ncih661 (ATCC)
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ncih661
Ncih661, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 164 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/nci+h661/NCI-H661/pm42174139-242-11-19
Average 95 stars, based on 164 article reviews
Ncih661, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 164 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/nci+h661/NCI-H661/pm42174139-242-11-19
Average 95 stars, based on 164 article reviews
ncih661 - by Bioz Stars,
2026-09
95/100 stars
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other:Article Title: Neurotensin Receptor 1 Regulates HER4 Tyrosine Phosphorylation in Lung Cancer Cells Article Snippet: NCI-H358, NCI-H522, A549, NCI-H661, NCI-H1299, and Article Title: DNA-PK inhibition sustains the antitumor innate immune response in small cell lung cancer Article Snippet: NCI-H661 , Article Title: DNA-PK inhibition sustains the antitumor innate immune response in small cell lung cancer Article Snippet: The SCLC cell lines NCI-H524 (ATCC Cat#CRL-5831; RRID:CVCL_1568), Cell Culture:Article Title: TMEM106B mediates ACE2-independent replication of the SARS-CoV-2 S-E484D variant in airway-derived cell models Article Snippet: .. The NCI-H522 (ATCC-CRL-5810) and Article Title: Gastrin-Releasing Peptide Receptors Stimulate MAPK-Mediated Growth of Lung Cancer Cells by Transactivating HER4 in a Neuregulin-1, MAP Kinase-Dependent Manner Requiring Activation of the ROS-System Article Snippet: .. NSCLC cell lines NCI-H157, NCI-H322, NCI-H441, NCI-H522, A549, Real-time Polymerase Chain Reaction:Article Title: Pan-KRAS Inhibitors BI-2493 and BI-2865 Display Potent Antitumor Activity in Tumors with KRAS Wild-type Allele Amplification Article Snippet: All master bank aliquots were routinely authenticated by short tandem repeat (STR, conducted at Eurofins Genomics) analysis and tested for the absence of Mycoplasma infection (MycoAlert assay, Lonza Bioscience, or Mycoplasma Real-Time PCR Applied Biosystems #4384772) at Boehringer Ingelheim. .. Source and testing dates for master bank aliquots of used cell lines were as follows: HEK293T (ATCC CRL-1573, RRID: CVCL_0045, MycoAlert August 21, 2020, STR profile September 29, 2020), A-375 (ATCC CRL-1619, RRID: CVCL_0132, MycoAlert July 11, 2023, STR profile August 16, 2023), NCI-H520 (ATCC HTB-182, RRID: CVCL_1566, MycoAlert April 14, 2021, STR profile April 21, 2021), SNU-1079 (KCLB 01079, RRID: CVCL_5008, MycoAlert September 01, 2022, STR profile November 22, 2022), SNU-478 (KCLB 00478, RRID: CVCL_5065, MycoAlert September 01, 2022, STR profile September 21, 2022), NCI-H838 (ATCC CRL-5844, RRID: CVCL_159, MycoAlert May 22, 2019, STR profile October 15, 2019), |
![DPPA2/4 multimerize for stability and nucleosome binding. ( A ) Western blot of whole-cell extracts from <t>NCI-H661</t> cells following CRISPR–Cas9-mediated knockout of DPPA2 and/or DPPA4 isogenic clones (WT) Wild type, (DPPA2 KO) DPPA2 single knockout, (DPPA4 KO) DPPA4 single knockout, (DKO) DPPA2+4 double knockout. Blots are anti-DPPA2 or antivinculin. “L” indicates a molecular ladder; sizes are annotated at the right . ( B ) Immunofluorescence images for DPPA2 (green) and DPPA4 (red) in NCI-H661 isogenic knockout clones. Single z -slice representative images are provided for each genotype. Scale bars, 50 µm. ( C ) Scatter plot of immunoprecipitation mass spectrometry (IP-MS) results following endogenous DPPA2 or DPPA4 IP from NCI-H661 whole-cell lysates ( n = 4 per condition). Enriched proteins were determined relative to species-matched IgG IP control by comparing label-free quantitation (LFQ-AUC) for each protein (log 2 FC ≥1 and BH-adjusted P -value of <0.05). The inset Venn diagram highlights the overlap of enriched proteins for DPPA2 and DPPA4. Proteins are colored based on whether they were enriched in a single IP or both IPs. ( D ) Box plots of enriched DPPA2 and DPPA4 protein levels from IP-MS of DPPA2/4 and matched IgG controls from NCI-H661 whole-cell lysates (log 2 LFQ-AUC; n = 4 per condition). ( E ) Box plots of DPPA2 and DPPA4 absolute protein levels relative to the