scholarly journals Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas

2021 ◽  
Author(s):  
Udit Parekh ◽  
Daniella McDonald ◽  
Amir Dailamy ◽  
Yan Wu ◽  
Thekla Cordes ◽  
...  
Keyword(s):  
Cell Cancer ◽  
Cancer Therapeutics ◽  
Cellular Transformation ◽  
Cell Types ◽  
Cancer Driver ◽  
Specific Effects ◽  
Novel Approach ◽  
Systematic Selection ◽  
Proliferative Advantage

SUMMARYDeconstructing tissue-specific effects of genes and variants on proliferative advantage is critical to understanding cellular transformation and to systematic selection of cancer therapeutics. Dissecting these specificities at scale requires integrated methods for multiplexed genetic screens tracking fitness across time, across human cell types, and in a suitable cellular niche since functional differences also depend on physiological cues. Towards this, we present a novel approach, harnessing single-cell cancer driver screens in teratomas coupled with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and gene variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serially injected teratomas. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. These drivers directed teratoma development to lineages representative of pediatric tumors such as medulloblastoma and rhabdomyosarcoma. Additionally, mutant MEK1S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful new platform for multi-lineage longitudinal study of oncogenesis.

scholarly journals Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

2016 ◽  
Vol 27 (22) ◽  
pp. 3616-3626 ◽  
Author(s):  
Tanumoy Saha ◽  
Isabel Rathmann ◽  
Abhiyan Viplav ◽  
Sadhana Panzade ◽  
Isabell Begemann ◽  
...  
Keyword(s):  
Protein Concentration ◽  
Growth Dynamics ◽  
Automated Analysis ◽  
Cell Types ◽  
Control Mechanisms ◽  
Spatially Resolved ◽  
Novel Approach ◽  
Associated Proteins

Filopodia are dynamic, actin-rich structures that transiently form on a variety of cell types. To understand the underlying control mechanisms requires precise monitoring of localization and concentration of individual regulatory and structural proteins as filopodia elongate and subsequently retract. Although several methods exist that analyze changes in filopodial shape, a software solution to reliably correlate growth dynamics with spatially resolved protein concentration along the filopodium independent of bending, lateral shift, or tilting is missing. Here we introduce a novel approach based on the convex-hull algorithm for parallel analysis of growth dynamics and relative spatiotemporal protein concentration along flexible filopodial protrusions. Detailed in silico tests using various geometries confirm that our technique accurately tracks growth dynamics and relative protein concentration along the filopodial length for a broad range of signal distributions. To validate our technique in living cells, we measure filopodial dynamics and quantify spatiotemporal localization of filopodia-associated proteins during the filopodial extension–retraction cycle in a variety of cell types in vitro and in vivo. Together these results show that the technique is suitable for simultaneous analysis of growth dynamics and spatiotemporal protein enrichment along filopodia. To allow readily application by other laboratories, we share source code and instructions for software handling.

scholarly journals Profound functional and molecular diversity of mitochondria revealed by cell type-specific profiling in vivo

2018 ◽  
Author(s):  
Caroline Fecher ◽  
Laura Trovò ◽  
Stephan A. Müller ◽  
Nicolas Snaidero ◽  
Jennifer Wettmarshausen ◽  
...  
Keyword(s):  
Molecular Diversity ◽  
Molecular Level ◽  
Cell Types ◽  
Long Chain Fatty Acids ◽  
Cell Type ◽  
Mitochondrial Proteome ◽  
Novel Approach ◽  
Cell Type Specific ◽  
And Function

AbstractMitochondria vary in morphology and function in different tissues, however little is known about their molecular diversity among cell types. To investigate mitochondrial diversity in vivo, we developed an efficient protocol to isolate cell type-specific mitochondria based on a new MitoTag mouse. We profiled the mitochondrial proteome of three major neural cell types in cerebellum and identified a substantial number of differential mitochondrial markers for these cell types in mice and humans. Based on predictions from these proteomes, we demonstrate that astrocytic mitochondria metabolize long-chain fatty acids more efficiently than neurons. Moreover, we identified Rmdn3 as a major determinant of ER-mitochondria proximity in Purkinje cells. Our novel approach enables exploring mitochondrial diversity on the functional and molecular level in many in vivo contexts.

