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K-562

RRID:CVCL_0004

Organism

Homo sapiens

Comments

Part of: Cancer Cell Line Encyclopedia (CCLE) project. Part of: COSMIC cell lines project. Part of: ENCODE project common cell types; tier 1. Part of: LL-100 blood cancer cell line panel. Part of: MD Anderson Cell Lines Project. Part of: NCI-60 cancer cell line panel. Doubling time: 47 hours (PubMed=25984343); 19.6 hours (NCI-DTP); ~30-40 hours (DSMZ). HLA typing: A*11:01:01,31:01:02; B*18,40; C*03; DPB1*04:01,04:02; DQB1*02:01,03:02; DRB1*03,04 (PubMed=15748285). HLA typing: A*11; B*40,35/39; C*05,03 (PubMed=25960936). Microsatellite instability: Stable (MSS) (PubMed=23671654; Sanger). Sequence variation: BCR-ABL1 gene fusion. Sequence variation: Homozygous for TP53 p.Gln136fs*13 (c.406_407insC) (PubMed=17088437; PubMed=18277095). Omics: Array-based CGH. Omics: CNV analysis. Omics: Deep antibody staining analysis. Omics: Deep exome analysis. Omics: Deep proteome analysis. Omics: Deep quantitative phosphoproteome analysis. Omics: Deep RNAseq analysis. Omics: DNA methylation analysis. Omics: Fluorescence phenotype profiling. Omics: Genome sequenced. Omics: H2A.Z; ChIP-seq epigenome analysis. Omics: H3K27ac ChIP-seq epigenome analysis. Omics: H3K27me3 ChIP-seq epigenome analysis. Omics: H3K36me3 ChIP-seq epigenome analysis. Omics: H3K4me1 ChIP-seq epigenome analysis. Omics: H3K4me2 ChIP-seq epigenome analysis. Omics: H3K4me3 ChIP-seq epigenome analysis. Omics: H3K79me2 ChIP-seq epigenome analysis. Omics: H3K9ac ChIP-seq epigenome analysis. Omics: H3K9me1 ChIP-seq epigenome analysis. Omics: H3K9me3 ChIP-seq epigenome analysis. Omics: H4K20me1 ChIP-seq epigenome analysis. Omics: Pol2; ChIP-seq epigenome analysis. Omics: lncRNA expression profiling. Omics: Metabolome analysis. Omics: Protein expression by reverse-phase protein arrays. Omics: shRNA library screening. Omics: SNP array analysis. Omics: Transcriptome analysis. Omics: Virome analysis using proteomics. Genome ancestry: African=5.19%; Native American=0%; East Asian, North=8.4%; East Asian, South=0%; South Asian=0%; European, North=43.44%; European, South=42.97% (PubMed=30894373). Misspelling: K-652; In Cosmic 1523829. Misspelling: K652; In Cosmic 1516632 and Cosmic 2024372. Derived from sampling site: Pleural effusion. DT Created: 04-04-12; Last updated: 05-07-19; Version: 31

Proper Citation

RCB Cat# RCB1897, RRID:CVCL_0004

Category

Cancer cell line DT Created: 04-04-12; Last updated: 05-07-19; Version: 31

Sex

DT Created: 04-04-12; Last updated: 05-07-19; Version: 31

Synonyms

K562, K 562, GM05372, GM05372E DT Created: 04-04-12, Last updated: 05-07-19, Version: 31

