The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society
Cheng, Y;Burrack, RK;Li, Q;
PMID: 35848523 | DOI: 10.1369/00221554221114174
Highly multiplexed protein and RNA in situ detection on a single tissue section concurrently is highly desirable for both basic and applied biomedical research. CO-detection by inDEXing (CODEX) is a new and powerful platform to visualize up to 60 protein biomarkers in situ, and RNAscope in situ hybridization (RNAscope) is a novel RNA detection system with high sensitivity and unprecedent specificity at a single-cell level. Nevertheless, to our knowledge, the combination of CODEX and RNAscope remained unreported until this study. Here, we report a simple and reproducible combination of CODEX and RNAscope. We also determined the cross-reactivities of CODEX anti-human antibodies to rhesus macaques, a widely used animal model of human disease.
Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer
Zowada, M;Tirier, S;Dieter, S;Krieger, T;Oberlack, A;Chua, R;Huerta, M;Ten, F;Laaber, K;Park, J;Jechow, K;Müller, T;Kalxdorf, M;Kriegsmann, M;Kriegsmann, K;Herbst, F;Krijgsveld, J;Schneider, M;Eils, R;Glimm, H;Conrad, C;Ball, C;
| DOI: 10.3390/cancers13051097
Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.
Astrocytes mediate the effect of oxytocin in the central amygdala on neuronal activity and affective states in rodents
Wahis, J;Baudon, A;Althammer, F;Kerspern, D;Goyon, S;Hagiwara, D;Lefevre, A;Barteczko, L;Boury-Jamot, B;Bellanger, B;Abatis, M;Da Silva Gouveia, M;Benusiglio, D;Eliava, M;Rozov, A;Weinsanto, I;Knobloch-Bollmann, HS;Kirchner, MK;Roy, RK;Wang, H;Pertin, M;Inquimbert, P;Pitzer, C;Siemens, J;Goumon, Y;Boutrel, B;Lamy, CM;Decosterd, I;Chatton, JY;Rouach, N;Young, WS;Stern, JE;Poisbeau, P;Stoop, R;Darbon, P;Grinevich, V;Charlet, A;
PMID: 33589833 | DOI: 10.1038/s41593-021-00800-0
Oxytocin (OT) orchestrates social and emotional behaviors through modulation of neural circuits. In the central amygdala, the release of OT modulates inhibitory circuits and, thereby, suppresses fear responses and decreases anxiety levels. Using astrocyte-specific gain and loss of function and pharmacological approaches, we demonstrate that a morphologically distinct subpopulation of astrocytes expresses OT receptors and mediates anxiolytic and positive reinforcement effects of OT in the central amygdala of mice and rats. The involvement of astrocytes in OT signaling challenges the long-held dogma that OT acts exclusively on neurons and highlights astrocytes as essential components for modulation of emotional states under normal and chronic pain conditions.
Picard N, Takesian AE, Fagiolini M, Hensch TK.
PMID: 30696941 | DOI: 10.1038/s41380-018-0341-9
Ketamine has emerged as a widespread treatment for a variety of psychiatric disorders when used at sub-anesthetic doses, but the neural mechanisms underlying its acute action remain unclear. Here, we identified NMDA receptors containing the 2A subunit (GluN2A) on parvalbumin (PV)-expressing inhibitory interneurons as a pivotal target of low-dose ketamine. Genetically deleting GluN2A receptors globally or selectively from PV interneurons abolished the rapid enhancement of visual cortical responses and gamma-band oscillations by ketamine. Moreover, during the follicular phase of the estrous cycle in female mice, the ketamine response was transiently attenuated along with a concomitant decrease of grin2A mRNA expression within PV interneurons. Thus, GluN2A receptors on PV interneurons mediate the immediate actions of low-dose ketamine treatment, and fluctuations in receptor expression across the estrous cycle may underlie sex-differences in drug efficacy.
Vasek, MJ;Mueller, SM;Fass, SB;Deajon-Jackson, JD;Liu, Y;Crosby, HW;Koester, SK;Yi, J;Li, Q;Dougherty, JD;
PMID: 37277487 | DOI: 10.1038/s41593-023-01353-0
Neurons, astrocytes and oligodendrocytes locally regulate protein translation within distal processes. Here, we tested whether there is regulated local translation within peripheral microglial processes (PeMPs) from mouse brain. We show that PeMPs contain ribosomes that engage in de novo protein synthesis, and these are associated with transcripts involved in pathogen defense, motility and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the formation of PeMP phagocytic cups, the localization of lysosomal proteins within them, and phagocytosis of apoptotic cells and pathogen-like particles. Finally, PeMPs severed from their somata exhibit and require de novo local protein synthesis to effectively surround pathogen-like particles. Collectively, these data argue for regulated local translation in PeMPs and indicate a need for new translation to support dynamic microglial functions.
Warren, R;Shaik, A;Teubner, L;Lyu, H;De Langhe, S;
PMID: 37302070 | DOI: 10.1016/j.xpro.2023.102353
Fluorescence in situ hybridization (FISH) is a useful tool for analyzing RNA expression, but difficulties arise with low-abundance RNA and in tissues that are formalin-fixed paraffin-embedded (FFPE) because reagents can be expensive. In this protocol, we adapt a previously designed FISH amplification protocol (SABER [signal amplification by exchange reaction]) for adult mouse FFPE lung sections by using probes that are extended and branched to amplify the signal. We combine FISH and immunostaining to identify cell-specific RNA. For complete details on the use and execution of this protocol, please refer to Kishi et al.1 and Lyu et al.2.
