Journal: Cell reports

Article Title: Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis.

doi: 10.1016/j.celrep.2025.115439

Figure Lengend Snippet: Figure 4. Emerin bidirectionally regulates protein synthesis, including translation factors and synaptic proteins (A–C) BONCAT-western blot (BONCAT-WB) analysis of NSPs with Emerin KD and OE. (A) Experimental workflow for BONCAT and FUNCAT. DIV12 neuronal cultures were treated with AHA for 1 h, followed by BONCAT-WB or FUNCAT- immunolabeling. (B) BONCAT-WB biotin signal with Emerin KD (shEmd vs. control shScramble) (left) or OE (Emd-mRuby vs. control mRuby) in excitatory (center) and inhibitory neurons (right).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Emerin monoclonal primary antibody Cell signaling #30853S RRID: AB_2798996 Mouse anti-Lamin A/C monoclonal primary antibody Cell signaling #4777S RRID: AB_10545756 Goat anti-biotin polyclonal primary antibody Invitrogen #31852 RRID: AB_228243 Rabbit anti-cFos monoclonal primary antibody Cell signaling #2250S RRID: AB_2247211 Guinea pig anti-Map2 polyclonal primary antibody Synaptic System #188004 RRID: AB_2138181 Mouse anti-Map2 monoclonal primary antibody Sigma-Aldrich #M9942 RRID: AB_477256 Rabbit anti-PDI monoclonal primary antibody Cell signaling #3501 RRID: AB_2156433 Rabbit anti-Synaptophysin monoclonal primary antibody Synaptic System #101008 RRID: AB_2864779 Mouse anti-PSD95 monoclonal primary antibody Cell signaling #36233 RRID: AB_2721262 Rabbit anti-vGlut1 monoclonal primary antibody Synaptic System #135308 RRID: AB_2864787 Guinea pig anti-Homer1 polyclonal primary antibody Synaptic System #160004 RRID: AB_10549720 Rabbit anti-vGat polyclonal primary antibody Synaptic System #131013 RRID: AB_2189938 Mouse anti-Gephyrin monoclonal primary antibody Synaptic System #147021 RRID: AB_2232546 Bacterial and virus strains NEB Stable competent E. coli NEB Bio-Lab Cat#C3040H AAV.dj capsid Gift from Maximov lab / Chemicals, peptides, and recombinant proteins L-azidonorleucine Chem Impex Cat#30456 L-azidohomoalanine Fisher Scientific Cat#502107772 Bicuculline Methiodine Tocris Cat# 2503 Actinomycin-D Sigma Aldrich Cat#A1410 Anisomycin Tocris Cat#22862-76-6 Paraformaldehyde Electron Microscopy Sciences Cat#15710-S TBTA Sigma-Aldrich Cat#678937 CuSO4 Sigma-Aldrich Cat#451657 Biotin-PEG4-alkyne Click Chemistry Tools Cat#TA105-25 Heavy isotope-labeled-biotin-alkyne Setareh Cat#7889 Light isotope-labeled-biotin-alkyne Setareh Cat#7884 TCEP Sigma-Aldrich Cat#C4706 Critical commercial assays BCA protein assay ThermoFisher Cat#23225 Duolink proximity ligation assay Sigma Aldrich Duolink Western blot Bio-Rad MiniPROTEAN Deposited data VE-induced cell type-specific nascent proteomic analysis ProteomeXchange Accession # PXD050926 Emerin overexpression nascent proteomic analysis ProteomeXchange Accession # PXD050926 Experimental models: Organisms/strains EMX1Cre mice Jackson laboratory JAX 005628 vGatCre mice Jackson laboratory JAX 16962 R26lsl GFP-mMetRS mice Jackson laboratory JAX 028071 C57BL/6 mice Scripps Research breeding colony / (Continued on next page) Cell Reports 44, 115439, April 22, 2025 19

Techniques: Western Blot, Immunolabeling, Control

Journal: Cell reports

Article Title: Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis.