Vendor

RCB

Cat Num

RCB1897

Cross References

BTO; BTO:0000664 CLO; CLO_0007050 CLO; CLO_0007059 CLO; CLO_0024880 CLO; CLO_0050123 CLO; CLO_0050124 CLO; CLO_0050126 EFO; EFO_0002067 MCCL; MCC:0000261 CLDB; cl2967 CLDB; cl2969 CLDB; cl2970 CLDB; cl2971 CLDB; cl2972 CLDB; cl2973 CLDB; cl2974 CLDB; cl2976 CLDB; cl2978 CLDB; cl2979 CLDB; cl2980 CLDB; cl2981 CLDB; cl2982 CLDB; cl2984 4DN; 4DNSRP5XBV7W 4DN; 4DNSRWQFKJYO AddexBio; C0003004/52 ArrayExpress; E-MTAB-2706 ArrayExpress; E-MTAB-2770 ArrayExpress; E-MTAB-3610 ArrayExpress; E-MTAB-7721 ArrayExpress; E-MTAB-7722 ATCC; CCL-243 BCRC; 60007 BCRJ; 0126 BioSample; SAMN03472111 BioSample; SAMN03473172 BioSample; SAMN03473407 BioSample; SAMN10988357 CCLE; K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE CCLV; CCLV-RIE 0439 CCRID; 3111C0001CCC000039 CCRID; 3111C0002000000026 CCRID; 3131C0001000700029 CCRID; 3142C0001000000037 CCRID; 3153C0001000000012 CCTCC; GDC0037 Cell_Model_Passport; SIDM00791 CGH-DB; 9215-4 ChEMBL-Cells; CHEMBL3308378 ChEMBL-Targets; CHEMBL385 CLS; 300224/p473_K-562 Coriell; GM05372 Cosmic; 683655 Cosmic; 755290 Cosmic; 759897 Cosmic; 760646 Cosmic; 787495 Cosmic; 798223 Cosmic; 798664 Cosmic; 850384 Cosmic; 851999 Cosmic; 875864 Cosmic; 897450 Cosmic; 905940 Cosmic; 919127 Cosmic; 922682 Cosmic; 924039 Cosmic; 932771 Cosmic; 949095 Cosmic; 974253 Cosmic; 991559 Cosmic; 994173 Cosmic; 998760 Cosmic; 999774 Cosmic; 1012074 Cosmic; 1019830 Cosmic; 1026565 Cosmic; 1037680 Cosmic; 1044253 Cosmic; 1067445 Cosmic; 1070699 Cosmic; 1078718 Cosmic; 1089521 Cosmic; 1092608 Cosmic; 1107181 Cosmic; 1118473 Cosmic; 1127251 Cosmic; 1175856 Cosmic; 1176584 Cosmic; 1191694 Cosmic; 1226862 Cosmic; 1305338 Cosmic; 1312324 Cosmic; 1319552 Cosmic; 1325761 Cosmic; 1465965 Cosmic; 1516632 Cosmic; 1523829 Cosmic; 1524846 Cosmic; 1601068 Cosmic; 1604867 Cosmic; 1779132 Cosmic; 1998450 Cosmic; 2009516 Cosmic; 2024372 Cosmic; 2089675 Cosmic; 2301564 Cosmic; 2649242 Cosmic; 2651386 Cosmic-CLP; 905940 DepMap; ACH-000551 DSMZ; ACC-10 ECACC; 89121407 ENCODE; ENCBS001TOZ ENCODE; ENCBS004ALC ENCODE; ENCBS005AIZ ENCODE; ENCBS005ZXA ENCODE; ENCBS007IVF ENCODE; ENCBS007ZNT ENCODE; ENCBS008XYP ENCODE; ENCBS010SYB ENCODE; ENCBS011IBX ENCODE; ENCBS013BQD ENCODE; ENCBS013ENT ENCODE; ENCBS013GDO ENCODE; ENCBS013VIB ENCODE; ENCBS014ZBK ENCODE; ENCBS014ZUQ ENCODE; ENCBS016BTC ENCODE; ENCBS016SET ENCODE; ENCBS016SXN ENCODE; ENCBS016YMK ENCODE; ENCBS017GMY ENCODE; ENCBS017IKU ENCODE; ENCBS017YLT ENCODE; ENCBS018CRO ENCODE; ENCBS019QZZ ENCODE; ENCBS020IUG ENCODE; ENCBS021PJN ENCODE; ENCBS022LAM ENCODE; ENCBS023DBL ENCODE; ENCBS023ECI ENCODE; ENCBS023EVI ENCODE; ENCBS023XVB ENCODE; ENCBS023YVH ENCODE; ENCBS024UMN ENCODE; ENCBS024ZBK ENCODE; ENCBS025CUE ENCODE; ENCBS025ONJ ENCODE; ENCBS026DNX ENCODE; ENCBS026IRF ENCODE; ENCBS026LKC ENCODE; ENCBS027GJN ENCODE; ENCBS029GNW ENCODE; ENCBS031HYV ENCODE; ENCBS031YPZ ENCODE; ENCBS036OIX ENCODE; ENCBS038KVF ENCODE; ENCBS038TWG ENCODE; ENCBS039ENC ENCODE; ENCBS039FPC ENCODE; ENCBS040EUG ENCODE; ENCBS040IKC ENCODE; ENCBS044UVO ENCODE; ENCBS044WJW ENCODE; ENCBS048GNZ ENCODE; ENCBS049QOP ENCODE; ENCBS049ZAC ENCODE; ENCBS051ELN ENCODE; ENCBS053JIZ ENCODE; ENCBS055ZTI ENCODE; ENCBS056HKT ENCODE; ENCBS058KXV ENCODE; ENCBS058MBJ ENCODE; ENCBS058XGI ENCODE; ENCBS060HRB ENCODE; ENCBS061SQD ENCODE; ENCBS061XBB ENCODE; ENCBS063NCT ENCODE; ENCBS063ROH ENCODE; ENCBS065RXZ ENCODE; ENCBS070OMK ENCODE; ENCBS071UNK ENCODE; ENCBS073JAL ENCODE; ENCBS074HIZ ENCODE; ENCBS078NQM ENCODE; ENCBS078OYF ENCODE; ENCBS079AJY ENCODE; ENCBS079MXX ENCODE; ENCBS081NLE ENCODE; ENCBS082JRQ ENCODE; ENCBS083ACT ENCODE; ENCBS083CLD ENCODE; ENCBS084MBW ENCODE; ENCBS086JQA ENCODE; ENCBS087RNA ENCODE; ENCBS088RNA ENCODE; ENCBS089OTW ENCODE; ENCBS091YRZ ENCODE; ENCBS092VTJ ENCODE; ENCBS093NNC