Darras, H;Berney, C;Hasin, S;Drescher, J;Feldhaar, H;Keller, L;
PMID: 37023182 | DOI: 10.1126/science.adf0419
Multicellular organisms typically develop from a single fertilized egg and therefore consist of clonal cells. We report an extraordinary reproductive system in the yellow crazy ant. Males are chimeras of haploid cells from two divergent lineages: R and W. R cells are overrepresented in the males' somatic tissues, whereas W cells are overrepresented in their sperm. Chimerism occurs when parental nuclei bypass syngamy and divide separately within the same egg. When syngamy takes place, the diploid offspring either develops into a queen when the oocyte is fertilized by an R sperm or into a worker when fertilized by a W sperm. This study reveals a mode of reproduction that may be associated with a conflict between lineages to preferentially enter the germ line.
Shu, M;Hong, D;Lin, H;Zhang, J;Luo, Z;Du, Y;Sun, Z;Yin, M;Yin, Y;Liu, L;Bao, S;Liu, Z;Lu, F;Huang, J;Dai, J;
PMID: 36495874 | DOI: 10.1016/j.devcel.2022.11.011
Spinal cord development is precisely orchestrated by spatiotemporal gene regulatory programs. However, the underlying epigenetic mechanisms remain largely elusive. Here, we profiled single-cell chromatin accessibility landscapes in mouse neural tubes spanning embryonic days 9.5-13.5. We identified neuronal-cell-cluster-specific cis-regulatory elements in neural progenitors and neurons. Furthermore, we applied a novel computational method, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression data and identify the hub enhancers within enhancer networks. It was experimentally validated in vivo for Atoh1 that knockout of the hub enhancers, but not the non-hub enhancers, markedly decreased Atoh1 expression and reduced dp1/dI1 cells. Together, our work provides insights into the epigenetic regulation of spinal cord development and a proof-of-concept demonstration of enhancer networks as a general mechanism in transcriptional regulation.
Brett, JO;Ritterhouse, LL;Newman, ET;Irwin, KE;Dawson, M;Ryan, LY;Spring, LM;Rivera, MN;Lennerz, JK;Dias-Santagata, D;Ellisen, LW;Bardia, A;Wander, SA;
PMID: 36493359 | DOI: 10.1093/oncolo/oyac248
In hormone receptor-positive metastatic breast cancer (HR+ MBC), endocrine resistance is commonly due to genetic alterations of ESR1, the gene encoding estrogen receptor alpha (ERα). While ESR1 point mutations (ESR1-MUT) cause acquired resistance to aromatase inhibition (AI) through constitutive activation, far less is known about the molecular functions and clinical consequences of ESR1 fusions (ESR1-FUS). This case series discusses 4 patients with HR+ MBC with ESR1-FUS in the context of the existing ESR1-FUS literature. We consider therapeutic strategies and raise the hypothesis that CDK4/6 inhibition (CDK4/6i) may be effective against ESR1-FUS with functional ligand-binding domain swaps. These cases highlight the importance of screening for ESR1-FUS in patients with HR+ MBC while continuing investigation of precision treatments for these genomic rearrangements.
Zeitschrift für Gastroenterologie
Qian, Y;Evert, K;Itzel, T;Albin, JE;
| DOI: 10.1055/s-0042-1754738
Background and aims Graft-versus-host-disease (GvHD) is a common complication following allogeneic hematopoietic stem cell transplantation (aHCT) that typically manifests as injury response to the skin, gastrointestinal mucosa and liver. In liver, late onset acute and chronic liver GvHD are more similar to an autoimmune reaction. The identification of valid GvHD biomarker is still an unmet clinical need. In our study, we therefore aimed to identify gene expression patterns, which could be used as potential indicators for the outcome of aHCTs with regard to acute or chronic GvHD. For this purpose, we expect to uncover similar and distinct gene signatures of GvHD in comparison to non-diseased liver tissues and detect potential candidates giving information about the outcome after aHCT. Method Microarray analyses from FFPE samples of patients were performed, and the following criteria were applied: fold change> [1] and a p- value
Huan, T;Cheng, S;Tian, B;Punzo, C;Lin, H;Daly, M;Seddon, J;
| DOI: 10.1016/j.xops.2022.100206
Purpose To select individuals and families with low genetic burden for age-related macular degeneration (AMD), to inform the clinical diagnosis of macular disorders, and to find novel genetic variants associated with macular disease in affected families. Design Genetic association study based on targeted and whole exome sequencing. Participants 758 subjects (481 individuals with maculopathy and 277 controls), including 316 individuals in 72 families. Methods We focused on 150 genes involved in the complement, coagulation, and inflammatory pathways. Single-variant tests were performed on 3062 variants shared among 5 or more subjects using logistic regression. Gene-based tests were used to evaluate aggregate effects from rare and low frequency variants (at minor allele frequency [MAF]
Xie, B;Johal, N;Jabr, R;Kanai, A;Ahmed, A;Fry, C;
| DOI: 10.1016/j.cont.2022.100458
Bladder exstrophy, as part of the exstrophy-epispadias complex, is characterised by a pathologically open and protruding organ. Despite improvements in surgical repair, many patients continue to have poorly contractile, low-capacity bladders. These pathophysiological features are associated with significant fibrosis and greater biomechanical stiffness of the bladder wall (1). The current investigation was designed to yield insight into changes to Wnt-signalling pathways, important in organ and tissue development, but also in the regulation of connective tissue deposition (2). The study used multiplex immunolabelling of target proteins and single mRNA molecules, followed by imaging and unbiased, quantitative image analysis. Data were obtained from children undergoing exstrophy repair and compared to those from children with functionally normal bladders (controls). We hypothesise that exstrophy bladders show excessive connective tissue deposition associated with altered regulation of Wnt-signalling targets.
