Journal: Cell reports

Article Title: A chromosome-level reference genome and pangenome for barn swallow population genomics

doi: 10.1016/j.celrep.2023.111992

Figure Lengend Snippet: (A) Flowchart of the VGP assembly pipeline 1.6 (redrawn from Rhie et al. ). (B) Genomescope2.0 k -mer profile for bHirRus1 generated from trimmed 10x Linked-Reads, used to estimate genome size, repetitiveness, and heterozygosity (top). The x axis represents multiplicity in the read set, while the y axis represents their cumulative frequency. (C) Merqury spectra-cn plots for bHirRus1. K -mer multiplicity in the 10x Linked-Reads (x axis) versus their frequency (y axis). Colored curves discriminate k -mer occurrences in the assembly. The bar at the origin of the graph represents k -mers found only in the assembly (assembly errors). Two frequency peaks are visible: a haploid peak at ~25× coverage (half average coverage, red), representing k -mers found once in the assembly (haplotype specific), and a diploid peak at ~50× (average coverage, blue) representing k -mers found twice in the assembly (shared between haplotypes). No k -mers resulting from artificial duplications (green, purple, yellow) are visible (duplication content 0.49%; ). (D) Hi-C interaction heatmaps for the curated bHirRus1 assembly. The linear sequence of the reference genome assembly is represented on both axes, and the diagonal shows 3D proximity of interacting pairs. The strength of the interaction is given by color intensity. A scaffold is considered a full chromosome when the number of interchromosomal interactions is negligible. No off-diagonal interactions are visible. Scaffolds are labeled by their chromosome number. (E) Hi-C interaction heatmaps for bHirRus1 assembly before curation. A number of off-diagonal interactions are still visible, which can either result from missing links between scaffolds of the same chromosome or from misassembly. (F) Hi-C interaction heatmaps for Chelidonia assembly. The assembly is still substantially fragmented, with several off-diagonal Hi-C interactions. (G) Snail plots and assembly summary statistics. The main plot is divided into 1,000 size-ordered bins around the circumference. Scaffold length distribution is shown in dark gray with the plot radius scaled to the longest scaffold (red). Orange and pale orange arcs show scaffold N50 and N90, respectively. The pale gray spiral shows the cumulative scaffold count on a log scale, with white scale lines showing successive orders of magnitude. The blue and pale blue areas around the plot show the GC, AT, and N content in the same bins as the inner plot. Top plot: bHirRus1 snail plot. Bottom plot: Chelidonia snail plot. The table summarizes the assembly summary statistics and BUSCO results (vertebrata_odb10) of Chelidonia and bHirRus1. (H) Dotplot alignment of bHirRus1 (blue) and Chelidonia (red) with the VGP chicken assembly GRCg7b. Chromosome numbers and coordinates are reported for GRCg7b (x axis), Chelidonia (y axis, red), and bHirRus1 (y axis, blue). Black vertical lines, red horizontal lines, and blue dashed horizontal lines define chromosome and scaffold boundaries in the chicken assembly, in Chelidonia, and in bHirRus1, respectively. See also and .

Article Snippet: Linked-reads libraries were generated using the 10x Genomics Chromium platform (Genome Library Kit & Gel Bead Kit v2 PN-120258, Genome Chip Kit v2 PN-120257, i7 Multiplex Kit PN-120262) and sequenced on an Illumina NovaSeq S4 150bp PE lane at ~60X coverage.

Techniques: Generated, Hi-C, Sequencing, Labeling

Journal: Cell reports

Article Title: A chromosome-level reference genome and pangenome for barn swallow population genomics

doi: 10.1016/j.celrep.2023.111992

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Linked-reads libraries were generated using the 10x Genomics Chromium platform (Genome Library Kit & Gel Bead Kit v2 PN-120258, Genome Chip Kit v2 PN-120257, i7 Multiplex Kit PN-120262) and sequenced on an Illumina NovaSeq S4 150bp PE lane at ~60X coverage.

Techniques: Recombinant, DNA Extraction, Multiplex Assay, cDNA Synthesis, Amplification, Sequencing, Sample Prep, Generated, Cell Culture, Software

Journal: Biomedicines

Article Title: One Year in the Extreme Isolation of Antarctica—Is This Enough to Modulate an “Allergic” Sensitization?

doi: 10.3390/biomedicines10020448

Figure Lengend Snippet: Overview of the ALEX test summary of all participants who returned the questionnaire, color explanation: no color/rose (0) = <0.3 kUA/L (negative or uncertain), yellow (1) = 0.3–1 kUA/L (low IgE level), orange (2) = 1–5 kUA/L (moderate IgE level), red (3) = 5–15 kUA/L(high IgE level), dark red (4) = >15 kUA/L (Very high IgE level). No color and rose lines show different subjects. Grey columns show separations of test clusters.

