dataset chembl  (Biogen Inc)

Journal: Results in chemistry

Article Title: Assessing the impact of data harmonization on human liver microsomal stability prediction model performance

doi: 10.1016/j.rechem.2026.103305

Figure Lengend Snippet: Visualization of chemical space diversity using a t-SNE plot of RDKit molecular descriptors for Biogen (green), ChEMBL (teal), NCATS (purple), AstraZeneca (orange), Polaris (magenta). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The single-dataset ChEMBL and single-dataset NCATS models showed comparable performance to each other across all metrics and both the single-dataset ChEMBL and single-dataset NCATS models generally improved with the addition of Biogen data.

Techniques:

Journal: Results in chemistry

Article Title: Assessing the impact of data harmonization on human liver microsomal stability prediction model performance

doi: 10.1016/j.rechem.2026.103305

Figure Lengend Snippet: Visualization of chemical space diversity using a t-SNE plot of RDKit molecular descriptors for Biogen (green), ChEMBL (teal), NCATS (purple), AstraZeneca (orange), Polaris (magenta). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The remaining three datasets were used for our analysis: Biogen, ChEMBL, and NCATS; and four combinations of those datasets: Biogen + ChEMBL, Biogen + NCATS, ChEMBL + NCATS, and a combined set of Biogen + ChEMBL + NCATS.

Techniques:

Journal: Results in chemistry

Article Title: Assessing the impact of data harmonization on human liver microsomal stability prediction model performance

doi: 10.1016/j.rechem.2026.103305

Figure Lengend Snippet: Visualization of chemical space diversity using a t-SNE plot of RDKit molecular descriptors for Biogen (green), ChEMBL (teal), NCATS (purple), AstraZeneca (orange), Polaris (magenta). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The remaining three datasets were used for our analysis: Biogen, ChEMBL, and NCATS; and four combinations of those datasets: Biogen + ChEMBL, Biogen + NCATS, ChEMBL + NCATS, and a combined set of Biogen + ChEMBL + NCATS.

Techniques:

Journal: Molecular Therapy Advances

Article Title: Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates

doi: 10.1016/j.omta.2026.201726

Figure Lengend Snippet: Experimental design (A) Vitrectomy and subretinal AAV gene therapies were performed to both right (RE) and left (LE) eyes of two wild-type non-human primates (NHPs). The left eyes of both animals also received monthly intravitreal injection of 1.5 mg adalimumab. Retinal structure and function were longitudinally monitored by multimodal imaging and ERG. Vitreous and blood samples were collected at key time points for cytokine analysis. Retinas were harvested at 12 weeks for immunohistochemistry, single-cell RNA-sequencing, and spatial transcriptomic analysis. (B) NHP1 received a total dose of 1.5 × 10 11 vg (vector genome) of Luxturna (AAV2-CAG- hRPE65 ) per eye via two subretinal blebs (denoted by dashed lines). (C) NHP2 received 1.25 × 10 11 vg of AAV8-GRK1- hRPGRco and 2.5 × 10 10 vg of an equivalent reporter vector AAV8-GRK1- mScarlet in two separate blebs (dashed lines). Note that all retinal images are vertically inverted (top of the image representing inferior retina) due to the imaging device approaching the supine animal from the top. Scale bars, 500 μm.

Article Snippet: More recently, clinical trials of another subretinal gene therapy (cotoretigene toliparvovec, Biogen Inc., USA) for X-linked retinitis pigmentosa (XLRP) demonstrated significant improvements in low-luminance visual acuity and retinal sensitivity., This consisted of an AAV8 vector expressing a codon-optimized human retinitis pigmentosa GTPase regulator ( hRPGRco ) transgene under the control of a photoreceptor-specific G protein-coupled receptor kinase 1 (GRK1) promoter.

Techniques: Injection, Imaging, Immunohistochemistry, Single Cell, RNA Sequencing, Plasmid Preparation

Journal: Molecular Therapy Advances

Article Title: Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates

doi: 10.1016/j.omta.2026.201726

Figure Lengend Snippet: Mild perturbation of retinal structure following subretinal AAV gene therapy in non-human primates Longitudinal multimodal retinal imaging following subretinal injection of AAV vectors over 12 weeks of both eyes of NHP1 and NHP2. The color lines represent the locations of OCT sections from inside the treated subretinal blebs. Note that all retinal images are vertically inverted (top of the image representing inferior retina). Red-dashed circles indicate subretinal infiltrates seen from 4 to 8 weeks. In the left eye inferior arcade of NHP2 (within an area treated by AAV8-GRK1-mScarlet), this was followed by RPE/outer retinal atrophy associated with hypo-autofluorescence (yellow-dashed circle). Note that the surrounded area treated by the mScarlet vector also demonstrated increased background hyper-autofluorescence, indicative of fluorescent reporter expression. Scale bars, 500 μm.