ENCODE; ENCBS099HZF ENCODE; ENCBS101QRF ENCODE; ENCBS103HEN ENCODE; ENCBS106FRJ ENCODE; ENCBS107DSY ENCODE; ENCBS109ENC ENCODE; ENCBS109VHI ENCODE; ENCBS110VVJ ENCODE; ENCBS111BRF ENCODE; ENCBS111GYT ENCODE; ENCBS111RFA ENCODE; ENCBS113YMQ ENCODE; ENCBS118YJZ ENCODE; ENCBS119EVP ENCODE; ENCBS119WDQ ENCODE; ENCBS123DAX ENCODE; ENCBS123QRB ENCODE; ENCBS123YCA ENCODE; ENCBS125ACM ENCODE; ENCBS125WRA ENCODE; ENCBS126AJR ENCODE; ENCBS128EWC ENCODE; ENCBS128UKH ENCODE; ENCBS131FDE ENCODE; ENCBS132EBC ENCODE; ENCBS133VWK ENCODE; ENCBS136ZNW ENCODE; ENCBS138SLH ENCODE; ENCBS139SNH ENCODE; ENCBS140MLH ENCODE; ENCBS140NYG ENCODE; ENCBS143LJI ENCODE; ENCBS143XSU ENCODE; ENCBS144YDQ ENCODE; ENCBS145IJT ENCODE; ENCBS146WJY ENCODE; ENCBS148ZBT ENCODE; ENCBS149SJX ENCODE; ENCBS151LUO ENCODE; ENCBS152EMG ENCODE; ENCBS152WCA ENCODE; ENCBS152XKV ENCODE; ENCBS153VBF ENCODE; ENCBS154XYR ENCODE; ENCBS155KGP ENCODE; ENCBS158FRU ENCODE; ENCBS158KSS ENCODE; ENCBS159KYP ENCODE; ENCBS159UIB ENCODE; ENCBS162AGB ENCODE; ENCBS162UQR ENCODE; ENCBS164AGP ENCODE; ENCBS164ITK ENCODE; ENCBS165ART ENCODE; ENCBS165NPS ENCODE; ENCBS166BGG ENCODE; ENCBS166SNL ENCODE; ENCBS169BBI ENCODE; ENCBS170ZQG ENCODE; ENCBS171PLV ENCODE; ENCBS172RAU ENCODE; ENCBS173WPT ENCODE; ENCBS174LOJ ENCODE; ENCBS174YKM ENCODE; ENCBS175JIH ENCODE; ENCBS175LWC ENCODE; ENCBS175LZM ENCODE; ENCBS177FZX ENCODE; ENCBS177LGN ENCODE; ENCBS180BMC ENCODE; ENCBS181AJG ENCODE; ENCBS182ISG ENCODE; ENCBS182RTT ENCODE; ENCBS182SAO ENCODE; ENCBS184UCR ENCODE; ENCBS185RGL ENCODE; ENCBS190TRO ENCODE; ENCBS192SEZ ENCODE; ENCBS193JEH ENCODE; ENCBS193QNA ENCODE; ENCBS193WKG ENCODE; ENCBS195ZWQ ENCODE; ENCBS198UTW ENCODE; ENCBS198YII ENCODE; ENCBS199SKB ENCODE; ENCBS200VZF ENCODE; ENCBS201EIP ENCODE; ENCBS201LYR ENCODE; ENCBS204NMW ENCODE; ENCBS205QYW ENCODE; ENCBS207UAM ENCODE; ENCBS209TDT ENCODE; ENCBS209TSR ENCODE; ENCBS210WPX ENCODE; ENCBS211WEE ENCODE; ENCBS215KUV ENCODE; ENCBS216WMI ENCODE; ENCBS217DFO ENCODE; ENCBS218LCA ENCODE; ENCBS218QRN ENCODE; ENCBS218ZAA ENCODE; ENCBS220ZHX ENCODE; ENCBS221UJD ENCODE; ENCBS221YFO ENCODE; ENCBS222CHH ENCODE; ENCBS222QCU ENCODE; ENCBS225YVR ENCODE; ENCBS226YIA ENCODE; ENCBS228CEB ENCODE; ENCBS230JWL ENCODE; ENCBS232KKV ENCODE; ENCBS237BHV ENCODE; ENCBS237MFM ENCODE; ENCBS237RBH ENCODE; ENCBS243YEC ENCODE; ENCBS243YPN ENCODE; ENCBS244ZUD ENCODE; ENCBS245AME ENCODE; ENCBS250CMV ENCODE; ENCBS250HLF ENCODE; ENCBS250IAJ ENCODE; ENCBS252OWV ENCODE; ENCBS253VOZ ENCODE; ENCBS254JMT ENCODE; ENCBS254KOX ENCODE; ENCBS254WUV ENCODE; ENCBS257HMY ENCODE; ENCBS257PZA ENCODE; ENCBS261MYX ENCODE; ENCBS262OLW ENCODE; ENCBS263GNB ENCODE; ENCBS268LPU ENCODE; ENCBS270GGH ENCODE; ENCBS270OAE ENCODE; ENCBS271BPH ENCODE; ENCBS271WWU ENCODE; ENCBS272SXA ENCODE; ENCBS274WIM ENCODE; ENCBS275HBP ENCODE; ENCBS278ISQ ENCODE; ENCBS278LNR ENCODE; ENCBS280PHL ENCODE; ENCBS283QAE ENCODE; ENCBS283TEI ENCODE; ENCBS284MJG ENCODE; ENCBS285VBM ENCODE; ENCBS287TWJ ENCODE; ENCBS288EEL ENCODE; ENCBS290OFW ENCODE; ENCBS292NBI ENCODE; ENCBS293BDC ENCODE; ENCBS293ZDP ENCODE; ENCBS298QZZ ENCODE; ENCBS301EZU ENCODE; ENCBS302IGJ ENCODE; ENCBS305KEA ENCODE; ENCBS306NPK ENCODE; ENCBS311LNQ ENCODE; ENCBS313HKT ENCODE; ENCBS316CKF ENCODE; ENCBS318IMK ENCODE; ENCBS320BUL ENCODE; ENCBS322JPK ENCODE; ENCBS323NUL ENCODE; ENCBS323WRW ENCODE; ENCBS324XGY ENCODE; ENCBS324YAG ENCODE; ENCBS326ULG ENCODE; ENCBS328LML ENCODE; ENCBS330LHC ENCODE; ENCBS331OZE ENCODE; ENCBS333OTT ENCODE; ENCBS334VOL ENCODE; ENCBS339WIS ENCODE; ENCBS340AMO ENCODE; ENCBS341TAT ENCODE; ENCBS344LIE ENCODE; ENCBS344ZTN ENCODE; ENCBS345PNA ENCODE; ENCBS346YOL ENCODE; ENCBS348UOE ENCODE; ENCBS349ULG ENCODE; ENCBS351GWD ENCODE; ENCBS354VJM ENCODE; ENCBS355BRH ENCODE; ENCBS356NKY ENCODE; ENCBS357GME ENCODE; ENCBS358PHP ENCODE; ENCBS359TRM