bait (DPPA2/4 stoichiometry) following IP-MS of DPPA2/4 from NCI-H661 whole-cell lysates (units are relative intensity-based absolute quantification [iBAQ]; n = 4 per condition). ( F ) Representative electrophoretic mobility shift assay (EMSA) of unmodified recombinant nucleosomes incubated in the absence/presence of increasing concentrations of recombinant DPPA2-Myc/FLAG and/or His-DPPA4 protein. Protein concentrations are denoted above the gel, and the percentage of nucleosomal DNA bound in each lane is annotated below . Percentage nucleosomes shifted represents the percentage loss of band compared with the input. The experiment was repeated three times. ( G ) Density histogram of enhanced chromatin occupancy (EChO) paired-end fragment size analysis from CUT&RUN experiments performed using DPPA2 (MAB4356) and DPPA4 (ab154642, AP21202c, and AP1438a) antibodies. The X -axis represents the mean CUT&RUN fragment size at peak foci (peaks called using MACS2 for each CUT&RUN relative to a matched IgG control). The vertical line at 150 bp represents the cutoff for nucleosomal DNA fragments. ( H ) Immunofluorescence imaging of DPPA2 (green) and DPPA4 immunostaining (red) in NCI-H661 parental cells. Representative images are projections (maximum five z -slices) for cells in different stages of mitosis. DAPI stain is shown in blue. Scale bars, 10 µm. The intensity profile for each channel in a single z -slice along the dotted line in the merged image is shown below the images.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8344/pmc13138344/pmc13138344__756f02.jpg)
![DPPA2/4 colocate at active gene regulatory regions marked by H3K4me3, H3K27ac, and H2AK119ub. ( A ) Genome view of the chromosome 20: 33,632,176–33,752,019 (hg38) locus. Gene annotation track and CpG islands (red) are shown above . Tracks depict individual replicate tracks of double-cross-linked input ChIPs ( top ) and CUT&RUN ( bottom ). ChIP tracks include control input (gray; n = 1), DPPA2 (blue; n = 2), and DPPA4 (purple; n = 2). CUT&RUN tracks include mouse and rabbit IgG (gray; n = 1 each), DPPA2 (blue; n = 1), and DPPA4 (two different antibodies; purple; n = 1). Consensus DPPA2+4 peaks are annotated at the bottom . Scales are in counts per million per base pair. ( B ) Genomic annotations of DPPA2+4 consensus peaks ( n = 16,620). Promoter TSS is defined as the TSS ± 1500 bp. ( C ) G/C content of ( left ) and GC/CG dinucleotide fraction within ( right ) DPPA2+4 consensus peaks ( n = 16,620) compared with size-matched random genomic regions ( n = 16,620). ( D ) Venn diagram showing the overlap of DPPA2/4 consensus peaks and KDM2A peaks. ( E ) Heat maps of ChIP-seq enrichment at DPPA2+4 consensus peaks (±5 kb from the center of each peak, split into 100 equal windows) grouped by KDM2A peak overlap ( top ) versus nonoverlap ( bottom ) for input (gray; n = 1), DPPA2 (purple; n = 2), DPPA4 (pink; n = 2), and KDM2A (orange; n = 1). ChIP counts per million per base pair values were scaled per bin across all regions for visualization. DNA methylation (WGBS; n = 3) and CpG island density are shown for comparison. WGBS represents the fraction of methylated DNA. ( F ) Pearson correlation of KDM2A versus DPPA2 ( left ) or DPPA4 ( right ) enrichment at CpG islands in NCI-H661 cells. Scatter plots show fold enrichment over input and are colored by percentage DNA methylation (red). ( G ) Genome view of the chromosome 5: 93,429,332–93,810,092 (hg38) locus. Gene annotation track and CpG islands (red) are shown above . Shown from top to bottom are the double-cross-linked (2×) input ChIP control ( n = 1); average DPPA2 ( n = 2) and DPPA4 ( n = 2) ChIP; single-cross-linked input ChIP control ( n = 1); average H3K4me3 ( n = 2), H3K27ac ( n = 2), H3K4me1 ( n = 2), H2AK119ub ( n = 2), H3K27me3 ( n = 2), H3K36me3 ( n = 2), H3K36me2 ( n = 2), and H3K9me3 ( n = 2) ChIP; and average DNA methylation (WGBS; n = 3). Consensus DPPA2+4 peaks are annotated below . Scales are in counts per million per base pair for ChIPs and in percentage methylated DNA for WGBS (0%–100%). ( H ) Genome-wide pairwise correlations of ChIP-seq (DPPA2, DPPA4, H3K4me3, H3K27ac, H3K4me1, H3K27me3, H2AK119ub, H3K9me3, H3K36me2, and H3K36me3 fold enrichment over the input control) and WGBS (fraction of methylated DNA) partitioned into 200 bp bins genome-wide. Dots are colored and sized by Pearson correlation coefficients ( r ) and ordered by hierarchical clustering, with red squares denoting major clusters. ( I ) Odds ratio tests of DPPA2+4 consensus regions in association with ChromHMM chromatin states (17-state model; three null states [i.e., no overlap with DPPA2+4 consensus regions] excluded). Tests reflect the representation of DPPA2+4 regions in a given chromatin state compared with all other DPPA2+4 regions falling within all other chromatin state annotations. States are ordered by decreasing odds ratio, reflecting enriched chromatin states (log 10 odds ratio >0; red) compared with depleted states (log 10 odds ratio <0; blue). Error bars represent the 95% confidence intervals for hazard ratios, and all shown states have a BH-adjusted P -value of <0.05. ( J ) Heat maps of genomic regions centered on DPPA2+4 consensus peaks (resized to ±5 kb from the center of each peak, split into 100 equal windows) overlapping enriched chromatin states: active TSS (orange; n = 9676), intragenic enhancer (yellow; n = 2577), bivalent TSS (purple; n = 890), flanking active TSS (orange; n = 1576e), strong transcription (green; n = 633), and background regions not bound by DPPA2/4 for comparison (selection; black; n = 1000). Columns represent the double-cross-linked input ChIP control ( n = 1); DPPA2 ChIP ( n = 2); DPPA2 CUT&RUN ( n = 1); DPPA4 ChIP ( n = 2); DPPA4 CUT&RUN ( n = 1); H3K4me3 ( n = 2), H3K27ac ( n = 2), H3K4me1 ( n = 2), H2AK119ub ( n = 2), H3K27me3 ( n = 2), H3K9me3 ( n = 2), H3K36me3 ( n = 2), and H3K36me2 ( n = 2) ChIPs; and DNA methylation (WGBS; n = 3). The last column depicts CpG island density. ChIP and CUT&RUN counts per million per base pair values were scaled per bin across all regions for visualization. WGBS represents the fraction of methylated DNA. ( K ) Heat maps of genomic regions centered on H3K4me3–H2AK119ub reChIP consensus peaks (resized to ±5 kb from the center of each peak, split into 100 equal windows; n = 4663) compared with a set of background regions ( n = 500). Columns represent the double-cross-linked input ChIP control ( n = 1); IgG–IgG reChIP control ( n = 2); H3K4me3 ( n = 2); H2AK119ub ( n = 2); H3K4me3–H2AK119ub reChIP (K4–K119; n = 2); H2AK119ub–H3K4me3 reChIP (K119–K4; n = 2); and H3K27me3 ( n = 2), DPPA2 ( n = 2), and DPPA4 ( n = 2) ChIPs. ( L ) Genome view of the chromosome 20: 56,435,664–56,677,328 (hg38) locus. Gene annotation track and CpG islands (red) are shown above . Tracks show input ChIP control ( n = 1); average reChIP IgG–IgG control ( n = 2); H3K4me3 ( n = 2) and H2AK119ub ( n = 2) ChIPs; H3K4me3–H2AK119ub (K4–K119; n = 2) and H2AK119ub–H3K4me3 (K119–K4; n = 2) reChIPs; and H3K27me3 ( n = 2), DPPA2 ( n = 2), and DPPA4 ( n = 2) ChIPs. Consensus DPPA2/4 (gray) and reChIP peaks (black) are depicted below . Scales are in counts per million per base pair. ( M ) Venn diagram showing the overlap between DPPA2/4 consensus peaks, H3K4me3–H2AK119ub reChIP peaks (consensus of both K4–K119 and K119–K4 peaks), and H3K27me3 ChIP peaks.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8344/pmc13138344/pmc13138344__756f03.jpg)
![Loss of DPPA2/4 leads to H2AK119ub depletion at H2AK119ub–H3K4me3 promoters. ( A ) Representative Western blot of chromatin extracts from stable inducible NCI-H661 cell lines following 7 day shRNA-mediated knockdown of DPPA2 and/or DPPA4 (induction with a vehicle control [H 2 O] or 2 µg/mL doxycycline [DOX]). Uninduced and induced conditions are provided per cell line. (shREN) Nontargeting control, (shDPPA2) DPPA2 single knockdown, (shDPPA4) DPPA4 single knockdown, (shDPPA2+4) DPPA2+4 double knockdown. Blots show anti-DPPA2, anti-H3K4me3, anti-H3K27me3, anti-H3K27ac, anti-H2AK119ub, anti-H2A, or anti-H3. “L” indicates a molecular ladder; sizes are annotated at the right . ( B ) Scatter plots of differential RNA-seq and consensus (union of overlapping peaks in two