Article Snippet: More recently, clinical trials of another subretinal gene therapy (cotoretigene toliparvovec, Biogen Inc., USA) for X-linked retinitis pigmentosa (XLRP) demonstrated significant improvements in low-luminance visual acuity and retinal sensitivity., This consisted of an AAV8 vector expressing a codon-optimized human retinitis pigmentosa GTPase regulator ( hRPGRco ) transgene under the control of a photoreceptor-specific G protein-coupled receptor kinase 1 (GRK1) promoter.

Techniques: Imaging, Injection, Plasmid Preparation, Expressing

Journal: Molecular Therapy Advances

Article Title: Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates

doi: 10.1016/j.omta.2026.201726

Figure Lengend Snippet: Single-cell transcriptomic analysis reveals a type 1 cell-mediated response in the retina 12 weeks after subretinal AAV gene therapy in non-human primates (NHPs) (A) Identification of immune population cells in the PTPRC + cluster. (B) Two-dimensional Fruchterman-Reingold (FR) force-directed graph of myeloid cells colored by unbiased Leiden cluster prior to trajectory inference analysis. (C) Pseudotime analysis of myeloid cells revealed one root (quiescent cells) and two branches—branch 1 (antigen presentation) and branch 2 (cell mobility). Gene ontology enrichment analysis identified the main biological processes linked with these branches. (D) T cell (CD3D + ) subclusters show presence of various CD4 and CD8 subsets, as well as a proliferating (“cycling”) cluster with high expression of cell-cycle genes. CD8 + subclusters labeled 1–4, DN, double-negative ( CD4 − CD8A − ). (E) Projection of our T cell dataset (black contour plot) onto the ProjecTILs reference dataset (colored UMAP). (F) Percentage of T cells projected onto each ProjecTILs cluster showing a prominent CD8 effector memory cell cluster.

Article Snippet: More recently, clinical trials of another subretinal gene therapy (cotoretigene toliparvovec, Biogen Inc., USA) for X-linked retinitis pigmentosa (XLRP) demonstrated significant improvements in low-luminance visual acuity and retinal sensitivity., This consisted of an AAV8 vector expressing a codon-optimized human retinitis pigmentosa GTPase regulator ( hRPGRco ) transgene under the control of a photoreceptor-specific G protein-coupled receptor kinase 1 (GRK1) promoter.

Techniques: Single Cell, Immunopeptidomics, Expressing, Labeling

Journal: The Journal of Comparative Neurology

Article Title: Na V 1.7 mRNA and Protein Expression in Resident Neurons of the Human Spinal Dorsal Horn

doi: 10.1002/cne.70168

Figure Lengend Snippet: Distribution of SCN9A (Na V 1.7) and TACR1 (NK1R) mRNAs in the human spinal dorsal horn using RNAscope. (A) Mosaic image of a human spinal cord (lumbar 5/sacral 1) labeled with RNAscope in situ hybridization for SCN9A (red) and TACR1 (green) mRNAs and co‐stained with DAPI (cyan). The 488 channel was left unstained (green) to reveal background autofluorescence and lipofuscin, which is present in all human neurons. Magenta line outlines gray matter. Higher magnification images for each channel are shown for (B) lamina I, (C) lamina II, (D) lamina III, (E) lamina IV, and (F) lamina V. (G) Percentage of SCN9A + nuclei that coexpressed TACR1 (red bar) and percentage of TACR1 + nuclei that coexpressed SCN9A (blue bar) for each lamina (LI–LV). (H) Percentage of TACR1 + nuclei that were copositive for SCN9A (blue bar) and percentage of SCN9A + nuclei that were copositive for TACR1 (red bar) for the entire dorsal horn (combined data of H). (I) S CN9A mRNA was also detected in (I) nuclei lining the central canal, likely ependymal cells, (J) preganglionic parasympathetic neurons in the sacral parasympathetic nucleus (SPSy), (K) motor neurons in the ventral horn, particularly Pes9, which contains motor neurons associated with the feet, and (L) preganglionic sympathetic neurons in the intermediolateral column (IML) from a lumbar 1 spinal cord section. LI–LV, lamina I–V; SPSy, sacral parasympathetic nucleus; Pes9, motor neurons of the foot; CC, central canal. Sample size: n = 4. Scale bars: A = 500 µm; B–F = 20 µm; I–L = 50 µm.