ENCODE; ENCBS360VVZ ENCODE; ENCBS360YEH ENCODE; ENCBS361MEX ENCODE; ENCBS362YBS ENCODE; ENCBS363HPO ENCODE; ENCBS365DFQ ENCODE; ENCBS366CLP ENCODE; ENCBS368MWR ENCODE; ENCBS370QIM ENCODE; ENCBS370ZIR ENCODE; ENCBS371NDR ENCODE; ENCBS373HMN ENCODE; ENCBS374DHY ENCODE; ENCBS376UCQ ENCODE; ENCBS378DFU ENCODE; ENCBS379NWT ENCODE; ENCBS380BDK ENCODE; ENCBS380IYL ENCODE; ENCBS380NDS ENCODE; ENCBS383JPN ENCODE; ENCBS383VKK ENCODE; ENCBS388NGV ENCODE; ENCBS388YAM ENCODE; ENCBS388ZVM ENCODE; ENCBS392QEL ENCODE; ENCBS393YUA ENCODE; ENCBS394LTC ENCODE; ENCBS396JPQ ENCODE; ENCBS396WFI ENCODE; ENCBS397GXE ENCODE; ENCBS397OLQ ENCODE; ENCBS398SSI ENCODE; ENCBS400CRG ENCODE; ENCBS400HFL ENCODE; ENCBS400IMH ENCODE; ENCBS400MFJ ENCODE; ENCBS402AEU ENCODE; ENCBS403VZZ ENCODE; ENCBS405GDI ENCODE; ENCBS406BAI ENCODE; ENCBS406RFF ENCODE; ENCBS407GJQ ENCODE; ENCBS409CCX ENCODE; ENCBS409HCD ENCODE; ENCBS410EIF ENCODE; ENCBS411BWT ENCODE; ENCBS413TJM ENCODE; ENCBS413UCH ENCODE; ENCBS415LMS ENCODE; ENCBS415MYO ENCODE; ENCBS416ZWV ENCODE; ENCBS417FMB ENCODE; ENCBS417QMS ENCODE; ENCBS418OCT ENCODE; ENCBS419NSL ENCODE; ENCBS422KVR ENCODE; ENCBS424RFS ENCODE; ENCBS425EWY ENCODE; ENCBS426MFA ENCODE; ENCBS430DZA ENCODE; ENCBS431YNM ENCODE; ENCBS432FLT ENCODE; ENCBS433HMF ENCODE; ENCBS433OVV ENCODE; ENCBS433WAM ENCODE; ENCBS438DSC ENCODE; ENCBS440DGS ENCODE; ENCBS441PSF ENCODE; ENCBS442NXE ENCODE; ENCBS442VLY ENCODE; ENCBS443DUP ENCODE; ENCBS445GUZ ENCODE; ENCBS448ECS ENCODE; ENCBS449PYL ENCODE; ENCBS450ITK ENCODE; ENCBS451AJS ENCODE; ENCBS452HCE ENCODE; ENCBS453KQD ENCODE; ENCBS455LFT ENCODE; ENCBS456EWO ENCODE; ENCBS456TNJ ENCODE; ENCBS460WQH ENCODE; ENCBS461TCT ENCODE; ENCBS463ABO ENCODE; ENCBS463GGK ENCODE; ENCBS464DIX ENCODE; ENCBS464YJN ENCODE; ENCBS465MWC ENCODE; ENCBS465RFQ ENCODE; ENCBS468YAY ENCODE; ENCBS472YQF ENCODE; ENCBS474CTB ENCODE; ENCBS474XLY ENCODE; ENCBS476AUA ENCODE; ENCBS476AXH ENCODE; ENCBS476WAQ ENCODE; ENCBS477JCG ENCODE; ENCBS477MKD ENCODE; ENCBS478TXQ ENCODE; ENCBS478USZ ENCODE; ENCBS482NAM ENCODE; ENCBS484NBA ENCODE; ENCBS486UBH ENCODE; ENCBS487XCP ENCODE; ENCBS488IUR ENCODE; ENCBS489AXI ENCODE; ENCBS489LOC ENCODE; ENCBS489PTQ ENCODE; ENCBS489ZOH ENCODE; ENCBS491FIM ENCODE; ENCBS492BQN ENCODE; ENCBS492SXA ENCODE; ENCBS494YUP ENCODE; ENCBS495MNB ENCODE; ENCBS497UCZ ENCODE; ENCBS498NIQ ENCODE; ENCBS499AAA ENCODE; ENCBS499ZBY ENCODE; ENCBS500AAA ENCODE; ENCBS501AAA ENCODE; ENCBS501AJP ENCODE; ENCBS501VGA ENCODE; ENCBS502AAA ENCODE; ENCBS502SUO ENCODE; ENCBS503AAA ENCODE; ENCBS504AAA ENCODE; ENCBS504EOJ ENCODE; ENCBS504SHW ENCODE; ENCBS505AAA ENCODE; ENCBS505ILK ENCODE; ENCBS506VSB ENCODE; ENCBS508YPA ENCODE; ENCBS509AAA ENCODE; ENCBS510AAA ENCODE; ENCBS511UGF ENCODE; ENCBS511YCF ENCODE; ENCBS512JXB ENCODE; ENCBS515TJK ENCODE; ENCBS516DKF ENCODE; ENCBS517UIR ENCODE; ENCBS517XSM ENCODE; ENCBS519PER ENCODE; ENCBS519VAI ENCODE; ENCBS521FNT ENCODE; ENCBS522JIE ENCODE; ENCBS523GIC ENCODE; ENCBS524AAA ENCODE; ENCBS526FPZ ENCODE; ENCBS526GWV ENCODE; ENCBS528AAA ENCODE; ENCBS530DUV ENCODE; ENCBS530IBU ENCODE; ENCBS530JOQ ENCODE; ENCBS530MLH ENCODE; ENCBS532KVA ENCODE; ENCBS533ETT ENCODE; ENCBS534MHY ENCODE; ENCBS534VZR ENCODE; ENCBS534WDC ENCODE; ENCBS537KCG ENCODE; ENCBS538WJZ ENCODE; ENCBS540TUC ENCODE; ENCBS540UNM ENCODE; ENCBS543YEP ENCODE; ENCBS544JRU ENCODE; ENCBS548BNW ENCODE; ENCBS549CBF ENCODE; ENCBS549CIX ENCODE; ENCBS551TRA ENCODE; ENCBS552DXA ENCODE; ENCBS552 IDC ENCODE; ENCBS552LNH ENCODE; ENCBS555BIW ENCODE; ENCBS555BYH ENCODE; ENCBS555MCX ENCODE; ENCBS556RPW ENCODE; ENCBS559ZAU ENCODE; ENCBS560YCY ENCODE; ENCBS561DIS ENCODE; ENCBS563BBS ENCODE; ENCBS565ULH ENCODE; ENCBS565XGU ENCODE; ENCBS566AKW ENCODE; ENCBS566NIL ENCODE; ENCBS569AYK ENCODE; ENCBS569WDT ENCODE; ENCBS572YNK ENCODE; ENCBS573CFY ENCODE; ENCBS574JXP