Protein Signature of LMP1 Signaling in PTLDs Identifies and Mimics Inter/Perifollicular CD30+ EBV− B Blasts.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3251-3251
Author(s):  
Rita Shaknovich ◽  
Katia Basso ◽  
Govind Bhagat ◽  
Bachir Alobeid ◽  
Giorgio Cattoretti
Keyword(s):  
B Cells ◽  
B Cell ◽  
Plasma Cells ◽  
Cell Subset ◽  
Cellular Transformation ◽  
Cell Types ◽  
Marginal Zone B Cells ◽  
Latently Infected ◽  
Protein Signature

Abstract EBV-associated B-cell Post-Transpant Lymphoproliferative Disorders (PTLDs) represent a diverse group of lesions morphologically, in clinical presentation and behaviour, ranging from early reversible lesions to monomorphic aggressive lymphomas. Polymorphic cases, which represent the focus of our analysis, contain a mixture of cells in various EBV latency stages, defined by EBNA1, EBNA2 and LMP1 immunostaining. LMP1 is a key viral protein for cellular transformation and, analogously to CD40, engages TNF Receptor Associated Proteins and activates NF-kB and NF-kB-responsive genes. We analyzed the protein signature of LMP1 in PTLDs and non-PTLD tonsils by double staining for LMP1, CD30, CD20, Pax5 and signaling molecules. A remarkably conserved set of proteins, associated with LMP1/CD40 signaling and NF-kB activation is expressed both in the EBV-infected lymphoid population in polymorphic PTLDs and in a normal B-cell subset(s) in reactive tonsils. These proteins include highly expressed CD30, JunB, nuclear cRel, TRAF-1, Bcl-XL, MUM1, CCL22 and downregulated BCL6 and CD10. We observed that EBV infection, possibly through LMP1 and LMP2A signaling, results in varioius degrees of differentiation within the neoplastic clone. EBER+ terminally differentiated mucosa-associated IRTA-1+ marginal zone B-cells and CD138+ plasma cells were identified in most cases, including control post-transplant tonsils with no overt disease. We document for the first time in situ, in-vivo evidence of EBV latently infected post-Germinal Center B cells of marginal and plasma cell types in PTLDs. Polymorphic PTLD cases represent EBV-induced expansion of B cells, mimicking CD40L-like activated Peri/Interfollicular CD30+ normal B-cells.

scholarly journals The function of SH2B3 (LNK) in the kidney

2016 ◽  
Vol 311 (4) ◽  
pp. F682-F685 ◽  
Author(s):  
Gregory Blass ◽  
David L. Mattson ◽  
Alexander Staruschenko
Keyword(s):  
Ex Vivo ◽  
Hematopoietic Cells ◽  
Adaptor Protein ◽  
Cell Types ◽  
In Vivo Studies ◽  
Renal Diseases ◽  
Cytokine Signaling ◽  
Specific Effects

Recent evidence indicates the adaptor protein SH2B3 has a major role in the progression of renal diseases. SH2B3 is highly expressed by hematopoietic cells and regulates cytokine signaling, inducing cell-specific effects. Additionally, its expression in other cell types suggests that SH2B3 may have a more extensive role within the kidney. Ex vivo studies have determined targets of SH2B3 cell-specific signaling, while in vivo studies have observed the SH2B3 overall affects in the progression of renal diseases. This mini-review covers the function of SH2B3-expressing cell types that contribute to renal pathologies and their regulation by SH2B3.

scholarly journals Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level

2021 ◽  
Vol 17 (9) ◽  
pp. e1009305
Author(s):  
Suraj Kannan ◽  
Michael Farid ◽  
Brian L. Lin ◽  
Matthew Miyamoto ◽  
Chulan Kwon
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Pancreatic Beta Cells ◽  
Ad Hoc ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Batch Effects ◽  
Biologically Relevant ◽  
Novel Approach

The immaturity of pluripotent stem cell (PSC)-derived tissues has emerged as a universal problem for their biomedical applications. While efforts have been made to generate adult-like cells from PSCs, direct benchmarking of PSC-derived tissues against in vivo development has not been established. Thus, maturation status is often assessed on an ad-hoc basis. Single cell RNA-sequencing (scRNA-seq) offers a promising solution, though cross-study comparison is limited by dataset-specific batch effects. Here, we developed a novel approach to quantify PSC-derived cardiomyocyte (CM) maturation through transcriptomic entropy. Transcriptomic entropy is robust across datasets regardless of differences in isolation protocols, library preparation, and other potential batch effects. With this new model, we analyzed over 45 scRNA-seq datasets and over 52,000 CMs, and established a cross-study, cross-species CM maturation reference. This reference enabled us to directly compare PSC-CMs with the in vivo developmental trajectory and thereby to quantify PSC-CM maturation status. We further found that our entropy-based approach can be used for other cell types, including pancreatic beta cells and hepatocytes. Our study presents a biologically relevant and interpretable metric for quantifying PSC-derived tissue maturation, and is extensible to numerous tissue engineering contexts.

