Journal: Brain

Article Title: Schizophrenia-associated changes in neuronal subpopulations in the human midbrain

doi: 10.1093/brain/awae321

Figure Lengend Snippet: Unsupervised clustering identifies 18 neuronal populations in the human midbrain . ( A ) Experimental design of the study . A schematic representation of the rostral midbrain at the level of the red nucleus and third cranial nerves (created with biorender.com ). The lines indicate where the superior colliculus (SC) and cerebral peduncles (CP) were removed before nuclei isolation, FANS and snRNAseq. ( B ) Unsupervised clustering of 31 669 neuronal nuclei from 14 schizophrenia (SZ) cases and 14 controls ( and ). Each dot indicates a nucleus, colours indicate clusters. ( C ) Average expression per cluster of selected neurotransmitter-, neuropeptide- or interneuron-related genes. ( D ) Bar plot depicting the total number of nuclei obtained per population, with the percentage of the total NEUN+ population enclosed in parentheses. ( E ) Violin plots depicting log-normalized expression levels of cluster markers (log 2 fold-change > 0.25, P -adjusted < 0.05) . ( F ) Violin plot depicting log-normalized expression level of DLX1 , a cluster marker for inh-CCK. ( G ) A schematic representation of the rostral midbrain indicating the periaqueductal grey and the third cranial nerve nucleus with a box and the reticular formation with a dotted box. In these regions the immunohistochemical staings, shown in H , were performed. ( H ) Representative images of immunohistochemical stainings for DLX1 (brown) and GFAP (black) in control midbrain ( n = 5). Scale bar = 50 μm. avg. = average; expr. = expression; FANS = fluorescence-activated nuclear sorting; log-norm. = log-normalized; snRNAseq = single nucleus RNA-sequencing; UMAP = Uniform Manifold Approximation and Projection.

Article Snippet: Briefly, after sucrose density centrifugation, nuclei were incubated with fluorescently-conjugated antibodies directed against neuronal marker NEUN (RBFOX3/NEUN 1B7 AF647 mouse mAB, Novus Biologicals, NBP1-92693AF647) and the transcription factor OLIG2 for the oligodendrocyte lineage (Anti-OLIG2 clone 211F1.1 AF488 mouse mAB, Merck Millipore, MABN50A4).

Techniques: Isolation, Expressing, Marker, Immunohistochemical staining, Control, Fluorescence, RNA Sequencing

Journal: Brain

Article Title: Schizophrenia-associated changes in neuronal subpopulations in the human midbrain

doi: 10.1093/brain/awae321

Figure Lengend Snippet: Schizophrenia-associated shifts in proportions of midbrain neuronal populations and subpopulations . ( A ) Uniform Manifold Approximation and Projection (UMAP) of the clusters split by diagnosis. The colour legend indicates the number of nuclei obtained per population and the percentage of the total NEUN+ population enclosed in brackets. ( B ) Box plot depicting the percentage of exc-VGLUT1 and 2 nuclei detected in midbrain samples of schizophrenia and control cases ( n = 14 per group; ). Outlier cases are labelled with grey diamond shapes, each dot represents a case, and horizontal lines indicate the median. Outliers were defined as proportions outside of the third quartile plus 1.5 times the interquartile range. ( C ) UMAP of the subclusters split by diagnosis. The colour legend indicates the number of nuclei obtained per population and the percentage of the total NEUN+ population enclosed in brackets. ( D ) Box plots depicting the percentage of nuclei detected per case in subclusters that had significantly altered proportions in schizophrenia; and . Outlier cases are labelled with grey diamond shapes and were defined as data points outside the third quartile + 1.5 × interquartile range. ( E ) Total count of differentially expressed genes (DEGs) between schizophrenia and controls within a neuronal population. Numbers above the bar indicate the total count of increased plus decreased gene expression changes in schizophrenia. ( F ) Volcano plot depicting differentially expressed genes (absolute log 2 fold-change > 0.25, P -adjusted < 0.05) between schizophrenia and controls within the neuronal population ‘inh-CCK’. The corresponding information on DEGs is available in . ( G ) Total count of differentially expressed genes between schizophrenia and controls within a neuronal subpopulation. Numbers above the bar indicate the total count of increased plus decreased gene expression changes in schizophrenia. ( H ) Volcano plot depicting DEGs (absolute log 2 fold-change > 0.25, P -adjusted < 0.05) between schizophrenia and controls within the neuronal subpopulation ‘inh-C’. The number of gene labels was reduced to avoid overlapping text; the full information on DEGs is available in . ( I ) Heat map with the number indicating the detected schizophrenia susceptibility genes per neuronal population . The colour indicates the normalized ratio of detected susceptibility genes over the total number of expressed genes per neuronal population. High-confidence schizophrenia susceptibility genes derived from Wang et al .

Article Snippet: Briefly, after sucrose density centrifugation, nuclei were incubated with fluorescently-conjugated antibodies directed against neuronal marker NEUN (RBFOX3/NEUN 1B7 AF647 mouse mAB, Novus Biologicals, NBP1-92693AF647) and the transcription factor OLIG2 for the oligodendrocyte lineage (Anti-OLIG2 clone 211F1.1 AF488 mouse mAB, Merck Millipore, MABN50A4).