ENCODE; ENCBS575FXP ENCODE; ENCBS576EJU ENCODE; ENCBS577JGM ENCODE; ENCBS577QZL ENCODE; ENCBS579CNZ ENCODE; ENCBS588YDJ ENCODE; ENCBS590KAM ENCODE; ENCBS590PKD ENCODE; ENCBS591LWJ ENCODE; ENCBS593BIQ ENCODE; ENCBS593CFU ENCODE; ENCBS594GNK ENCODE; ENCBS595QXS ENCODE; ENCBS598STC ENCODE; ENCBS599BAS ENCODE; ENCBS600AAA ENCODE; ENCBS600EDY ENCODE; ENCBS601AAA ENCODE; ENCBS601MXN ENCODE; ENCBS602AAA ENCODE; ENCBS602RSX ENCODE; ENCBS602TPG ENCODE; ENCBS603CUX ENCODE; ENCBS603PMU ENCODE; ENCBS609MYU ENCODE; ENCBS611GYD ENCODE; ENCBS613LBH ENCODE; ENCBS614RYV ENCODE; ENCBS615ZVR ENCODE; ENCBS619KUS ENCODE; ENCBS621XIY ENCODE; ENCBS622KGA ENCODE; ENCBS624RXT ENCODE; ENCBS626KTH ENCODE; ENCBS626OHB ENCODE; ENCBS626TPH ENCODE; ENCBS627GSN ENCODE; ENCBS628JQT ENCODE; ENCBS629DNR ENCODE; ENCBS630MQK ENCODE; ENCBS630NVQ ENCODE; ENCBS630OAS ENCODE; ENCBS631FGS ENCODE; ENCBS632QPM ENCODE; ENCBS636RQT ENCODE; ENCBS637RKV ENCODE; ENCBS638EYY ENCODE; ENCBS638OEZ ENCODE; ENCBS638QCL ENCODE; ENCBS639AAA ENCODE; ENCBS641AAS ENCODE; ENCBS642DEU ENCODE; ENCBS643CHR ENCODE; ENCBS643OWK ENCODE; ENCBS645RVR ENCODE; ENCBS647KYQ ENCODE; ENCBS649DTO ENCODE; ENCBS649VHZ ENCODE; ENCBS651RVZ ENCODE; ENCBS652YOG ENCODE; ENCBS654OPT ENCODE; ENCBS654PMT ENCODE; ENCBS654VZH ENCODE; ENCBS655HQL ENCODE; ENCBS656VZE ENCODE; ENCBS657MGB ENCODE; ENCBS657ZYP ENCODE; ENCBS658KIL ENCODE; ENCBS659SAO ENCODE; ENCBS661YYO ENCODE; ENCBS664AAA ENCODE; ENCBS664AUV ENCODE; ENCBS664VDB ENCODE; ENCBS666SJB ENCODE; ENCBS667AAA ENCODE; ENCBS667PRV ENCODE; ENCBS670KPG ENCODE; ENCBS673MZQ ENCODE; ENCBS674MPN ENCODE; ENCBS674VNC ENCODE; ENCBS675OVW ENCODE; ENCBS676KLB ENCODE; ENCBS677BWZ ENCODE; ENCBS677GYI ENCODE; ENCBS677HPS ENCODE; ENCBS677KBE ENCODE; ENCBS680QCR ENCODE; ENCBS681CCH ENCODE; ENCBS684JMW ENCODE; ENCBS688EQJ ENCODE; ENCBS688QTO ENCODE; ENCBS688VYK ENCODE; ENCBS690NWI ENCODE; ENCBS691GWJ ENCODE; ENCBS693EWC ENCODE; ENCBS695KRB ENCODE; ENCBS697QYY ENCODE; ENCBS697XFI ENCODE; ENCBS698AAA ENCODE; ENCBS698ZKR ENCODE; ENCBS699AAA ENCODE; ENCBS700AAA ENCODE; ENCBS701AAA ENCODE; ENCBS701VZK ENCODE; ENCBS702AAA ENCODE; ENCBS703AAA ENCODE; ENCBS703API ENCODE; ENCBS704AAA ENCODE; ENCBS704IXT ENCODE; ENCBS704YXA ENCODE; ENCBS708KJA ENCODE; ENCBS709SOB ENCODE; ENCBS709TUN ENCODE; ENCBS713VDJ ENCODE; ENCBS714PSX ENCODE; ENCBS714TRH ENCODE; ENCBS715AAA ENCODE; ENCBS715BML ENCODE; ENCBS715XGH ENCODE; ENCBS718GJU ENCODE; ENCBS719UQU ENCODE; ENCBS719YVT ENCODE; ENCBS720HYG ENCODE; ENCBS720UTF ENCODE; ENCBS721AAA ENCODE; ENCBS721OCY ENCODE; ENCBS722AAA ENCODE; ENCBS723AAA ENCODE; ENCBS723ZIW ENCODE; ENCBS724AAA ENCODE; ENCBS725AAA ENCODE; ENCBS726AAA ENCODE; ENCBS726ZFM ENCODE; ENCBS728WBV ENCODE; ENCBS729ELF ENCODE; ENCBS729IGE ENCODE; ENCBS730QNJ ENCODE; ENCBS731EBS ENCODE; ENCBS731WEZ ENCODE; ENCBS731WGV ENCODE; ENCBS732IZQ ENCODE; ENCBS732XZP ENCODE; ENCBS734NZL ENCODE; ENCBS736PRC ENCODE; ENCBS737CUP ENCODE; ENCBS739ZIJ ENCODE; ENCBS741EFJ ENCODE; ENCBS741VGS ENCODE; ENCBS744CXB ENCODE; ENCBS745CIF ENCODE; ENCBS745UXY ENCODE; ENCBS746GKH ENCODE; ENCBS746KYH ENCODE; ENCBS746YXR ENCODE; ENCBS747AAA ENCODE; ENCBS748AAA ENCODE; ENCBS748FCA ENCODE; ENCBS749AAA ENCODE; ENCBS749FNX ENCODE; ENCBS750AAA ENCODE; ENCBS751AAA ENCODE; ENCBS751EBU ENCODE; ENCBS751SXP ENCODE; ENCBS751WKI ENCODE; ENCBS752AAA ENCODE; ENCBS753DCN ENCODE; ENCBS753LXR ENCODE; ENCBS757HMX ENCODE; ENCBS764AAA ENCODE; ENCBS765AAA ENCODE; ENCBS766AAA ENCODE; ENCBS767AAA ENCODE; ENCBS767HRR ENCODE; ENCBS767XGD ENCODE; ENCBS768AAA ENCODE; ENCBS769AAA ENCODE; ENCBS770AAA ENCODE; ENCBS770VHR ENCODE; ENCBS771AAA ENCODE; ENCBS771FYB ENCODE; ENCBS771FYZ ENCODE; ENCBS771NTZ ENCODE; ENCBS772AAA ENCODE; ENCBS772SKD ENCODE; ENCBS774KGY ENCODE; ENCBS775AAA ENCODE; ENCBS775HUY ENCODE; ENCBS776AAA ENCODE; ENCBS776WTE ENCODE; ENCBS777AAA