Halothane-induced synaptic depression at both in vivo and in vitro reconstructed synapses between identified Lymnaea neurons

1995 ◽  
Vol 74 (6) ◽  
pp. 2604-2613 ◽  
Author(s):  
G. E. Spencer ◽  
N. I. Syed ◽  
K. Lukowiak ◽  
W. Winlow
Keyword(s):  
Synaptic Transmission ◽  
Lymnaea Stagnalis ◽  
Cell Types ◽  
Inhibitory Synapses ◽  
General Anesthetics ◽  
General Anesthetic ◽  
Presynaptic Neuron ◽  
Novel Approach

1. In the present study we tested the ability of the general anesthetic, halothane, to affect synaptic transmission at in vivo and in vitro reconstructed peptidergic synapses between identified neurons of Lymnaea stagnalis. 2. An identified respiratory interneuron, visceral dorsal 4 (VD4), innervates a number of postsynaptic cells in the central ring ganglia of Lymnaea. Because VD4 has previously been shown to exhibit immunoreactivity for FMRFamide-related peptides, it was hypothesized that these peptides may be utilized by VD4 during synaptic transmission. In the intact, isolated CNS of Lymnaea, we have identified novel connections between VD4 and the pedal A (PeA) cells. We demonstrate that VD4 makes inhibitory connections with the PeA neurons, in particular PeA4, and that these synaptic responses are mimicked by exogenous application of FMRFamide. 3. The synaptic transmission between VD4 and the PeA cells in an intact, isolated CNS preparation was completely blocked in 2%, but not 1% halothanc. Interestingly, the postsynaptic responses (PeA) to exogenous FMRFamide were maintained in the presence of both 1 and 2% halothane. 4. To determine the specificity of the observed responses and to determine the precise synaptic site of anesthetic action, we reconstructed the VD4/PeA synapses in vitro. After isolation from their respective ganglia, both cell types extended processes and established neuritic contact. We demonstrated that not only did the presynaptic neuron reestablish the appropriate inhibitory synapses with the PeA neurons, but that the PeA cells also maintained their responsiveness to exogenous FMRFamide. 5. Superfusion of the in vitro synaptically connected VD4 and PeA cells with 2% halothane completely abolished the synaptic transmission between these cells. However, even higher concentrations of 4% halothane failed to block the responsiveness of the PeA neurons to exogenous FMRFamide. Moreover, both 1 and 2% halothane enhanced the duration of the postsynaptic response to exogenously applied FMRFamide. These data suggest that the halothane-induced depression of synaptic transmission most likely occurred at the presynaptic level. 6. This study provides the first direct evidence that peptidergic transmission in the nervous system may also be susceptible to the actions of general anesthetics. In addition, we utilized a novel approach of in vitro reconstructed synapses for studying the effects of general anesthetics on monosynaptic transmission in the absence of other synaptic influences.

scholarly journals Dissecting T cell lineage relationships by cellular barcoding

2008 ◽  
Vol 205 (10) ◽  
pp. 2309-2318 ◽  
Author(s):  
Koen Schepers ◽  
Erwin Swart ◽  
Jeroen W.J. van Heijst ◽  
Carmen Gerlach ◽  
Maria Castrucci ◽  
...  
Keyword(s):  
T Cells ◽  
Cd8 T Cells ◽  
Family Relationships ◽  
Detection System ◽  
Cell Lineage ◽  
Cell Types ◽  
Kinship Analysis ◽  
Novel Approach ◽  
Cellular Barcoding

T cells, as well as other cell types, are composed of phenotypically and functionally distinct subsets. However, for many of these populations it is unclear whether they develop from common or separate progenitors. To address such issues, we developed a novel approach, termed cellular barcoding, that allows the dissection of lineage relationships. We demonstrate that the labeling of cells with unique identifiers coupled to a microarray-based detection system can be used to analyze family relationships between the progeny of such cells. To exemplify the potential of this technique, we studied migration patterns of families of antigen-specific CD8+ T cells in vivo. We demonstrate that progeny of individual T cells rapidly seed independent lymph nodes and that antigen-specific CD8+ T cells present at different effector sites are largely derived from a common pool of precursors. These data show how locally primed T cells disperse and provide a technology for kinship analysis with wider utility.

scholarly journals Development of a VLP-Based Vaccine Displaying an xCT Extracellular Domain for the Treatment of Metastatic Breast Cancer

