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It has been 50 years since cellular senescence was first described in human diploid fibroblasts (HDFs),yet its mechanism as well as its physiological and clinical implications are still not fully appreciated. Recent progress suggests that cellular senescence is a collective phenotype,composed of complex networks of effector programs. The balance and quality within the effector network varies depending on the cell type,the nature of the stress as well as the context. Therefore,understanding each of these effectors in the context of the whole network will be necessary in order to fully understand senescence as a whole. Furthermore,searching for new effector programs of senescence will help to define this heterogeneous and complex phenotype according to cellular contexts. View Publication

The quantification of cellular mechanical properties is of tremendous interest in biology and medicine. Recent microfluidic technologies that infer cellular mechanical properties based on analysis of cellular deformations during microchannel traversal have dramatically improved throughput over traditional single-cell rheological tools,yet the extraction of material parameters from these measurements remains quite complex due to challenges such as confinement by channel walls and the domination of complex inertial forces. Here,we describe a simple microfluidic platform that uses hydrodynamic forces at low Reynolds number and low confinement to elongate single cells near the stagnation point of a planar extensional flow. In tandem,we present,to our knowledge,a novel analytical framework that enables determination of cellular viscoelastic properties (stiffness and fluidity) from these measurements. We validated our system and analysis by measuring the stiffness of cross-linked dextran microparticles,which yielded reasonable agreement with previously reported values and our micropipette aspiration measurements. We then measured viscoelastic properties of 3T3 fibroblasts and glioblastoma tumor initiating cells. Our system captures the expected changes in elastic modulus induced in 3T3 fibroblasts and tumor initiating cells in response to agents that soften (cytochalasin D) or stiffen (paraformaldehyde) the cytoskeleton. The simplicity of the device coupled with our analytical model allows straightforward measurement of the viscoelastic properties of cells and soft,spherical objects. View Publication

Germinal centres (GC) are lymphoid structures in which B cells acquire affinity-enhancing somatic hypermutations (SHM),with surviving clones differentiating into memory B cells (MBCs) and long-lived bone marrow plasma cells1-5 (BMPCs). SARS-CoV-2 mRNA vaccination induces a persistent GC response that lasts for at least six months in humans6-8. The fate of responding GC B cells as well as the functional consequences of such persistence remain unknown. Here,we detected SARS-CoV-2 spike protein-specific MBCs in 42 individuals who had received two doses of the SARS-CoV-2 mRNA vaccine BNT162b2 six month earlier. Spike-specific IgG-secreting BMPCs were detected in 9 out of 11 participants. Using a combined approach of sequencing the B cell receptors of responding blood plasmablasts and MBCs,lymph node GC B cells and plasma cells and BMPCs from eight individuals and expression of the corresponding monoclonal antibodies,we tracked the evolution of 1,540 spike-specific B cell clones. On average,early blood spike-specific plasmablasts exhibited the lowest SHM frequencies. By contrast,SHM frequencies of spike-specific GC B cells increased by 3.5-fold within six months after vaccination. Spike-specific MBCs and BMPCs accumulated high levels of SHM,which corresponded with enhanced anti-spike antibody avidity in blood and enhanced affinity as well as neutralization capacity of BMPC-derived monoclonal antibodies. We report how the notable persistence of the GC reaction induced by SARS-CoV-2 mRNA vaccination in humans culminates in affinity-matured long-term antibody responses that potently neutralize the virus. View Publication

Human norovirus (HNoV) is a global health and socioeconomic burden,estimated to infect every individual at least five times during their lifetime. The underlying mechanism for the potential lack of long-term immune protection from HNoV infections is not understood and prompted us to investigate HNoV susceptibility of primary human B cells and its functional impact. Primary B cells isolated from whole blood were infected with HNoV-positive stool samples and harvested at 3??days postinfection (dpi) to assess the viral RNA yield by reverse transcriptase quantitative PCR (RT-qPCR). A 3- to 18-fold increase in the HNoV RNA yield was observed in 50 to 60% of donors. Infection was further confirmed in B cells derived from splenic and lymph node biopsy specimens. Next,we characterized infection of whole-blood-derived B cells by flow cytometry in specific functional B cell subsets (naive CD27- IgD+,memory-switched CD27+ IgD-,memory-unswitched CD27+ IgD+,and double-negative CD27- IgD- cells). While the susceptibilities of the subsets were similar,changes in the B cell subset distribution upon infection were observed,which were also noted after treatment with HNoV virus-like particles and the predicted recombinant NS1 protein. Importantly,primary B cell stimulation with the predicted recombinant NS1 protein triggered B cell activation and induced metabolic changes. These data demonstrate that primary B cells are susceptible to HNoV infection and suggest that the NS1 protein can alter B cell activation and metabolism in vitro,which could have implications for viral pathogenesis and immune responses in vivo. IMPORTANCE Human norovirus (HNoV) is the most prevalent causative agent of gastroenteritis worldwide. Infection results in a self-limiting disease that can become chronic and severe in the immunocompromised,the elderly,and infants. There are currently no approved therapeutic and preventative strategies to limit the health and socioeconomic burdens associated with HNoV infections. Moreover,HNoV does not elicit lifelong immunity as repeat infections are common,presenting a challenge for vaccine development. Given the importance of B cells for humoral immunity,we investigated the susceptibility and impact of HNoV infection on human B cells. We found that HNoV replicates in human primary B cells derived from blood,spleen,and lymph node specimens,while the nonstructural protein NS1 can activate B cells. Because of the secreted nature of NS1,we put forward the hypothesis that HNoV infection can modulate bystander B cell function with potential impacts on systemic immune responses. View Publication