ENCODE; ENCBS778AAA ENCODE; ENCBS779AAA ENCODE; ENCBS782AAA ENCODE; ENCBS782UIO ENCODE; ENCBS783AAA ENCODE; ENCBS783CHO ENCODE; ENCBS783CHQ ENCODE; ENCBS783PTA ENCODE; ENCBS783WYV ENCODE; ENCBS784AAA ENCODE; ENCBS785AAA ENCODE; ENCBS786AAA ENCODE; ENCBS787AAA ENCODE; ENCBS788AAA ENCODE; ENCBS788CSD ENCODE; ENCBS789AAA ENCODE; ENCBS789DTV ENCODE; ENCBS790AAA ENCODE; ENCBS790JBM ENCODE; ENCBS790YFX ENCODE; ENCBS791AAA ENCODE; ENCBS792SRL ENCODE; ENCBS797SGL ENCODE; ENCBS798HJU ENCODE; ENCBS799TLB ENCODE; ENCBS800RVX ENCODE; ENCBS802AYH ENCODE; ENCBS803KFY ENCODE; ENCBS808AAA ENCODE; ENCBS808FZK ENCODE; ENCBS808ZQB ENCODE; ENCBS809AAA ENCODE; ENCBS809UHL ENCODE; ENCBS810AAA ENCODE; ENCBS811AAA ENCODE; ENCBS812AAA ENCODE; ENCBS812OIJ ENCODE; ENCBS813AAA ENCODE; ENCBS813JVE ENCODE; ENCBS814AAA ENCODE; ENCBS815AAA ENCODE; ENCBS815LSY ENCODE; ENCBS816AAA ENCODE; ENCBS818EBR ENCODE; ENCBS818WVG ENCODE; ENCBS820QHU ENCODE; ENCBS821KLW ENCODE; ENCBS822TRA ENCODE; ENCBS823LKQ ENCODE; ENCBS824PND ENCODE; ENCBS827AAA ENCODE; ENCBS827YSZ ENCODE; ENCBS828AAA ENCODE; ENCBS828OIW ENCODE; ENCBS829AAA ENCODE; ENCBS829QEL ENCODE; ENCBS829VJO ENCODE; ENCBS830AAA ENCODE; ENCBS830FSQ ENCODE; ENCBS831AAA ENCODE; ENCBS831ATS ENCODE; ENCBS831COV ENCODE; ENCBS831RAD ENCODE; ENCBS832AAA ENCODE; ENCBS833AAA ENCODE; ENCBS833OVZ ENCODE; ENCBS836YTS ENCODE; ENCBS839CNN ENCODE; ENCBS839VND ENCODE; ENCBS840AAA ENCODE; ENCBS841AAA ENCODE; ENCBS841YJV ENCODE; ENCBS842AAA ENCODE; ENCBS843AAA ENCODE; ENCBS843LHE ENCODE; ENCBS843ZIK ENCODE; ENCBS844AAA ENCODE; ENCBS846HWI ENCODE; ENCBS847CMA ENCODE; ENCBS849TDY ENCODE; ENCBS850BRB ENCODE; ENCBS850LWJ ENCODE; ENCBS850QNJ ENCODE; ENCBS851FLL ENCODE; ENCBS851WPL ENCODE; ENCBS852AAA ENCODE; ENCBS852JTF ENCODE; ENCBS852VOH ENCODE; ENCBS854WQM ENCODE; ENCBS855MYK ENCODE; ENCBS855ZEG ENCODE; ENCBS857RNB ENCODE; ENCBS861PFY ENCODE; ENCBS862RBC ENCODE; ENCBS863CBS ENCODE; ENCBS863MAI ENCODE; ENCBS864MCX ENCODE; ENCBS864OKZ ENCODE; ENCBS865CZC ENCODE; ENCBS865HYV ENCODE; ENCBS865KGU ENCODE; ENCBS865VEQ ENCODE; ENCBS869IGF ENCODE; ENCBS870PSR ENCODE; ENCBS870VQI ENCODE; ENCBS871KRX ENCODE; ENCBS871MOK ENCODE; ENCBS871QLJ ENCODE; ENCBS872JXE ENCODE; ENCBS873YKY ENCODE; ENCBS877QTV ENCODE; ENCBS877RXF ENCODE; ENCBS878WRC ENCODE; ENCBS884PXY ENCODE; ENCBS885HUO ENCODE; ENCBS885ULI ENCODE; ENCBS886PEW ENCODE; ENCBS889HPN ENCODE; ENCBS889HVK ENCODE; ENCBS889MQU ENCODE; ENCBS891EMR ENCODE; ENCBS894CLK ENCODE; ENCBS895IMG ENCODE; ENCBS895KNQ ENCODE; ENCBS897EVB ENCODE; ENCBS897PRR ENCODE; ENCBS903OGK ENCODE; ENCBS904ISV ENCODE; ENCBS904ULB ENCODE; ENCBS905JDP ENCODE; ENCBS905KZI ENCODE; ENCBS905LQS ENCODE; ENCBS906KIP ENCODE; ENCBS907QMF ENCODE; ENCBS910WHE ENCODE; ENCBS917PHA ENCODE; ENCBS918DLF ENCODE; ENCBS922LYA ENCODE; ENCBS922RYG ENCODE; ENCBS923TYZ ENCODE; ENCBS926CWO ENCODE; ENCBS931MQO ENCODE; ENCBS934FPI ENCODE; ENCBS936VOR ENCODE; ENCBS937ULR ENCODE; ENCBS941WQP ENCODE; ENCBS943ICN ENCODE; ENCBS943ODH ENCODE; ENCBS946FNG ENCODE; ENCBS946SUX ENCODE; ENCBS946YFO ENCODE; ENCBS947EGW ENCODE; ENCBS947VKK ENCODE; ENCBS947YKG ENCODE; ENCBS948HVW ENCODE; ENCBS948PVM ENCODE; ENCBS948QXW ENCODE; ENCBS949ESX ENCODE; ENCBS949FLF ENCODE; ENCBS953HJY ENCODE; ENCBS953YBZ ENCODE; ENCBS954RIE ENCODE; ENCBS957NCU ENCODE; ENCBS958BUA ENCODE; ENCBS960IYL ENCODE; ENCBS962ZXU ENCODE; ENCBS963QYF ENCODE; ENCBS963XMS ENCODE; ENCBS964MCW ENCODE; ENCBS964YGP ENCODE; ENCBS967BUS ENCODE; ENCBS967GAK ENCODE; ENCBS969AZO ENCODE; ENCBS972JLR ENCODE; ENCBS972KMH ENCODE; ENCBS973CSB ENCODE; ENCBS973MAW ENCODE; ENCBS973NFP ENCODE; ENCBS975JQF ENCODE; ENCBS978JIM ENCODE; ENCBS982AOH ENCODE; ENCBS983KMD ENCODE; ENCBS983TNS ENCODE; ENCBS984GCA ENCODE; ENCBS985INM ENCODE; ENCBS990XUV ENCODE; ENCBS992SGT ENCODE; ENCBS993NMB ENCODE; ENCBS994EIH