Article Snippet: As only small amounts of blood existed for further sensitization analyses, the study team decided to use the chip based multiplex ALEX Allergy Explorer (MacroArray Diagnostics GmbH, Vienna, Austria) containing more than 280 allergen extracts and molecular allergens.

Techniques: Fluorescence In Situ Hybridization

Journal: bioRxiv

Article Title: Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

doi: 10.64898/2026.10.08.757800

Figure Lengend Snippet: (a) Experimental design of the conditioned-medium (CM) model. Mice received daily intraperitoneal injections of TRAMP-C1 CM or matched blank medium (Control) for 2 weeks; BM was collected after 1 or 2 weeks. (b) Flow-cytometric quantification of CCR3-positive neutrophils, CD8Temra cells, intermediate monocytes (intMono) and non-classical monocytes (ncMono) during niche establishment. Each dot represents one mouse; for CCR3 neutrophils, intMono and ncMono measurements, n = 6, 7 and 7 mice for Control, 1 week and 2 weeks groups, respectively. For CD8 T cells, n = 3 mice per group. (c) Representative multiplex immunofluorescence images of BM stained for DAPI, CCR3 and Ly6G. Scale bars, 50 µm in the main images and 5 µm in the insets. (d) Frequency of CCR3-positive Ly6G-positive neutrophils in BM, liver, lung, peripheral blood (PB) and spleen from sham-operated and orthotopic prostate-tumor-bearing mice. Each dot represents one mouse; n = 3 mice per group. (e) Differential expression in epithelial cells from primary prostate cancer versus normal prostate datasets; selected tumor-secreted factors are labeled. (f) Activity of IGF1-, CXCL8-and ERBB-family downstream gene modules across neutrophil states. (g) Representative immunohistochemical staining of IGF1 in normal prostate and prostate cancer tissues from patients with low/medium risk, high risk or established bone metastasis. Scale bar, 200 µm. (h) Quantification of prostate-tissue IGF1 staining and plasma IGF1 bioavailability across normal, low/medium-risk, high-risk and bone-metastatic prostate cancer groups. For tissue IGF1 staining, normal prostate, n = 15 patients; low/medium-risk PCa, n = 16; high-risk PCa, n = 21; bone-metastatic PCa, n = 11. For plasma IGF1 bioavailability, normal prostate, n = 6 patients; low/medium-risk PCa, n = 13; high-risk PCa, n = 14; bone-metastatic PCa, n = 10. (i) Paired plasma IGF1 bioavailability before and after radical prostatectomy (RP); n = 9 matched patient pairs. (j) IGF1 staining in primary prostate cancer tissues and plasma IGF1 bioavailability in patients with advanced localized PCa, stratified according to subsequent bone metastasis development during follow-up (non-BMets, remained free of bone metastasis; BMets, subsequently developed bone metastases). For tissue IGF1 staining, non-BMets, n = 36 patients; BMets, n = 33. For plasma IGF1 bioavailability, non-BMets, n = 18 patients; BMets, n = 8. (k) Flow-cytometric quantification of IGF1R mean fluorescence intensity (MFI) on neutrophils from PB, spleen and BM. Each dot represents one mouse; n = 4, 4 and 3 mice for PB, spleen and BM, respectively. (l) UMAP of epithelial cells in metastatic BM samples. Early and late subtypes were labeled. (m) Diffusion-map and RNA-velocity analysis of epithelial-subtype progression. (n) UMAP feature plots of IGF1 , COL5A2 , ACAD8 , FOS , FOSB and JUN . (o) Malignant epithelial cells from paired primary-prostate cancer and BM samples from patients M8 and M9, shown by cluster identity and tissue-specific density. (p) EMP scores across paired-sample epithelial clusters. (q) Patient-specific diffusion maps with RNA-velocity vectors, colored by cluster identity. Unless otherwise indicated, bar plots with error bars show mean ± s.d. Statistical significance was assessed using two-sided unpaired Student’s t-tests (b,d,h,j,k), a paired Student’s t-test (i), Fisher’s exact tests with multiple-testing correction (e). Student’s t-test P values were adjusted using the Benjamini-Hochberg method where multiple comparisons were performed.