The role of negative checkpoint regulators (NCRs) in human health and disease cannot be overstated. V-domain Ig-containing Suppressor of T-cell Activation (VISTA) is an Ig superfamily protein predominantly expressed within the hematopoietic compartment and has been studied for its role in the negative regulation of T cell responses. The findings presented in this study show that,unlike all other NCRs,VISTA deficiency dramatically impacts on macrophage cytokine and chemokine production,as well as the chemotactic response of VISTA-deficient macrophages. A select group of inflammatory chemokines,including CCL2,CCL3,CCL4,and CCL5,was strikingly elevated in culture supernatants from VISTA KO macrophages. VISTA deficiency also altered chemokine receptor recycling and profoundly disrupted myeloid chemotaxis. The impact of VISTA deficiency on chemotaxis in vivo was apparent with the reduced ability of both KO macrophages and MDSCs to migrate to the tumor microenvironment. This is the first demonstration of an NCR impacting on myeloid mediator production and chemotaxis,and will guide the use of anti-VISTA therapeutics to manipulate the chemotaxis of inflammatory macrophages or immunosuppressive MDSCs in inflammatory diseases and cancer. View Publication

Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways,including fatty acid oxidation,degradation of amino acids,and biosynthesis of ether lipids. Consequently,peroxisome dysfunction leads to pediatric-onset neurodegenerative conditions,including Peroxisome Biogenesis Disorders (PBD). Due to the dynamic,tissue-specific,and context-dependent nature of their biogenesis and function,live cell imaging of peroxisomes is essential for studying peroxisome regulation,as well as for the diagnosis of PBD-linked abnormalities. However,the peroxisomal imaging toolkit is lacking in many respects,with no reporters for substrate import,nor cell-permeable probes that could stain dysfunctional peroxisomes. Here we report that the BODIPY-C12 fluorescent fatty acid probe stains functional and dysfunctional peroxisomes in live mammalian cells. We then go on to improve BODIPY-C12,generating peroxisome-specific reagents,PeroxiSPY650 and PeroxiSPY555. These probes combine high peroxisome specificity,bright fluorescence in the red and far-red spectrum,and fast non-cytotoxic staining,making them ideal tools for live cell,whole organism,or tissue imaging of peroxisomes. Finally,we demonstrate that PeroxiSPY enables diagnosis of peroxisome abnormalities in the PBD CRISPR/Cas9 cell models and patient-derived cell lines. The array of tools to image peroxisome regulation is still limited. Here,the authors develop improved fatty acid-based probes with high peroxisome specificity and bright fluorescence in the red/far-red spectrum,which makes them ideal to study peroxisomes in live cells and whole organisms. View Publication

SummaryProtein turnover is a critical component of gene expression regulation and cellular homeostasis,yet methods for measuring turnover rates that are scalable and applicable to different models are still needed. We introduce an improved D2O (heavy water) labeling strategy to investigate the landscape of protein turnover in cell culture,with accurate calibration of per-residue deuterium incorporation in multiple cell types. Applying this method,we mapped the proteome-wide turnover landscape of pluripotent and differentiating human induced pluripotent stem cells (hiPSCs). Our analysis highlights the role of APC/C (anaphase-promoting complex/cyclosome) and SPOP (speckle-type POZ protein) degrons in the fast turnover of cell-cycle-related and DNA-binding hiPSC proteins. Upon pluripotency exit,many short-lived hiPSC proteins are depleted,while RNA-binding and -splicing proteins become hyperdynamic. The ability to identify fast-turnover proteins also facilitates secretome profiling,as exemplified in hiPSC-cardiomyocyte and primary human cardiac fibroblast analysis. This method is broadly applicable to protein turnover studies in primary,pluripotent,and transformed cells. Graphical abstract Highlights•D2O labeling measures protein turnover in primary,pluripotent,and transformed cells•D2O incorporates into multiple amino acids in vitro,including Ala,Glu,Asp,and Pro•Protein turnover analysis shows hiPSC differentiation alters fast-turnover proteins•We show application to secretome analysis in human cardiac myocytes and fibroblasts MotivationDynamic stable isotope labeling by amino acids in cell culture coupled with mass spectrometry is commonly used to measure protein turnover in cell culture but requires altering culture medium composition and may not label some peptides. We describe a simple and convenient alternative for measuring protein turnover kinetics in cultured cells by adding low-volume D2O (heavy water) to standard tissue culture media. Addressing a critical gap,we determined the number of deuterium-accessible atoms on all 20 proteinogenic amino acids across multiple cell types. This allows accurate interpretation of D2O-labeled mass spectra to measure protein turnover kinetics and secretome flux on a proteome scale. Alamillo et al. present a D2O labeling mass spectrometry method to measure protein turnover rates that is compatible with multiple cell cultures and medium formulations. The method reveals a parsimonious protein turnover landscape in human induced pluripotent stem cells and identifies hyperdynamic proteins that are unique to self-renewal states. View Publication