doi: 10.1016/j.celrep.2025.115439

Figure Lengend Snippet: Figure 6. Emerin is required for normal visual responses in mice (A–G) Visually-evoked potential (VEP) recordings with Emerin KD. (A) Experimental workflow of unilateral Emerin KD and bilateral VEPs recording. (B) Representative coronal brain image showing AAV targeting and coverage. Left hemispheres are marked during sectioning for post hoc data interpretation. (C) Workflow for pre-recording preparation. (D) Visual stimulation and data acquisition protocol. (E) Representative VEP traces when both eyes were covered (left) and with normal visual stimulation (right). Recordings from KD (blue) and control (gray) hemispheres are aligned to the stimulus. (F) Trough-peak amplitude comparing left vs. right hemispheres (left) and shEmd vs. shScramble treatments (right). (G) VEP latency comparing left vs. right hemispheres (left) and shEmd vs. shScramble treatments (right). n = 8 mice, paired t test. (H–J) VE-induced cFos expression with Emerin KD. (H) Experimental workflow of unilateral Emerin KD and VE paradigm. (I) Representative image of VE-induced cFos immunolabeling in the primary visual cortex. (J) cFos+ neurons in shEmd vs. shScramble treatments. n = 5 mice, paired t test.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Emerin monoclonal primary antibody Cell signaling #30853S RRID: AB_2798996 Mouse anti-Lamin A/C monoclonal primary antibody Cell signaling #4777S RRID: AB_10545756 Goat anti-biotin polyclonal primary antibody Invitrogen #31852 RRID: AB_228243 Rabbit anti-cFos monoclonal primary antibody Cell signaling #2250S RRID: AB_2247211 Guinea pig anti-Map2 polyclonal primary antibody Synaptic System #188004 RRID: AB_2138181 Mouse anti-Map2 monoclonal primary antibody Sigma-Aldrich #M9942 RRID: AB_477256 Rabbit anti-PDI monoclonal primary antibody Cell signaling #3501 RRID: AB_2156433 Rabbit anti-Synaptophysin monoclonal primary antibody Synaptic System #101008 RRID: AB_2864779 Mouse anti-PSD95 monoclonal primary antibody Cell signaling #36233 RRID: AB_2721262 Rabbit anti-vGlut1 monoclonal primary antibody Synaptic System #135308 RRID: AB_2864787 Guinea pig anti-Homer1 polyclonal primary antibody Synaptic System #160004 RRID: AB_10549720 Rabbit anti-vGat polyclonal primary antibody Synaptic System #131013 RRID: AB_2189938 Mouse anti-Gephyrin monoclonal primary antibody Synaptic System #147021 RRID: AB_2232546 Bacterial and virus strains NEB Stable competent E. coli NEB Bio-Lab Cat#C3040H AAV.dj capsid Gift from Maximov lab / Chemicals, peptides, and recombinant proteins L-azidonorleucine Chem Impex Cat#30456 L-azidohomoalanine Fisher Scientific Cat#502107772 Bicuculline Methiodine Tocris Cat# 2503 Actinomycin-D Sigma Aldrich Cat#A1410 Anisomycin Tocris Cat#22862-76-6 Paraformaldehyde Electron Microscopy Sciences Cat#15710-S TBTA Sigma-Aldrich Cat#678937 CuSO4 Sigma-Aldrich Cat#451657 Biotin-PEG4-alkyne Click Chemistry Tools Cat#TA105-25 Heavy isotope-labeled-biotin-alkyne Setareh Cat#7889 Light isotope-labeled-biotin-alkyne Setareh Cat#7884 TCEP Sigma-Aldrich Cat#C4706 Critical commercial assays BCA protein assay ThermoFisher Cat#23225 Duolink proximity ligation assay Sigma Aldrich Duolink Western blot Bio-Rad MiniPROTEAN Deposited data VE-induced cell type-specific nascent proteomic analysis ProteomeXchange Accession # PXD050926 Emerin overexpression nascent proteomic analysis ProteomeXchange Accession # PXD050926 Experimental models: Organisms/strains EMX1Cre mice Jackson laboratory JAX 005628 vGatCre mice Jackson laboratory JAX 16962 R26lsl GFP-mMetRS mice Jackson laboratory JAX 028071 C57BL/6 mice Scripps Research breeding colony / (Continued on next page) Cell Reports 44, 115439, April 22, 2025 19

Techniques: Control, Expressing, Immunolabeling

Journal: Cell reports

Article Title: Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis.