ENCODE; ENCBS994NNW ENCODE; ENCBS994WPS ENCODE; ENCBS995UMN ENCODE; ENCBS997MUA ENCODE; ENCBS998FPD ENCODE; ENCBS998ZJJ ENCODE; ENCBS999HDT GDSC; 905940 GEO; GSM2134 GEO; GSM2136 GEO; GSM2172 GEO; GSM50195 GEO; GSM50259 GEO; GSM236784 GEO; GSM236820 GEO; GSM472910 GEO; GSM472926 GEO; GSM472927 GEO; GSM482508 GEO; GSM733651 GEO; GSM733653 GEO; GSM733656 GEO; GSM733658 GEO; GSM733675 GEO; GSM733680 GEO; GSM733692 GEO; GSM733714 GEO; GSM733719 GEO; GSM733776 GEO; GSM733777 GEO; GSM733778 GEO; GSM733786 GEO; GSM736566 GEO; GSM736629 GEO; GSM749690 GEO; GSM749733 GEO; GSM750811 GEO; GSM788082 GEO; GSM788085 GEO; GSM788087 GEO; GSM788088 GEO; GSM799347 GEO; GSM799410 GEO; GSM803378 GEO; GSM803379 GEO; GSM803380 GEO; GSM803383 GEO; GSM803384 GEO; GSM803401 GEO; GSM803402 GEO; GSM803407 GEO; GSM803408 GEO; GSM803410 GEO; GSM803414 GEO; GSM803431 GEO; GSM803439 GEO; GSM803440 GEO; GSM803441 GEO; GSM803442 GEO; GSM803443 GEO; GSM803446 GEO; GSM803447 GEO; GSM803469 GEO; GSM803470 GEO; GSM803471 GEO; GSM803473 GEO; GSM803494 GEO; GSM803504 GEO; GSM803505 GEO; GSM803515 GEO; GSM803520 GEO; GSM803523 GEO; GSM803524 GEO; GSM803525 GEO; GSM803540 GEO; GSM816655 GEO; GSM822275 GEO; GSM822310 GEO; GSM822311 GEO; GSM887193 GEO; GSM888266 GEO; GSM923448 GEO; GSM935310 GEO; GSM935311 GEO; GSM935319 GEO; GSM935336 GEO; GSM935337 GEO; GSM935338 GEO; GSM935340 GEO; GSM935343 GEO; GSM935344 GEO; GSM935355 GEO; GSM935356 GEO; GSM935358 GEO; GSM935361 GEO; GSM935368 GEO; GSM935371 GEO; GSM935372 GEO; GSM935373 GEO; GSM935374 GEO; GSM935385 GEO; GSM935392 GEO; GSM935394 GEO; GSM935401 GEO; GSM935402 GEO; GSM935407 GEO; GSM935410 GEO; GSM935411 GEO; GSM935414 GEO; GSM935425 GEO; GSM935429 GEO; GSM935433 GEO; GSM935439 GEO; GSM935464 GEO; GSM935479 GEO; GSM935481 GEO; GSM935490 GEO; GSM935494 GEO; GSM935495 GEO; GSM935496 GEO; GSM935497 GEO; GSM935499 GEO; GSM935501 GEO; GSM935502 GEO; GSM935503 GEO; GSM935516 GEO; GSM935520 GEO; GSM935532 GEO; GSM935539 GEO; GSM935540 GEO; GSM935544 GEO; GSM935547 GEO; GSM935565 GEO; GSM935568 GEO; GSM935569 GEO; GSM935574 GEO; GSM935575 GEO; GSM935576 GEO; GSM935594 GEO; GSM935595 GEO; GSM935597 GEO; GSM935598 GEO; GSM935600 GEO; GSM935616 GEO; GSM935632 GEO; GSM935633 GEO; GSM935634 GEO; GSM935642 GEO; GSM935645 GEO; GSM945165 GEO; GSM945228 GEO; GSM945294 GEO; GSM945302 GEO; GSM1003445 GEO; GSM1003447 GEO; GSM1003448 GEO; GSM1003449 GEO; GSM1003450 GEO; GSM1003452 GEO; GSM1003478 GEO; GSM1003492 GEO; GSM1003504 GEO; GSM1003507 GEO; GSM1003510 GEO; GSM1003545 GEO; GSM1003560 GEO; GSM1003563 GEO; GSM1003565 GEO; GSM1003566 GEO; GSM1003567 GEO; GSM1003568 GEO; GSM1003569 GEO; GSM1003570 GEO; GSM1003574 GEO; GSM1003575 GEO; GSM1003576 GEO; GSM1003583 GEO; GSM1003586 GEO; GSM1003608 GEO; GSM1003609 GEO; GSM1003610 GEO; GSM1003611 GEO; GSM1003620 GEO; GSM1003621 GEO; GSM1003622 GEO; GSM1003625 GEO; GSM1008567 GEO; GSM1008558 GEO; GSM1008580 GEO; GSM1008601 GEO; GSM1008602 GEO; GSM1010722 GEO; GSM1010732 GEO; GSM1010782 GEO; GSM1010820 GEO; GSM1010849 GEO; GSM1010877 GEO; GSM1010878 GEO; GSM1010890 GEO; GSM1010895 GEO; GSM1010906 GEO; GSM1153418 GEO; GSM1181317 GEO; GSM1181332 GEO; GSM1374583 GEO; GSM1669971 GEO; GSM2124641 IARC_TP53; 1985 IARC_TP53; 21424 IARC_TP53; 30210 IBRC; C10081 ICLC; HTL94001 IGRhCellID; K562 IZSLER; BS TCL 33 JCRB; JCRB0019 KCB; KCB 90029YJ KCLB; 10243 LiGeA; CCLE_012 LINCS_LDP; LCL-1103 Lonza; 101 MeSH; D020014 NCBI_Iran; C122 NCI-DTP; K-562 PRIDE; PRD000032 PRIDE; PRD000229 PRIDE; PXD000216 PRIDE; PRD000345 PRIDE; PXD001352 PRIDE; PXD002383 PRIDE; PXD002395 PRIDE; PXD002836 PRIDE; PXD003664 PRIDE; PXD005942 RCB; RCB0027 RCB; RCB1635 RCB; RCB1897 SKY/M-FISH/CGH; 2811 TKG; TKG 0210 TOKU-E; 2086 TOKU-E; 3631 Wikidata; Q6324626 DT Created: 04-04-12; Last updated: 05-07-19; Version: 31