Article Snippet: Several Na V 1.7 inhibitors have been developed, and a series of clinical trials have been conducted with mixed reports on pain outcomes and cardiovascular safety (Alles and Smith ; Biogen ; Dormer et al. ; Eagles et al. ; Kingwell ; McDonnell et al. ; Price et al. ).

Techniques: RNAscope, Labeling, In Situ Hybridization, Staining

Journal: The Journal of Comparative Neurology

Article Title: Na V 1.7 mRNA and Protein Expression in Resident Neurons of the Human Spinal Dorsal Horn

doi: 10.1002/cne.70168

Figure Lengend Snippet: Distribution of SCN9A (Na V 1.7) and GPR83 mRNAs in the human spinal dorsal horn using RNAscope. (A) Mosaic image of a human spinal cord section (lumbar 3) labeled with RNAscope in situ hybridization for SCN9A (red) and GPR83 (green) mRNAs and co‐stained with DAPI (cyan). The 488 channel was left unstained (green) to reveal background autofluorescence and lipofuscin, which is present in all human neurons. Magenta line outlines gray matter. Higher magnification images for each channel are shown for (B) lamina I, (C) lamina II, (D) lamina III, (E) lamina IV, and (F) lamina V. (G) Percentage of SCN9A + nuclei in that coexpressed GPR83 (red bar) and percentage of GPR83 + nuclei that coexpressed SCN9A (blue bar) for each lamina (LI–LV). (H) Percentage of GPR83 + nuclei that were copositive for SCN9A (blue bar) and percentage of SCN9A + nuclei that were copositive for GPR83 (red bar) for the entire dorsal horn (combined data of H). LI–LV, lamina I–V; D, dorsal nucleus; CC, central canal. Sample size: n = 4. Scale bars: A = 500 µm; B–F = 20 µm.

Article Snippet: Several Na V 1.7 inhibitors have been developed, and a series of clinical trials have been conducted with mixed reports on pain outcomes and cardiovascular safety (Alles and Smith ; Biogen ; Dormer et al. ; Eagles et al. ; Kingwell ; McDonnell et al. ; Price et al. ).

Techniques: RNAscope, Labeling, In Situ Hybridization, Staining

Journal: The Journal of Comparative Neurology

Article Title: Na V 1.7 mRNA and Protein Expression in Resident Neurons of the Human Spinal Dorsal Horn

doi: 10.1002/cne.70168

Figure Lengend Snippet: Na V 1.7 protein expression in the human lumbar spinal cord. Mosaic image of Na V 1.7 (red) protein staining in the human lumbar spinal cord (lumbar 5), co‐stained with DAPI (blue). White outline demarcates the gray matter. (B) Na V 1.7 protein gave an axonal and neuropil (synaptic) pattern in the spinal dorsal horn, mostly localized to lamina I–II (LI–LII). (C) Nav1.7 protein was also detected in the cytoplasm of large motor neurons in the ventral horn and (D) in axons in the anterior commissure (white arrows), as well as the cytoplasm of ependymal cells (cells outlining the central canal). (E) Representative 10x magnification confocal image of Na V 1.7 protein (red) co‐stained with the nociceptive presynaptic marker CGRP (blue), the presynaptic active zone marker Bassoon (green), and DAPI (cyan) in LI–LII of the spinal dorsal horn. (F) Overlay image (488, 555, 647, DAPI) of LI–LII in the negative control that was exposed to all of the same reagents except primary antibody and imaged and adjusted to the same settings as shown in E. (G) A higher magnification (100x) confocal view of the area outlined in yellow in the overlay image in C. (F) A digitally magnified view of the area outlined in white in E showing Na V 1.7 signal colocalized with CGRP and/or Bassoon (white arrows) or in close proximity to these proteins. LI–LV, lamina I–V; CC, central canal. Sample size: n = 4. Scale bars: A = 1 mm; B–C = 500 µm; D–F = 200 µm; G = 20 µm; H = 10 µm.