doi: 10.1016/j.celrep.2025.115439

Figure Lengend Snippet: Figure 7. Emerin is required for visual depth perception in mice (A) Side view schematic of the visual cliff arena (left) and top view showing the 25/75 distribution of safe and unsafe zones (right). (B) Experimental workflow of bilateral Emerin knockdown and visual cliff test sessions 5 days and 30 days after AAV injection. (C) Representative movement tracking of mice within the visual cliff arena using DeepLabCut. The safe zone is highlighted in gray. (D) Raster plots of time spent in safe (green) and unsafe (orange) zones of the shEmd and shScramble groups. (E–G) Quantification of behavioral parameters from the day 30 session. (E) Percent total time spent moving and relative time spent in the safe and unsafe zones. (F) Distance traveled in the entire arena, safe zone, and unsafe zone. (G) Average moving speed in the entire arena, safe zone, and unsafe zone. n = 6 mice, Welch’s t test between shEmd and shScramble. Lines indicate median and 95% CI. (H) Time spent in the safe zone comparing day 5 and day 30 after AAV injection. n = 6 mice, paired t test. Scale bars: 5 mm (B) and 200 mm (I).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Emerin monoclonal primary antibody Cell signaling #30853S RRID: AB_2798996 Mouse anti-Lamin A/C monoclonal primary antibody Cell signaling #4777S RRID: AB_10545756 Goat anti-biotin polyclonal primary antibody Invitrogen #31852 RRID: AB_228243 Rabbit anti-cFos monoclonal primary antibody Cell signaling #2250S RRID: AB_2247211 Guinea pig anti-Map2 polyclonal primary antibody Synaptic System #188004 RRID: AB_2138181 Mouse anti-Map2 monoclonal primary antibody Sigma-Aldrich #M9942 RRID: AB_477256 Rabbit anti-PDI monoclonal primary antibody Cell signaling #3501 RRID: AB_2156433 Rabbit anti-Synaptophysin monoclonal primary antibody Synaptic System #101008 RRID: AB_2864779 Mouse anti-PSD95 monoclonal primary antibody Cell signaling #36233 RRID: AB_2721262 Rabbit anti-vGlut1 monoclonal primary antibody Synaptic System #135308 RRID: AB_2864787 Guinea pig anti-Homer1 polyclonal primary antibody Synaptic System #160004 RRID: AB_10549720 Rabbit anti-vGat polyclonal primary antibody Synaptic System #131013 RRID: AB_2189938 Mouse anti-Gephyrin monoclonal primary antibody Synaptic System #147021 RRID: AB_2232546 Bacterial and virus strains NEB Stable competent E. coli NEB Bio-Lab Cat#C3040H AAV.dj capsid Gift from Maximov lab / Chemicals, peptides, and recombinant proteins L-azidonorleucine Chem Impex Cat#30456 L-azidohomoalanine Fisher Scientific Cat#502107772 Bicuculline Methiodine Tocris Cat# 2503 Actinomycin-D Sigma Aldrich Cat#A1410 Anisomycin Tocris Cat#22862-76-6 Paraformaldehyde Electron Microscopy Sciences Cat#15710-S TBTA Sigma-Aldrich Cat#678937 CuSO4 Sigma-Aldrich Cat#451657 Biotin-PEG4-alkyne Click Chemistry Tools Cat#TA105-25 Heavy isotope-labeled-biotin-alkyne Setareh Cat#7889 Light isotope-labeled-biotin-alkyne Setareh Cat#7884 TCEP Sigma-Aldrich Cat#C4706 Critical commercial assays BCA protein assay ThermoFisher Cat#23225 Duolink proximity ligation assay Sigma Aldrich Duolink Western blot Bio-Rad MiniPROTEAN Deposited data VE-induced cell type-specific nascent proteomic analysis ProteomeXchange Accession # PXD050926 Emerin overexpression nascent proteomic analysis ProteomeXchange Accession # PXD050926 Experimental models: Organisms/strains EMX1Cre mice Jackson laboratory JAX 005628 vGatCre mice Jackson laboratory JAX 16962 R26lsl GFP-mMetRS mice Jackson laboratory JAX 028071 C57BL/6 mice Scripps Research breeding colony / (Continued on next page) Cell Reports 44, 115439, April 22, 2025 19

Techniques: Knockdown, Injection

Journal: Clinical Cancer Research

Article Title: Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity That Associate with a Clinically Aggressive Subtype of Prostate Cancer

doi: 10.1158/1078-0432.CCR-24-3660

Figure Lengend Snippet: Loss of EMD results in the vsn phenotype of decreased nuclear size, increased invasiveness, and features suggesting lineage plasticity. A, EMD expression by immunofluorescence in DU145 EMD knockdown cells by siRNA. B–D, Nuclear size of ( B ) DU145, ( C ) 22Rv1, and ( D ) C4-2B EMD knockdown cells by siRNA. E, EMD knockdown induces invasion in C4-2B EMD knockdown cells by siRNA. F and G, Expression of lineage plasticity markers in ( F ) C4-2B and ( G ) DU145 EMD knockdown cells by siRNA. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, nonsignificant.