Article Snippet: Purified BM neutrophils were treated with saline vehicle (Control) or recombinant IGF1 (100 ng/ml; MCE, HY-P70698A).

Techniques: Control, Multiplex Assay, Immunofluorescence, Staining, Quantitative Proteomics, Labeling, Activity Assay, Immunohistochemical staining, Tissue, Clinical Proteomics, Fluorescence, Diffusion-based Assay, Analysis

Journal: bioRxiv

Article Title: Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

doi: 10.64898/2026.10.08.757800

Figure Lengend Snippet: (a) Heatmap of genes differentially expressed in control and IGF1-treated mouse BM neutrophils; values are scaled expressions. Two mice were analysed per group, with each mouse serving as an independent biological replicate. (b) Gene-set enrichment analysis of the TAN signature in IGF1-treated versus control neutrophils using the RNA-seq data shown in a (n = 2 mice per group). (c) Representative immunofluorescence images of peripheral-blood and BM neutrophils from control- or IGF1-treated mice stained for DAPI, CD274, Ly6G and CCR3. Scale bars, 10 µm. (d) Frequencies of CCR3-positive and CD274-positive neutrophils in peripheral blood and BM; n = 3 mice per group. (e) Transcription-factor motifs enriched in accessible chromatin after IGF1 stimulation. n = 2 biologically independent neutrophil preparations per group. (f) Intersection of IGF1-upregulated genes (RNA-seq), IGF1-regulated transcription factors (ATAC-seq) and TAN-upregulated genes (scRNA-seq), identifying KLF4 as a candidate regulator. (g) KLF4 MFI in neutrophils after IGF1 stimulation with or without MAPK/ERK inhibition; n = 3 biologically independent samples per group. (h) ChIP-qPCR analysis of c-Myc occupancy at the KLF4 promoter after IGF1 stimulation; normal IgG served as the negative control. n = 3 biologically independent samples per group. (i) Experimental design for IGF1-induced BM preconditioning in mice receiving matched vehicle (Control), IGF1 or IGF1 plus the IGF1R inhibitor picropodophyllin (PPP). (j) CCR3 and ICAM1 MFIs in BM neutrophils after the indicated treatments; n = 6 mice per group. (k) Representative BM immunofluorescence images stained for DAPI, CCR3 and Ly6G. Scale bars, 50 µm in the main images and 5 µm in the insets. (l) Experimental design of the CM-induced BM-preconditioning model using matched blank medium (Control), wild-type TRAMP-C1 conditioned-medium (WT CM), Igf1-knockdown CM (Igf1-KD CM) or wild-type CM combined with an IGF1R-blocking antibody. (m) Frequencies of CCR3-positive neutrophils, PD-1-positive CD8 T cells and Tregs after the indicated CM treatments; n = 3 mice per group. (n) Experimental design for analysis of IGF1-induced BM remodeling in neutrophil-specific Igf1r conditional-knockout (cKO) mice and littermate controls. (o) CD274, CCR3 and ICAM1 MFIs in neutrophils, intermediate-monocyte frequency and CD8Temra frequency in control and cKO mice after IGF1 treatment; n = 3 mice per group. (p) Design of the mouse BM scRNA-seq experiment comprising saline-control, IGF1-induced HMP-like, and IGF1-preconditioned TRAMP-C1 metastatic groups. For each experimental group, BM cells from three mice were pooled to generate one scRNA-seq sample. (q) UMAP of all mouse BM cells, colored by major cell type. (r) UMAP of mouse neutrophil states with group-specific embeddings. (s) Human-derived TAN signature scores across mouse neutrophil states. (t) Differential abundance of mouse neutrophil states across experimental groups. Color indicates the log odds ratio, and “+” or “-” denotes significant enrichment or depletion, respectively. (u) UMAP of mouse BM CD8 T cell subtypes with group-specific embeddings. (v) Differential abundance of CD8 T cell subtypes across experimental groups. (w) IL-1β-induced signature scores in CD8Temra cells across saline-control, IGF1-induced HMP and TRAMP-C1 metastatic groups. Unless otherwise indicated, bar plots with error bars show mean ± s.d. Statistical comparisons in panels d, g, h, j, m and o were performed using two-sided Student’s t-tests. P values were adjusted using the Benjamini–Hochberg method where multiple comparisons were performed. For the GSEA in panel b, nominal P values and normalized enrichment scores are shown.

