Query: human cell size

title: The influence of cell size on cytokinesis in situ and genomic interrogation of human cell size regulation

title: Magnetic resonance imaging of mean cell size in human breast tumors
abstract: Cell size is a fundamental characteristic of all tissues, and changes in cell size in cancer reflect tumor status and response to treatments, such as apoptosis and cell cycle arrest. Unfortunately, cell size can currently be obtained only by pathological evaluation of tumor tissue samples obtained invasively. Previous imaging approaches are limited to preclinical MRI scanners or require relatively long acquisition times that are impractical for clinical imaging. There is a need to develop cell size imaging for clinical applications.

title: Cell size dependent upregulation of HGF expression in dermal fibroblasts: Impact on human skin connective tissue aging.
abstract: Aged human skin is primarily attributable to loss of collagen, the main structural component of skin. Hepatocyte growth factor (HGF) acts as an anti fibrotic factor by suppression of collagen production. It is not known whether HGF is involved in age related collagen deficit in human skin.  The objective of this study was to investigate the expression of HGF in human skin, and the underlying mechanisms of age related elevation of HGF expression.  The expression of HGF in young (25+ 5years, six subjects) and aged (75+ 6years, six subjects) human skin was determined by laser capture microdissection (LCM) coupled real time PCR and immunohistology. The underlying mechanisms of age related elevation of HGF were investigated by reducing dermal fibroblast size, which is a prominent feature of aged skin fibroblast in vivo.  HGF is predominantly expressed in human skin dermal fibroblasts, the major cells responsible for collagen production, and is significantly elevated in aged human skin in vivo. Mechanistically, reduced fibroblast size, which is a prominent feature of aged skin fibroblasts in vivo, is responsible for age related elevation of HGF expression. Cell size dependent upregulation of HGF expression is driven by increased c Jun and impaired TGF b signaling. Restoration of fibroblast size normalizes increased c Jun expression and impaired TGF b signaling, and thus reversed the elevated HGF expression. Finally, we confirmed that application of retinoid (ROL) which has been shown to improve aged human skin, significantly reduced elevated HGF mRNA expression in aged human skin in vivo (78+ 4years, six subjects)  These data reveal a novel mechanism by which reduction of fibroblast size upregulates HGF expression, which in turn contributes to loss of collagen, a prominent feature of aged skin.

title: The Human Cell Atlas White Paper
abstract: The Human Cell Atlas (HCA) will be made up of comprehensive reference maps of all human cells the fundamental units of life as a basis for understanding fundamental human biological processes and diagnosing, monitoring, and treating disease. It will help scientists understand how genetic variants impact disease risk, define drug toxicities, discover better therapies, and advance regenerative medicine. A resource of such ambition and scale should be built in stages, increasing in size, breadth, and resolution as technologies develop and understanding deepens. We will therefore pursue Phase 1 as a suite of flagship projects in key tissues, systems, and organs. We will bring together experts in biology, medicine, genomics, technology development and computation (including data analysis, software engineering, and visualization) We will also need standardized experimental and computational methods that will allow us to compare diverse cell and tissue types and samples across human communities in consistent ways, ensuring that the resulting resource is truly global. This document, the first version of the HCA White Paper, was written by experts in the field with feedback and suggestions from the HCA community, gathered during recent international meetings. The White Paper, released at the close of this yearlong planning process, will be a living document that evolves as the HCA community provides additional feedback, as technological and computational advances are made, and as lessons are learned during the construction of the atlas.

title: MAP4K4 Inhibition Promotes Survival of Human Stem Cell Derived Cardiomyocytes and Reduces Infarct Size In Vivo
abstract: Heart disease is a paramount cause of global death and disability. Although cardiomyocyte death plays a causal role and its suppression would be logical, no clinical counter measures target the responsible intracellular pathways. Therapeutic progress has been hampered by lack of preclinical human validation. Mitogen activated protein kinase kinase kinase kinase 4 (MAP4K4) is activated in failing human hearts and relevant rodent models. Using human induced pluripotent stem cell derived cardiomyocytes (hiPSC CMs) and MAP4K4 gene silencing, we demonstrate that death induced by oxidative stress requires MAP4K4. Consequently, we devised a small molecule inhibitor, DMX 5804, that rescues cell survival, mitochondrial function, and calcium cycling in hiPSC CMs. As proof of principle that drug discovery in hiPSC CMs may predict efficacy in vivo, DMX 5804 reduces ischemia reperfusion injury in mice by more than 50% We implicate MAP4K4 as a well posed target toward suppressing human cardiac cell death and highlight the utility of hiPSC CMs in drug discovery to enhance cardiomyocyte survival.

title: Cell size control and gene expression homeostasis in single cells.
abstract: Growth of a cell and its subsequent division into daughters is a fundamental aspect of all cellular living systems. During these processes, how do individual cells correct size aberrations so that they do not grow abnormally large or small? How do cells ensure that the concentration of essential gene products are maintained at desired levels, in spite of dynamic/stochastic changes in cell size during growth and division? Both these questions have fascinated researchers for over a century. We review how advances in singe cell technologies and measurements are providing unique insights into these questions across organisms from prokaryotes to human cells. More specifically, diverse strategies based on timing of cell cycle events, regulating growth, and number of daughters are employed to maintain cell size homeostasis. Interestingly, size homeostasis often results in size optimality proliferation of individual cells in a population is maximized at an optimal cell size. We further discuss how size dependent expression or gene replication timing can buffer concentration of a gene product from cell to cell size variations within a population. Finally, we speculate on an intriguing hypothesis that specific size control strategies may have evolved as a consequence of gene product concentration homeostasis.

