processes, including cell migration, wound healing, morphogenesis, and cancer metastasis. Quantifying such forces in vivo is technically challenging and requires novel strategies that capture mechanical information across molecular, cellular, and tissue length scales, while allowing these studies to be performed in physiologically realistic biological models. Advanced biomaterials can be designed to non-destructively measure these stresses in vitro, and here, we review mechanical characterizations and force-sensing biomaterial-based technologies to provide insight into the mechanical nature of tissue processes. We specifically and uniquely focus on the use of these techniques to identify characteristics of cell and tissue "tensegrity:" the hierarchical and modular interplay between tension and compression that provide biological tissues with remarkable mechanical properties and behaviors. Based on these observed patterns, we highlight and discuss the emerging role of tensegrity at multiple length scales in tissue dynamics from homeostasis, to morphogenesis, to pathological dysfunction.

Mechanobiological regulation of placental trophoblast fusion and function through extracellular matrix rigidity.

The syncytiotrophoblast is a multinucleated layer that plays a critical role in regulating functions of the human placenta during pregnancy. Maintaining the syncytiotrophoblast layer relies on ongoing fusion of mononuclear cytotrophoblasts throughout pregnancy, and errors in this fusion process are associated with complications such as preeclampsia. While biochemical factors are known to drive fusion, the role of disease-specific extracellular biophysical cues remains undefined. Since substrate mechanics play a crucial role in several diseases, and preeclampsia is associated with placental stiffening, we hypothesize that trophoblast fusion is mechanically regulated by substrate stiffness. We developed stiffness-tunable polyacrylamide substrate formulations that match the linear elasticity of placental tissue in normal and disease conditions, and evaluated trophoblast morphology, fusion, and function on these surfaces. Our results demonstrate that morphology, fusion, and hormone release is mechanically-regulated via myosin-II; optimal on substrates that match healthy placental tissue stiffness; and dysregulated on disease-like and supraphysiologically-stiff substrates. We further demonstrate that stiff regions in heterogeneous substrates provide dominant physical cues that inhibit fusion, suggesting that even focal tissue stiffening limits widespread trophoblast fusion and tissue function. These results confirm that mechanical microenvironmental cues influence fusion in the placenta, provide critical information needed to engineer better in vitro models for placental disease, and may ultimately be used to develop novel mechanically-mediated therapeutic strategies to resolve fusion-related disorders during pregnancy.

Mapping cellular-scale internal mechanics in 3D tissues with thermally responsive hydrogel probes.

Local tissue mechanics play a critical role in cell function, but measuring these properties at cellular length scales in living 3D tissues can present considerable challenges. Here we present thermoresponsive, smart material microgels that can be dispersed or injected into tissues and optically assayed to measure residual tissue elasticity after creep over several weeks. We first develop and characterize the sensors, and demonstrate that internal mechanical profiles of live multicellular spheroids can be mapped at high resolutions to reveal broad ranges of rigidity within the tissues, which vary with subtle differences in spheroid aggregation method. We then show that small sites of unexpectedly high rigidity develop in invasive breast cancer spheroids, and in an in vivo mouse model of breast cancer progression. These focal sites of increased intratumoral rigidity suggest new possibilities for how early mechanical cues that drive cancer cells towards invasion might arise within the evolving tumor microenvironment.

Micropocket hydrogel devices for all-in-one formation, assembly, and analysis of aggregate-based tissues.

Multicellular aggregated tissues have grown critically important in benchtop biomedical research, both as stand-alone spheroids and when assembled into larger bioengineered constructs. However, typical systems for aggregate formation are limited in their capacity to reliably handle such cultures at various experimental stages in a broadly accessible, consistent, and scalable manner. In this work, we develop a broadly versatile all-in-one biofabrication strategy to form uniform, spherical, multicellular aggregates that can be maintained at precisely defined positions for analysis or transfer into a larger tissue. The 3D-printed MicroPocket Culture (MPoC) system consists of an array of simple geometry-based valves in a polyacrylamide hydrogel, and is able to produce hundreds of uniformly-sized aggregates in standard tissue culture well plates, using simple tools that are readily available in all standard biological wet-labs. The model breast cancer aggregates formed in these experiments are retained in defined positions on chip during all liquid handling steps required to stimulate, label, and image the experiment, enabling high-throughput studies on this culture model. Furthermore, MPoCs enable robust formation of aggregates in cell types that do not conventionally form such structures. Finally, we demonstrate that this single platform can also be used to generate complex 3D tissues from the precisely-positioned aggregate building blocks. To highlight the unique and broad versatility of this technique, we develop a simple 3D invasion assay and show that cancer cells preferentially migrate towards nearby model tumors; demonstrating the importance of spatial precision when engineering 3D tissues. Together, this platform presents a broadly accessible and uniquely capable system with which to develop advanced aggregate-based models for tissue engineering, fundamental research, and applied drug discovery.

Functional Redundancy between ß1 and ß3 Integrin in Activating the IR/Akt/mTORC1 Signaling Axis to Promote ErbB2-Driven Breast Cancer.