Article Snippet: Purified BM neutrophils were treated with saline vehicle (Control) or recombinant IGF1 (100 ng/ml; MCE, HY-P70698A).

Techniques: Control, Analysis, RNA Sequencing, Immunofluorescence, Staining, Inhibition, ChIP-qPCR, Negative Control, Knockdown, Blocking Assay, Gene Knockout, Saline, Derivative Assay, Oligomer Restriction

Journal: bioRxiv

Article Title: Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

doi: 10.64898/2026.10.08.757800

Figure Lengend Snippet: (a) Experimental design for testing whether conditioned-medium (CM)-induced BM preconditioning promotes bone metastasis and whether PPP prevents this effect. Mice received matched blank medium (Control), wild-type TRAMP-C1 CM or CM plus PPP before intracardiac TRAMP-C1 injection. (b) Experimental design for testing whether recombinant IGF1-induced BM preconditioning promotes bone metastasis and whether PPP prevents this effect. Control mice received matched IGF1 and PPP vehicles. (c, d) Bone-metastasis-free curves and longitudinal bone bioluminescence imaging (BLI) signals after CM (c) or IGF1 (d) preconditioning, with or without PPP. For longitudinal BLI analyses, the area under the curve (AUC) was calculated for each mouse from ln(signal + 1)-transformed serial BLI measurements, and per-mouse AUC values were compared between groups; n = 10 mice per group. P 1 denotes Control versus CM in c and Control versus IGF1 in d; P 2 denotes CM versus CM plus PPP in c and IGF1 versus IGF1 plus PPP in d. (e) Experimental design using neutrophil-specific Igf1r conditional-knockout (cKO) mice and littermate controls to evaluate IGF1-induced BM preconditioning and subsequent bone metastasis. (f) Bone-metastasis-free curves and longitudinal bone BLI signals in control and cKO mice. BLI signals were natural-log transformed as ln(signal + 1); n = 10 mice per group. (g) Experimental design of the metastatic model evaluating Control, anti-IGF1R, anti-PD-1 or combined anti-IGF1R plus anti-PD-1 treatment. Control mice received matched saline. (h) Bone-metastasis-free curves and longitudinal bone BLI signals across treatment groups. BLI signals were natural-log transformed as ln(signal + 1); n = 10 mice per group. P values for the prespecified pairwise comparisons are shown in the panel: P 1, P 2 and P 3 denote Control versus Combination, Saline versus anti-IGF1R and Saline versus anti-PD-1, respectively. (i) Representative haematoxylin-and-eosin-stained bone sections from control, anti-IGF1R-, anti-PD-1- and combination-treated mice. Dashed lines outline tumor regions (T); B denotes bone. Scale bar, 400 µm. (j) Quantification of tumor area in the indicated treatment groups; each dot represents one mouse. (k) Frequencies of CCR3-positive neutrophils, IFNG-positive and PD1-positive CD8 T cells, and Tregs, together with BM IL-1β concentrations, across treatment groups; n = 3 mice per group. (l) Flowchart of the investigator-initiated trial of teprotumumab plus tislelizumab in metastatic castration-resistant prostate cancer; seven patients were enrolled and received treatment; one subsequently withdrew from the study. (m) Best percentage change in serum prostate-specific antigen (PSA) from baseline. (n) PSA progression-free survival from the first dose. (o) Representative axial PET/CT images before treatment and at day 84. (p) Best percentage change in serum alkaline phosphatase (ALP) from baseline. (q) Patient-reported pain outcomes at days 28, 56 and 84 after the first dose, categorized as improved, stable or worse relative to the immediately preceding assessment (day 28 versus baseline, day 56 versus day 28 and day 84 versus day 56); n = 6 evaluable patients at each time point. Unless otherwise indicated, bar plots with error bars show mean ± s.d. Bone-metastasis-free curves were compared using log-rank tests. Longitudinal BLI data were compared using a two-sided Welch’s t-test. Pairwise cellular or histological comparisons were analyzed using two-sided Student’s t-tests, with Benjamini-Hochberg adjustment where multiple comparisons were performed. Exact P values are shown in the panels.

Article Snippet: Purified BM neutrophils were treated with saline vehicle (Control) or recombinant IGF1 (100 ng/ml; MCE, HY-P70698A).

Techniques: Control, Injection, Recombinant, Imaging, Transformation Assay, Gene Knockout, Saline, Staining, Positron Emission Tomography-Computed Tomography