title: Classification of Single Particles from Human Cell Extract Reveals Distinct Structures
abstract: Multi protein complexes are necessary for nearly all cellular processes, and understanding their structure is required for elucidating their function. Current high resolution strategies in structural biology are effective but lag behind other fields (e.g. genomics and proteomics) due to their reliance on purified samples rather than heterogeneous mixtures. Here, we present a method combining single particle analysis by electron microscopy with protein identification by mass spectrometry to structurally characterize macromolecular complexes from human cell extract. We identify HSP60 through two dimensional classification and obtain three dimensional structures of native proteasomes directly from ab initio classification of a heterogeneous mixture of protein complexes. In addition, we reveal an ~1 MDa size structure of unknown composition and reference our proteomics data to suggest possible identities. Our study shows the power of using a shotgun approach to electron microscopy (shotgun EM) when coupled with mass spectrometry as a tool to uncover the structures of macromolecular machines.

title: DEPDC5 and NPRL3 modulate cell size, filopodial outgrowth, and localization of mTOR in neural progenitor cells and neurons
abstract: Mutations in DEPDC5 and NPRL3 subunits of GATOR1, a modulator of mechanistic target of rapamycin (mTOR) are linked to malformations of cortical development (MCD) Brain specimens from these individuals reveal abnormal cortical lamination, altered cell morphology, and hyperphosphorylation of ribosomal S6 protein (PS6) a marker for mTOR activation. While numerous studies have examined GATOR1 subunit function in non neuronal cell lines, few have directly assessed loss of GATOR1 subunit function in neuronal cell types. We hypothesized that DEPDC5 or NPRL3 shRNA mediated knockdown (DEPDC5/NPRL3 KD) leads to inappropriate functional activation of mTOR and mTOR dependent alterations in neuronal morphology. Neuronal size was determined in human specimens harboring DEPDC5 or NPRL3 mutations resected for epilepsy treatment. DEPDC5/NPRL3 KD effects on cell size, filopodial extension, subcellular mTOR complex 1 (mTORC1) localization, and mTORC1 activation during nutrient deprivation were assayed in mouse neuroblastoma cells (N2aC) and mouse subventricular zone derived neural progenitor cells (mNPCs) mTORC1 dependent effects of DEPDC5/NPRL3 KD were determined using the mTOR inhibitor rapamycin. Changes in mTOR subcellular localization and mTORC1 pathway activation following DEPDC5/NPRL3 KD were determined by examining the proximity of mTOR to the lysosomal surface during amino acid starvation. Neurons exhibiting PS6 immunoreactivity (Ser 235/236) in human specimens were 1.5x larger than neurons in post mortem control samples. DEPDC5/NPRL3 KD caused mTORC1, but not mTORC2, hyperactivation, soma enlargement, and increased filopodia in N2aC and mNPCs compared with wildtype cells. DEPDC5/NPRL3 KD led to inappropriate mTOR localization at the lysosome along with constitutive mTOR activation following amino acid deprivation. DEPDC5/NPRL3 KD effects on morphology and functional mTOR activation were reversed by rapamycin. mTOR dependent effects of DEPDC5/NPRL3 KD on morphology and subcellular localization of mTOR in neurons suggests that loss of function in GATOR1 subunits may play a role in MCD formation during fetal brain development.

title: 3D microniches reveal the importance of cell size and shape
abstract: Geometrical cues have been shown to alter gene expression and differentiation on 2D substrates. However, little is known about how geometrical cues affect cell function in 3D. One major reason for this lack of understanding is rooted in the difficulties of controlling cell geometry in a complex 3D setting and for long periods of culture. Here, we present a robust method to control cell volume and shape of individual human mesenchymal stem cells (hMSCs) inside 3D microniches with a range of different geometries (e.g. cylinder, triangular prism, cubic, and cuboid) We find that the actin filaments, focal adhesions, nuclear shape, YAP/TAZ localization, cell contractility, nuclear accumulation of histone deacetylase 3, and lineage selection are all sensitive to cell volume. Our 3D microniches enable fundamental studies on the impact of biophysical cues on cell fate, and have potential applications in investigating how multicellular architectures organize within geometrically well defined 3D spaces.Little is known about how geometric cues affect cell function and gene expression in 3D settings. Here the authors use microniches of different geometries to control cell volume and shape, and by extension cell phenotype and lineage.

title: Quantifying size and diversity of the human T cell alloresponse.
abstract: Alloreactive T lymphocytes are the primary mediators of immune responses in transplantation, both in the graft versus host and host versus graft directions. While essentially all clones comprising the human T cell repertoire have been selected on self peptide presented by self human leukocyte antigens (self HLAs) much remains to be understood about the nature of clones capable of responding to allo HLA molecules. Quantitative tools to study these cells are critical to understand fundamental features of this important response; however, the large size and diversity of the alloreactive T cell repertoire in humans presents a great technical challenge. We have developed a high throughput T cell receptor (TCR) sequencing approach to characterize the human alloresponse. We present a statistical method to model T cell clonal frequency distribution and quantify repertoire diversity. Using these approaches, we measured the diversity and frequency of distinct alloreactive CD4+ and CD8+ T cell populations in HLA mismatched responder stimulator pairs. Our findings indicate that the alloimmune repertoire is highly specific for a given pair of individuals, that most alloreactive clones circulate at low frequencies, and that a high proportion of TCRs is likely able to recognize alloantigens.