Article Snippet: C4-2B, 22Rv1, and DU145 cells were transfected with EMD siRNA (sc-35296, Santa Cruz Biotechnology; RRID: SCR_026442) and control scramble siRNA (sc-37007, Santa Cruz; RRID: SCR_026443) using Lipofectamine 3000 (Thermo Fisher Scientific), as described by the manufacturer.

Techniques: Expressing, Immunofluorescence, Knockdown

Journal: Clinical Cancer Research

Article Title: Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity That Associate with a Clinically Aggressive Subtype of Prostate Cancer

doi: 10.1158/1078-0432.CCR-24-3660

Figure Lengend Snippet: EMD knockdown induces metastasis- and dedifferentiation-related pathways in prostate cancer cells. A–C, Bar graph depicting GSEA results for enriched pathways associated with metastasis and dedifferentiation. Representative GSEA enrichment plots are shown for EMD knockdown by shRNA in ( A ) C4-2B, ( B ) 22Rv1, and ( C ) DU145 cells, compared with nontargeting controls. EMT, epithelial–mesenchymal transition; NES, normalized enrichment score; UP, Up; DN, Down; Alt, alteration; LOF, loss of function; Diff, difference; Mod, Modulation.

Article Snippet: C4-2B, 22Rv1, and DU145 cells were transfected with EMD siRNA (sc-35296, Santa Cruz Biotechnology; RRID: SCR_026442) and control scramble siRNA (sc-37007, Santa Cruz; RRID: SCR_026443) using Lipofectamine 3000 (Thermo Fisher Scientific), as described by the manufacturer.

Techniques: Knockdown, shRNA

Journal: Clinical Cancer Research

Article Title: Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity That Associate with a Clinically Aggressive Subtype of Prostate Cancer

doi: 10.1158/1078-0432.CCR-24-3660

Figure Lengend Snippet: Characterization of ARSI impact on vsn cells and morphologic and molecular features of ARSI-resistant cells. A and B, Nuclear size measurements of ARSI-resistant C4-2B sublines and parental controls by ( A ) NanoVelcro assay and ( B ) confocal microscopy. C, EMD expression in C4-2B ARSI-resistant sublines was assessed by immunofluorescence. D, Invasion capacity of C4-2B ARSI-resistant sublines by transwell assay. E, The expression of lineage plasticity markers in C4-2B ARSI-resistant sublines. NE, neuroendocrine. F, Cell viability of C4-2B EMD knockdown cells by siRNA after 5 days of treatment with 10 μmol/L Abi acetate and 1 μmol/L Enza. **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

Article Snippet: C4-2B, 22Rv1, and DU145 cells were transfected with EMD siRNA (sc-35296, Santa Cruz Biotechnology; RRID: SCR_026442) and control scramble siRNA (sc-37007, Santa Cruz; RRID: SCR_026443) using Lipofectamine 3000 (Thermo Fisher Scientific), as described by the manufacturer.

Techniques: Confocal Microscopy, Expressing, Immunofluorescence, Transwell Assay, Knockdown

Journal: Oncology Reports

Article Title: Image analysis of the nuclear characteristics of emerin protein and the correlation with nuclear grooves and intranuclear cytoplasmic inclusions in lung adenocarcinoma

doi: 10.3892/or.2018.6848

Figure Lengend Snippet: Flow chart of the analysis in this study shows the Feulgen reaction and emerin IHC. IHC, immunohistochemistry.

Article Snippet: After the solution was removed by tapping, the specimens were treated with mouse monoclonal anti-human emerin antibody (1:500 dilution, clone CL0201; cat. no. NBP2-52876; Novus Biologicals, Littleton, CO, USA) at 4°C overnight.

Techniques: Immunohistochemistry

Journal: Oncology Reports

Article Title: Image analysis of the nuclear characteristics of emerin protein and the correlation with nuclear grooves and intranuclear cytoplasmic inclusions in lung adenocarcinoma

doi: 10.3892/or.2018.6848

Figure Lengend Snippet: (A-D) Representative effect of specimen thickness in the nuclear analysis of emerin-stained specimens after image analysis and (E-G) representative data of the correlation analysis for nuclear size, NP or ENML for specimens stained by immunohistochemistry (IHC) for emerin. Effect of section thickness is shown in case no. 14: (A and B) 1-µm-thick, (C and D) 2-µm-thick. NP as detected by our protocol is indicated in red, while the emerin-stained membrane-traced line is indicated in green (B and D). (E-G) Correlation of nuclear area (Avg), NP (Avg), and ENML. Emerin in the x-axis in (G) stands for ENML (emerin-stained nuclear membrane length). Images in A-D were captured using VS (×40 objective lens). NP, nuclear perimeter; VS, virtual slide scanner.