Ab-targeted vaccination involves targeting a receptor of choice expressed by dendritic cells (DCs) with Ag-coupled Abs. Currently,there is little consensus as to which criteria determine receptor selection to ensure superior Ag presentation and immunity. In this study,we investigated parameters of DC receptor internalization and determined how they impact Ag presentation outcomes. First,using mixed bone marrow chimeras,we established that Ag-targeted,but not nontargeted,DCs are responsible for Ag presentation in settings of Ab-targeted vaccination in vivo. Next,we analyzed parameters of DEC205 (CD205),Clec9A,CD11c,CD11b,and CD40 endocytosis and obtained quantitative measurements of internalization speed,surface turnover,and delivered Ag load. Exploiting these parameters in MHC class I (MHC I) and MHC class II (MHC II) Ag presentation assays,we showed that receptor expression level,proportion of surface turnover,or speed of receptor internalization did not impact MHC I or MHC II Ag presentation efficiency. Furthermore,the Ag load delivered to DCs did not correlate with the efficiency of MHC I or MHC II Ag presentation. In contrast,targeting Ag to CD8(+) or CD8(-) DCs enhanced MHC I or MHC II Ag presentation,respectively. Therefore,receptor expression levels,speed of internalization,and/or the amount of Ag delivered can be excluded as major determinants that dictate Ag presentation efficiency in setting of Ab-targeted vaccination. View Publication

The ST6Gal-I sialyltransferase adds an $$2-6-linked sialic acid to the N-glycans of certain receptors. ST6Gal-I mRNA has been reported to be upregulated in human cancer,but a prior lack of antibodies has limited immunochemical analysis of the ST6Gal-I protein. Here,we show upregulated ST6Gal-I protein in several epithelial cancers,including many colon carcinomas. In normal colon,ST6Gal-I localized selectively to the base of crypts,where stem/progenitor cells are found,and the tissue staining patterns were similar to the established stem cell marker ALDH1. Similarly,ST6Gal-I expression was restricted to basal epidermal layers in skin,another stem/progenitor cell compartment. ST6Gal-I was highly expressed in induced pluripotent stem (iPS) cells,with no detectable expression in the fibroblasts from which iPS cells were derived. On the basis of these observations,we investigated further an association of ST6Gal-I with cancer stem cells (CSC). Selection of irinotecan resistance in colon carcinoma cells led to a greater proportion of CSCs compared with parental cells,as measured by the CSC markers CD133 and ALDH1 activity (Aldefluor). These chemoresistant cells exhibited a corresponding upregulation of ST6Gal-I expression. Conversely,short hairpin RNA (shRNA)-mediated attenuation of ST6Gal-I in colon carcinoma cells with elevated endogenous expression decreased the number of CD133/ALDH1-positive cells present in the cell population. Collectively,our results suggest that ST6Gal-I promotes tumorigenesis and may serve as a regulator of the stem cell phenotype in both normal and cancer cell populations. View Publication

Granzyme B (grB) is a serine proteinase released by cytotoxic lymphocytes (CLs) to kill abnormal cells. GrB-mediated apoptotic pathways are conserved in nucleated cells; hence,CLs require mechanisms to protect against ectopic or misdirected grB. The nucleocytoplasmic serpin,proteinase inhibitor 9 (PI-9),is a potent inhibitor of grB that protects cells from grB-mediated apoptosis in model systems. Here we show that PI-9 is present in CD4(+) cells,CD8(+) T cells,NK cells,and at lower levels in B cells and myeloid cells. PI-9 is up-regulated in response to grB production and degranulation,and associates with grB-containing granules in activated CTLs and NK cells. Intracellular complexes of PI-9 and grB are evident in NK cells,and overexpression of PI-9 enhances CTL potency,suggesting that cytoplasmic grB,which may threaten CL viability,is rapidly inactivated by PI-9. Because dendritic cells (DCs) acquire characteristics similar to those of target cells to activate naive CD8(+) T cells and therefore may also require protection against grB,we investigated the expression of PI-9 in DCs. PI-9 is evident in thymic DCs (CD3(-),CD4(+),CD8(-),CD45(+)),tonsillar DCs,and DC subsets purified from peripheral blood (CD16(+) monocytes and CD123(+) plasmacytoid DCs). Furthermore,PI-9 is expressed in monocyte-derived DCs and is up-regulated upon TNF-alpha-induced maturation of monocyte-derived DCs. In conclusion,the presence and subcellular localization of PI-9 in leukocytes and DCs are consistent with a protective role against ectopic or misdirected grB during an immune response. View Publication