Article Snippet: Several Na V 1.7 inhibitors have been developed, and a series of clinical trials have been conducted with mixed reports on pain outcomes and cardiovascular safety (Alles and Smith ; Biogen ; Dormer et al. ; Eagles et al. ; Kingwell ; McDonnell et al. ; Price et al. ).

Techniques: Expressing, Staining, Marker, Negative Control

Journal: The Journal of Comparative Neurology

Article Title: Na V 1.7 mRNA and Protein Expression in Resident Neurons of the Human Spinal Dorsal Horn

doi: 10.1002/cne.70168

Figure Lengend Snippet: Investigation of Na V 1.7 protein in the soma of resident neurons in the dorsal horn. (A) Mosaic image of a human spinal cord section (lumbar 5–sacral 1) immunolabeled with Na V 1.7 (red), NeuN (green, soma and nucleus of neurons), and DAPI (blue, nuclei). Magenta line outlines the gray matter. Representative 40x images of Na V 1.7 (red), NeuN (green), and DAPI (blue) in (B) lamina I, (C) lamina II, (D) lamina III, (E) lamina IV, and (F) lamina V and their corresponding negative control that was exposed to all of the same reagents except primary antibody and imaged and adjusted with the same settings of each subregion. Na V 1.7 was not detected in the soma of any of the dorsal horn (lamina I–V) neurons. However, it was detected in the cell bodies of motor neurons and in preganglionic parasympathetic neurons. LI–LV, lamina I–V; SPSy, sacral parasympathetic nucleus; Pes9, motor neurons of the foot; CC, central canal. Sample size: n = 4. Scale bars: A = 500 µm; B–F = 100 µm.

Article Snippet: Several Na V 1.7 inhibitors have been developed, and a series of clinical trials have been conducted with mixed reports on pain outcomes and cardiovascular safety (Alles and Smith ; Biogen ; Dormer et al. ; Eagles et al. ; Kingwell ; McDonnell et al. ; Price et al. ).

Techniques: Immunolabeling, Negative Control

Journal: The Journal of Comparative Neurology

Article Title: Na V 1.7 mRNA and Protein Expression in Resident Neurons of the Human Spinal Dorsal Horn

doi: 10.1002/cne.70168

Figure Lengend Snippet: Evidence for postsynaptic Na V 1.7 expression in the human spinal cord. (A) Representative 10x image of Na V 1.7 (red), MAP2 (green), and DAPI (blue) staining in the human lumbar dorsal horn. The white outlines lamina I and lamina II. Representative 40x images of Na V 1.7 (red), MAP2 (green), and DAPI (blue) in (B) lamina I and (C) lamina II. White arrows point to the MAP2 signal that is localized around resident neurons (appears to be the plasma membrane) but is absent of Na V 1.7 signal. The image inset in panel C shows a 100x image of a large, LII neuron with a large apical dendrite that is devoid of Na V 1.7 signal. (D) Representative 20x image of Na V 1.7‐positive axonal fibers in the deeper lamina around LIV–LV. The white arrow points to Na V 1.7 and MAP2 copositive signal (yellow in overlay) that does not have a nucleus and is not a cell body. (E) Representative 20x image of Na V 1.7 staining in the anterior commissure (ac), where intensely labeled Na V 1.7‐positive axons are highlighted (white arrow). (F) A 100x image of Na V 1.7 (red), Ankyrin‐G (green), and DAPI (blue) staining in a motor neuron in the ventral horn. (G) A cropped, zoomed‐in image of Na V 1.7 (red), Ankyrin‐G (green), and DAPI (blue) signal in a lamina II dorsal horn neuron. LI–LV, lamina I–V; ac, anterior commissure. Sample size: n = 3–4. Scale bars: A = 200 µm; B and C = 50 µm; D and E = 100 µm; F = 20 µm; G = 5 µm.

Article Snippet: Several Na V 1.7 inhibitors have been developed, and a series of clinical trials have been conducted with mixed reports on pain outcomes and cardiovascular safety (Alles and Smith ; Biogen ; Dormer et al. ; Eagles et al. ; Kingwell ; McDonnell et al. ; Price et al. ).

Techniques: Expressing, Staining, Clinical Proteomics, Membrane, Labeling