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1492 ◽  
Author(s):  
Valeria Rolih ◽  
Jerri Caldeira ◽  
Elisabetta Bolli ◽  
Ahmad Salameh ◽  
Laura Conti ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Metastatic Breast Cancer ◽  
De Novo ◽  
Metastatic Breast ◽  
Cell Types ◽  
Metastasis Formation ◽  
Poor Overall Survival ◽  
Novel Approach

Metastatic breast cancer (MBC) is the leading cause of cancer death in women due to recurrence and resistance to conventional therapies. Thus, MBC represents an important unmet clinical need for new treatments. In this paper we generated a virus-like particle (VLP)-based vaccine (AX09) to inhibit de novo metastasis formation and ultimately prolong the survival of patients with MBC. To this aim, we engineered the bacteriophage MS2 VLP to display an extracellular loop of xCT, a promising therapeutic target involved in tumor progression and metastasis formation. Elevated levels of this protein are observed in a high percentage of invasive mammary ductal tumors including triple negative breast cancer (TNBC) and correlate with poor overall survival. Moreover, xCT expression is restricted to only a few normal cell types. Here, we tested AX09 in several MBC mouse models and showed that it was well-tolerated and elicited a strong antibody response against xCT. This antibody-based response resulted in the inhibition of xCT’s function in vitro and reduced metastasis formation in vivo. Thus, AX09 represents a promising novel approach for MBC, and it is currently advancing to clinical development.

scholarly journals Polyphenol-Mediated Autophagy in Cancer: Evidence of In Vitro and In Vivo Studies

2020 ◽  
Vol 21 (18) ◽  
pp. 6635 ◽  
Author(s):  
Monica Benvenuto ◽  
Loredana Albonici ◽  
Chiara Focaccetti ◽  
Sara Ciuffa ◽  
Sara Fazi ◽  
...  
Keyword(s):  
Cell Death ◽  
Stress Responses ◽  
Current Knowledge ◽  
Cellular Transformation ◽  
Degradation Process ◽  
In Vivo Studies ◽  
Type I ◽  
Specific Effects

One of the hallmarks of cellular transformation is the altered mechanism of cell death. There are three main types of cell death, characterized by different morphological and biochemical features, namely apoptosis (type I), autophagic cell death (type II) and necrosis (type III). Autophagy, or self-eating, is a tightly regulated process involved in stress responses, and it is a lysosomal degradation process. The role of autophagy in cancer is controversial and has been associated with both the induction and the inhibition of tumor growth. Autophagy can exert tumor suppression through the degradation of oncogenic proteins, suppression of inflammation, chronic tissue damage and ultimately by preventing mutations and genetic instability. On the other hand, tumor cells activate autophagy for survival in cellular stress conditions. Thus, autophagy modulation could represent a promising therapeutic strategy for cancer. Several studies have shown that polyphenols, natural compounds found in foods and beverages of plant origin, can efficiently modulate autophagy in several types of cancer. In this review, we summarize the current knowledge on the effects of polyphenols on autophagy, highlighting the conceptual benefits or drawbacks and subtle cell-specific effects of polyphenols for envisioning future therapies employing polyphenols as chemoadjuvants.

scholarly journals Injectable Hydrogels for Improving Cardiac Cell Therapy—In Vivo Evidence and Translational Challenges

Gels ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 7
Author(s):  
Cecilie Hoeeg ◽  
Alireza Dolatshahi-Pirouz ◽  
Bjarke Follin
Keyword(s):  
Cell Therapy ◽  
Cardiac Tissue ◽  
Controlled Trial ◽  
Cell Types ◽  
Cardiac Cell ◽  
Injectable Hydrogels ◽  
Novel Approach ◽  
Cardiac Cell Therapy ◽  
Different Cell Types

Cell therapy has the potential to regenerate cardiac tissue and treat a variety of cardiac diseases which are currently without effective treatment. This novel approach to treatment has demonstrated clinical efficiency, despite low retention of the cell products in the heart. It has been shown that improving retention often leads to improved functional outcome. A feasible method of improving cell graft retention is administration of injectable hydrogels. Over the last decade, a variety of injectable hydrogels have been investigated preclinically for their potential to improve the effects of cardiac cell therapy. These hydrogels are created with different polymers, properties, and additional functional motifs and differ in their approaches for encapsulating different cell types. Only one combinational therapy has been tested in a clinical randomized controlled trial. In this review, the latest research on the potential of injectable hydrogels for delivery of cell therapy is discussed, together with potential roadblocks for clinical translation and recommendations for future explorations to facilitate future translation.

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