Article Snippet: After the solution was removed by tapping, the specimens were treated with mouse monoclonal anti-human emerin antibody (1:500 dilution, clone CL0201; cat. no. NBP2-52876; Novus Biologicals, Littleton, CO, USA) at 4°C overnight.

Techniques: Staining, Immunohistochemistry, Membrane

Journal: Oncology Reports

Article Title: Image analysis of the nuclear characteristics of emerin protein and the correlation with nuclear grooves and intranuclear cytoplasmic inclusions in lung adenocarcinoma

doi: 10.3892/or.2018.6848

Figure Lengend Snippet: A representative case with predominantly smooth nuclei (case no. 24) (A and C) and a case with eccentric nuclei (case no. 97) (B and D) as shown by emerin immunohistochemistry (IHC). In B and D, the NP is indicated in red and the ENML traced by the software is shown in green. Avg data of NP and ENML (emerin) and NP minus ENML is shown at the bottom of the figure. All images were captured by a VS (×40 objective lens). NP, nuclear perimeter; ENML, emerin-stained nuclear membrane length; VS, virtual slide scanner.

Article Snippet: After the solution was removed by tapping, the specimens were treated with mouse monoclonal anti-human emerin antibody (1:500 dilution, clone CL0201; cat. no. NBP2-52876; Novus Biologicals, Littleton, CO, USA) at 4°C overnight.

Techniques: Immunohistochemistry, Software, Staining, Membrane

Journal: Oncology Reports

Article Title: Image analysis of the nuclear characteristics of emerin protein and the correlation with nuclear grooves and intranuclear cytoplasmic inclusions in lung adenocarcinoma

doi: 10.3892/or.2018.6848

Figure Lengend Snippet: (A and C) Representative nuclear groove and intracytoplasmic inclusion, and (B and D) the relationship among nuclear grooves and intracytoplasmic inclusions, and a high nuclear deformity rate among all nuclei (NP minus the ENML-negative nuclei ratio out of all nuclei) in emerin-stained specimens. (E) The correlation between nuclear area and high nuclear deformity rate (HNDR) out of all nuclei. (A and C) A representative nuclear groove is seen as a ‘coffee bean shape’, indicated by arrows in A. A representative intracytoplasmic inclusion is indicated by an arrow in C. On the left is an H&E-stained section, whereas the right panel shows emerin IHC (×100 objective lens). (B and D) On the x-axis, a high nuclear deformity rate out of all nuclei was categorized for every 5%. The total number of cases in each category is shown in the gray bar. The percentage of cases with nuclear grooves (NGs) (B) or intranuclear cytoplasmic inclusions (ICIs) (D) out of all cases in each category is shown in the line plot. (E) Correlation between nuclear area and the rate of HNDN. NP, nuclear perimeter; ENML, emerin-stained nuclear membrane length.

Article Snippet: After the solution was removed by tapping, the specimens were treated with mouse monoclonal anti-human emerin antibody (1:500 dilution, clone CL0201; cat. no. NBP2-52876; Novus Biologicals, Littleton, CO, USA) at 4°C overnight.

Techniques: Staining, Membrane

Journal: Oncology Reports

Article Title: Image analysis of the nuclear characteristics of emerin protein and the correlation with nuclear grooves and intranuclear cytoplasmic inclusions in lung adenocarcinoma

doi: 10.3892/or.2018.6848

Figure Lengend Snippet: Comparison of cases with low emerin expression (n=34) and cases with positive emerin expression (n=54). (A) Nuclear area, (B) NP, (C) shape factor, and (D) staining intensity of each group were analyzed by Student's t-test. NP, nuclear perimeter.

Article Snippet: After the solution was removed by tapping, the specimens were treated with mouse monoclonal anti-human emerin antibody (1:500 dilution, clone CL0201; cat. no. NBP2-52876; Novus Biologicals, Littleton, CO, USA) at 4°C overnight.

Techniques: Comparison, Expressing, Staining