Techniques: Biomarker Discovery, Control, Gene Expression, Derivative Assay

Journal: NPJ Precision Oncology

Article Title: Characterizing circulating rare cells in peripheral blood for detecting and monitoring multiple myeloma and precursor states

doi: 10.1038/s41698-025-01175-2

Figure Lengend Snippet: The composite image and each individual biomarker channels are provided. The cell groups were classified into 12 classes based on the combination of DAPI (D) and 3 markers: CD138, BCMA (membrane [Memb] and perinuclear [Peri] localization), and CD45. A D | CD138 | BCMA | CD45, B D | CD138 | BCMA, C D | BCMA | CD45, D D | CD138 | CD45, E D | CD138, F D | BCMA, G D | CD45, H DAPI-only. BCMA membrane and perinuclear localization examples provided in the left and right columns, respectively. Images taken at 100x magnification. Blue: DAPI, Red: CD138, White: BCMA, Green: CD45.

Article Snippet: Slides were fixed with 2% paraformaldehyde for 20 min, blocked with 10% goat serum for 30 min, and incubated with a primary antibody mix consisting of CD138 (2 μg/mL, Exbio, clone A-38, cat# 10-520-C100, Vestec, Czech Republic), CD45 Alexa647 (1.6 μg/mL, AbD Serotec, cat# MCA87A647, Raleigh, NC, USA), and BCMA (2.5 μg/mL, Abcam, cat# ab253242, Cambridge UK) for 1 h. Next, slides were blocked again with 10% goat serum for 1 h prior to incubation with secondary antibodies AlexaFluor555 goat anti-mouse (1:500, Invitrogen, cat# A21127, Waltham, MA, USA), AlexaFluorPLUS488 goat anti-rabbit (1:500, Invitrogen, cat# A32731, Waltham, MA, USA), and DAPI (4’,6-diamidino-2-phenylindole; D) for 40 min.

Techniques: Biomarker Discovery, Membrane

Journal: NPJ Precision Oncology

Article Title: Characterizing circulating rare cells in peripheral blood for detecting and monitoring multiple myeloma and precursor states

doi: 10.1038/s41698-025-01175-2

Figure Lengend Snippet: A Morphology UMAP plot of rare cells by channel-type classification and separated by disease state: MGUS, SMM, NDMM, RRMM. B Probability density distribution plots for select morphometric parameters across channel-type classifications of median CD138 signal intensity, median BCMA signal intensity, median CD45 signal intensity, nuclear area, nuclear eccentricity, cellular area, and cellular eccentricity.

Article Snippet: Slides were fixed with 2% paraformaldehyde for 20 min, blocked with 10% goat serum for 30 min, and incubated with a primary antibody mix consisting of CD138 (2 μg/mL, Exbio, clone A-38, cat# 10-520-C100, Vestec, Czech Republic), CD45 Alexa647 (1.6 μg/mL, AbD Serotec, cat# MCA87A647, Raleigh, NC, USA), and BCMA (2.5 μg/mL, Abcam, cat# ab253242, Cambridge UK) for 1 h. Next, slides were blocked again with 10% goat serum for 1 h prior to incubation with secondary antibodies AlexaFluor555 goat anti-mouse (1:500, Invitrogen, cat# A21127, Waltham, MA, USA), AlexaFluorPLUS488 goat anti-rabbit (1:500, Invitrogen, cat# A32731, Waltham, MA, USA), and DAPI (4’,6-diamidino-2-phenylindole; D) for 40 min.

Techniques:

Journal: Scientific Reports

Article Title: Galectin 9 rescues the inducibility of IL-10 expression in regulatory B cells of patients with food allergy

doi: 10.1038/s41598-024-84079-8

Figure Lengend Snippet: Induction of IL-10 in B cells of FA patients is impaired. ( A , B ) CD19 + CD45R + naïve B cells were isolated from PBMCs of HC subjects ( n = 10) and FA patients ( n = 10), and exposed to LPS at indicated concentrations for two days. Bars show mean ± SD of IL10 mRNA levels in B cells (A) and IL-10 in culture supernatant ( B ). ( C − E ) naïve B cells were stimulated by LPS (10 µg/ml) or PBS for 48 h and analyzed by indicated procedures. Bars show mean ± SD of MAF mRNA ( C ), MAF ( D ) or Pol II ( E ) in IL10 promoter locus of B cells. Each dot in bars presents one sample. Statistics: ANOVA + Bonferroni test ( A , B ) or Student’s t -test ( C – E ). p values are presented in figures where appropriate. HC healthy control, FA food allergy, FA B cell B cell of FA patients, HC.BC B cells of HC subjects, FA.BC B cells of FA patients.

Article Snippet: Antibodies (Abs) of CD19 (Cat#: sc-390244, fluorochrome: AF488), IL-10 (sc-8438, AF594), CD45R (sc-19597, AF647), IgD (sc-53345, AF546), MAF (sc-293420), and Pol II (sc-21751) were purchased from Santa Cruz Biotech (Santa Cruz, CA).

Techniques: Isolation, Control