replicates per condition) ATAC-seq, H3K4me3 ChIP-seq, H3K27me3 ChIP-seq, and H2AK119ub ChIP-seq peaks (columns) for the four stable inducible cell lines (shREN control [ top row], shDPPA2 [second row], shDPPA4 [third row], and shDPPA2+shDPPA4 [ bottom row]) comparing 7 day shRNA induction (doxycycline [DOX]) with vehicle control (H 2 O). Differentially expressed genes (RNA-seq, FDR <0.05, absolute log 2 FC ≥1, edgeR-TMM) or peaks (ATAC-seq, ChIP-seq FDR <0.05, absolute log 2 FC ≥0.5, edgeR-TMM) are shown in red for enriched/upregulated genes and in blue for depleted/downregulated genes. ATAC-seq and ChIP-seq data were normalized using edgeR-TMM against large 10 kb genomic bins genome-wide. The Y -axes indicate log 2 FC for DOX versus H 2 O, and the X -axes indicate log counts per million (logCPM) in the H 2 O controls. All differential tests represent testing between three (RNA-seq) or two (ATAC-seq and ChIP-seq) biological replicates per condition. RNA-seq plots also denote miR30A, which is part of the shRNA hairpin. ( C ) Genome view of the chromosome 6: 108,541,111–108,580,815 (hg38) locus. Gene annotation track, CpG islands (red), and DPPA2/4 peaks (purple) are shown above . Tracks show averaged DPPA2 ( n = 2) and DPPA4 ( n = 2) ChIPs and DPPA2 ( n = 1) and DPPA4 ( n = 1) CUT&RUN. The bottom eight tracks show averaged ATAC-seq, H3K4me3 ChIP-seq, H3K27me3 ChIP-seq, and H2AK119ub ChIP-seq for control versus DOX-induced shDPPA2+shRPPA4 cells ( n = 2 each for H 2 O and DOX). Differential H2AK119ub peaks are depicted below . All scales are in counts per million per base pair. ( D ) Heat maps of genomic regions centered on depleted H2AK119ub peaks ( top three row groups;depleted in both shDPPA4 and shDPPA2+4 [peach; n = 1070], depleted in shDPPA4 [purple; n = 2918], and depleted in shDPPA2+4 [blue; n = 859]) versus stable random regions ( bottom group of rows; black; n = 500). Regions have been resized to ±5 kb from the center of each peak and split into 100 equal windows. Columns represent average DPPA2 ( n = 2) and DPPA4 ( n = 2) ChIPs and DPPA2 ( n = 1) and DPPA4 ( n = 1) CUT&RUN in parental cells (scaled counts per million per base pair values across all regions for visualization) and averaged ATAC-seq, H3K4me3, H3K27me3, and H2AK119ub ChIP-seq for shDPPA4 and shDPPA2+4 ( n = 2 each for H 2 O and DOX; unscaled counts per million per base pair). ( E ) Proportional bar plot of overlapping histone modifications (H3K4me3 and H3K27me3) and/or DPPA2+4 binding in all ( left column) or subsets of H2AK119ub regions depleted in shDPPA4 (second column), shDPPA2+4 (third column), or both shDPPA4 and shDPPA2+4 ( right column). Total number of peaks per category are annotated above each bar. ( F ) Box plots of averaged RNA-seq data from parental NCI-H661 cells ( n = 3) across different categories of H2AK119ub-marked promoters as well as the top 10% and bottom 10% of all expressed genes as controls. Units are in transcripts per million (log 10 TPM+1). ( G ) Venn diagram showing the overlap of DPPA2 RIME and DPPA4 RIME hits. ( H ) Scatter plot showing average fold enrichment over IgG for RING1B ( X -axis) and PCGF1 ( Y -axis) over 200 bp bins genome-wide. Highlighted are regions overlapping H2AK119ub peaks that are depleted in shDPPA4 (purple), shDPPA2+4 (blue), or both shDPPA4 and shDPPA2+4 (orange). ( I ) Genome view of the chromosome 11: 31,686,162–31,937,375 (hg38) locus. Gene annotation track and CpG islands (red) are shown above , and DPPA2/4 peaks (purple) and H2AK119ub-depleted peaks (red) are shown below . Tracks show individual mouse IgG ( n = 1), rabbit IgG ( n = 1), DPPA4 ( n = 1), RING1B ( n = 1), and PCGF1 ( n = 1) CUT&RUN for control versus DOX-induced shDPPA4 or shDPPA2+shDPPA4 cells. All scales are in counts per million per base pair. ( J ) Box plots of RING1B enrichment in counts per million (log 2 CPM) between control (gray) and DOX-treated (orange) shDPPA2+4 cells at H2AK119ub peaks downregulated in shDPPA4 and/or DPPA2+4 compared with a subset of stable H2AK119ub peaks.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8344/pmc13138344/pmc13138344__756f04.jpg)