Integrin receptors coordinate cell adhesion to the extracellular matrix (ECM) to facilitate many cellular processes during malignant transformation. Despite their pro-tumorigenic roles, therapies targeting integrins remain limited. Here, we provide genetic evidence supporting a functional redundancy between ß1 and ß3 integrin during breast cancer progression. Although ablation of ß1 or ß3 integrin alone has limited effects on ErbB2-driven mammary tumorigenesis, deletion of both receptors resulted in a significant delay in tumor onset with a corresponding impairment in lung metastasis. Mechanistically, stiff ECM cooperates with integrin receptors to recruit insulin receptors (IRs) to focal adhesion through the formation of integrin/IR complexes, thereby preventing their lysosomal degradation. ß1/ß3 integrin-deficient tumors that eventually emerged exhibit impaired Akt/mTORC1 activity. Murine and human breast cancers exhibiting enhanced integrin-dependent activity also display elevated IR/Akt/mTORC1 signaling activity. Together, these observations argue that integrin/IR crosstalk transduces mechanical cues from the tumor microenvironment to promote ErbB2-dependent breast cancer progression.

Dispersible hydrogel force sensors reveal patterns of solid mechanical stress in multicellular spheroid cultures.

Understanding how forces orchestrate tissue formation requires technologies to map internal tissue stress at cellular length scales. Here, we develop ultrasoft mechanosensors that visibly deform under less than 10 Pascals of cell-generated stress. By incorporating these mechanosensors into multicellular spheroids, we capture the patterns of internal stress that arise during spheroid formation. We experimentally demonstrate the spontaneous generation of a tensional 'skin', only a few cell layers thick, at the spheroid surface, which correlates with activation of mechanobiological signalling pathways, and balances a compressive stress profile within the tissue. These stresses develop through cell-driven mechanical compaction at the tissue periphery, and suggest that the tissue formation process plays a critically important role in specifying mechanobiological function. The broad applicability of this technique should ultimately provide a quantitative basis to design tissues that leverage the mechanical activity of constituent cells to evolve towards a desired form and function.

Thinking big by thinking small: advances in mechanobiology across the length scales.

The field of mechanobiology provides an integrative understanding of biology and engineering principles. Mechanical forces are now well-established to provide a physical stimulus to help maintain normal tissue function, yet little is understood as to how forces experienced at various length scales influence cell behaviour and tissue function. In this Research Highlight, we describe recent technical innovations that have enabled advanced insight into the cellular microenvironment across a range of length scales.

Infusion-based manganese-enhanced MRI: a new imaging technique to visualize the mouse brain.

Manganese-enhanced magnetic resonance imaging is a technique that employs the divalent ion of the paramagnetic metal manganese (Mn(2+)) as an effective contrast agent to visualize, in vivo, the mammalian brain. As total achievable contrast is directly proportional to the net amount of Mn(2+) accumulated in the brain, there is a great interest in optimizing administration protocols to increase the effective delivery of Mn(2+) to the brain while avoiding the toxic effects of Mn(2+) overexposure. In this study, we investigated outcomes following continuous slow systemic infusion of manganese chloride (MnCl(2)) into the mouse via mini-osmotic pump administration. The effects of increasing fractionated rates of Mn(2+) infusion on signal enhancement in regions of the brain were analyzed in a three-treatment study. We acquired whole-brain 3-D T1-weighted images and performed region of interest quantitative analysis to compare mean normalized signal in Mn(2+) treatments spanning 3, 7, or 14 days of infusion (rates of 1, 0.5, and 0.25 µL/h, respectively). Evidence of Mn(2+) transport at the conclusion of each infusion treatment was observed throughout the brains of normally behaving mice. Regions of particular Mn(2+) accumulation include the olfactory bulbs, cortex, infralimbic cortex, habenula, thalamus, hippocampal formation, amygdala, hypothalamus, inferior colliculus, and cerebellum. Signals measured at the completion of each infusion treatment indicate comparable means for all examined fractionated rates of Mn(2+) infusion. In this current study, we achieved a significantly higher dose of Mn(2+) (180 mg/kg) than that employed in previous studies without any observable toxic effects on animal physiology or behavior.

Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly.

Although transcription factors that repress gene expression play critical roles in nervous system development, their mechanism of action remains to be understood. Here, we report that the Olig-related transcription factor Bhlhb5 (also known as Bhlhe22) forms a repressor complex with the PR/SET domain protein, Prdm8. We find that Bhlhb5 binds to sequence-specific DNA elements and then recruits Prdm8, which mediates the repression of target genes. This interaction is critical for repressor function since mice lacking either Bhlhb5 or Prdm8 have strikingly similar cellular and behavioral phenotypes, including axonal mistargeting by neurons of the dorsal telencephalon and abnormal itch-like behavior. We provide evidence that Cadherin-11 functions as target of the Prdm8/Bhlhb5 repressor complex that must be repressed for proper neural circuit formation to occur. These findings suggest that Prdm8 is an obligate partner of Bhlhb5, forming a repressor complex that directs neural circuit assembly in part through the precise regulation of Cadherin-11.

Loss of inhibitory interneurons in the dorsal spinal cord and elevated itch in Bhlhb5 mutant mice.

Itch is the least well understood of all the somatic senses, and the neural circuits that underlie this sensation are poorly defined. Here we show that the atonal-related transcription factor Bhlhb5 is transiently expressed in the dorsal horn of the developing spinal cord and appears to play a role in the formation and regulation of pruritic (itch) circuits. Mice lacking Bhlhb5 develop self-inflicted skin lesions and show significantly enhanced scratching responses to pruritic agents. Through genetic fate-mapping and conditional ablation, we provide evidence that the pruritic phenotype in Bhlhb5 mutants is due to selective loss of a subset of inhibitory interneurons in the dorsal horn. Our findings suggest that Bhlhb5 is required for the survival of a specific population of inhibitory interneurons that regulate pruritus, and provide evidence that the loss of inhibitory synaptic input results in abnormal itch.