Unbiased Combinatorial Screening Identifies a Bispecific IgG1 that Potently Inhibits HER3 Signaling via HER2-Guided Ligand Blockade.

  • Geuijen CAW
  • Cancer Cell
  • 2018 May 14

Literature context:


Abstract:

HER2-driven cancers require phosphatidylinositide-3 kinase (PI3K)/Akt signaling through HER3 to promote tumor growth and survival. The therapeutic benefit of HER2-targeting agents, which depend on PI3K/Akt inhibition, can be overcome by hyperactivation of the heregulin (HRG)/HER3 pathway. Here we describe an unbiased phenotypic combinatorial screening approach to identify a bispecific immunoglobulin G1 (IgG1) antibody against HER2 and HER3. In tumor models resistant to HER2-targeting agents, the bispecific IgG1 potently inhibits the HRG/HER3 pathway and downstream PI3K/Akt signaling via a "dock & block" mechanism. This bispecific IgG1 is a potentially effective therapy for breast cancer and other tumors with hyperactivated HRG/HER3 signaling.

Funding information:
  • Wellcome Trust - (United Kingdom)

Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing bisphosphonates.

  • Yu Z
  • Elife
  • 2018 May 10

Literature context:


Abstract:

Nitrogen-containing-bisphosphonates (N-BPs) are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here, we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance.

Funding information:
  • NIA NIH HHS - K99 AG047255()
  • NIA NIH HHS - R00 AG047255()
  • NIDDK NIH HHS - DK59512(United States)

Overcoming Resistance to Targeted Anticancer Therapies through Small-Molecule-Mediated MEK Degradation.

  • Peh J
  • Cell Chem Biol
  • 2018 May 18

Literature context:


Abstract:

The discovery of mutant or fusion kinases that drive oncogenesis, and the subsequent approval of specific inhibitors for these enzymes, has been instrumental in the management of some cancers. However, acquired resistance remains a significant problem in the clinic, limiting the long-term effectiveness of most of these drugs. Here we demonstrate a general strategy to overcome this resistance through drug-induced MEK cleavage (via direct procaspase-3 activation) combined with targeted kinase inhibition. This combination effect is shown to be general across diverse tumor histologies (melanoma, lung cancer, and leukemia) and driver mutations (mutant BRAF or EGFR, fusion kinases EML4-ALK and BCR-ABL). Caspase-3-mediated degradation of MEK kinases results in sustained pathway inhibition and substantially delayed or eliminated resistance in cancer cells in a manner far superior to combinations with MEK inhibitors. These data suggest the generality of drug-mediated MEK kinase cleavage as a therapeutic strategy to prevent resistance to targeted anticancer therapies.

Funding information:
  • NCI NIH HHS - R01 CA120439()
  • NIAID NIH HHS - R01-AI043356(United States)
  • NIGMS NIH HHS - T32 GM070421()

CD69 partially inhibits apoptosis and erythroid differentiation via CD24, and their knockdown increase imatinib sensitivity in BCR-ABL-positive cells.

  • Huang SY
  • J. Cell. Physiol.
  • 2018 Apr 18

Literature context:


Abstract:

Chronic myeloid leukemia (CML) is caused by a constitutively active BCR-ABL tyrosine kinase. Tyrosine kinase inhibitors (TKIs) imatinib and its derivatives represent a breakthrough for CML therapy, but the use of TKI alone is ineffective for many CML patients. CD69, an early activation marker of lymphocytes, participates in immune and inflammatory responses. Previous studies revealed that BCR-ABL upregulates CD69 expression; however, the role of CD69 in CML cells is unknown. Here, we demonstrate that BCR-ABL induced CD69 promoter activity and mRNA and protein expression via the NF-κB pathway. CD69 knockdown partially increased apoptosis and expression of erythroid differentiation markers, α-globin, ζ-globin, and glycophorin A, and increased imatinib sensitivity in K562 and KU812 CML cells. Gene microarray analysis and quantitative real-time PCR verified that CD24, an oncogenic gene, downregulated in K562 cells upon CD69 knockdown. CD69 overexpression increased, whereas CD69 knockdown inhibited CD24 promoter activity and mRNA and protein levels. CD24 knockdown also partially increased apoptosis, erythroid differentiation, and imatinib sensitivity in K562 cells, whereas its overexpression inhibited the effects of CD69 knockdown on apoptosis, erythroid differentiation, and imatinib sensitivity in K562 cells. Imatinib-induced apoptosis and erythroid differentiation were also inhibited by CD69 or CD24 overexpression in BCR-ABL-expressing CML cell lines and CD34+ cells. Taken together, CD24 is a downstream effector of CD69. CD69 and CD24 partially inhibit apoptosis and erythroid differentiation in CML cells; thus, they may be potential targets to increase imatinib sensitivity.

Funding information:
  • NCI NIH HHS - UO1CA153086(United States)

Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.

  • Nussbacher JK
  • Mol. Cell
  • 2018 Mar 15

Literature context:


Abstract:

RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced UV crosslinking followed by immunoprecipitation (eCLIP) datasets for 126 RBPs to discover miR-encoding genomic loci that are statistically enriched for RBP binding. We find that 92% of RBPs interact directly with at least one miR locus, and that some interactions are cell line specific despite expression of the miR locus in both cell lines evaluated. We validated that ILF3 and BUD13 directly interact with and stabilize miR-144 and that BUD13 suppresses mir-210 processing to the mature species. We also observed that DDX3X regulates primary miR-20a, while LARP4 stabilizes precursor mir-210. Our approach to identifying regulators of miR loci can be applied to any user-defined RNA annotation, thereby guiding the discovery of uncharacterized regulators of RNA processing.

Funding information:
  • Howard Hughes Medical Institute - 5T32GM007454(United States)

The Histone Chaperones ASF1 and CAF-1 Promote MMS22L-TONSL-Mediated Rad51 Loading onto ssDNA during Homologous Recombination in Human Cells.

  • Huang TH
  • Mol. Cell
  • 2018 Mar 1

Literature context:


Abstract:

The access-repair-restore model for the role of chromatin in DNA repair infers that chromatin is a mere obstacle to DNA repair. However, here we show that blocking chromatin assembly, via knockdown of the histone chaperones ASF1 or CAF-1 or a mutation that prevents ASF1A binding to histones, hinders Rad51 loading onto ssDNA during homologous recombination. This is a consequence of reduced recruitment of the Rad51 loader MMS22L-TONSL to ssDNA, resulting in persistent RPA foci, extensive DNA end resection, persistent activation of the ATR-Chk1 pathway, and cell cycle arrest. In agreement, histones occupy ssDNA during DNA repair in yeast. We also uncovered DNA-PKcs-dependent DNA damage-induced ASF1A phosphorylation, which enhances chromatin assembly, promoting MMS22L-TONSL recruitment and, hence, Rad51 loading. We propose that transient assembly of newly synthesized histones onto ssDNA serves to recruit MMS22L-TONSL to efficiently form the Rad51 nucleofilament for strand invasion, suggesting an active role of chromatin assembly in homologous recombination.

Funding information:
  • Intramural NIH HHS - (United States)
  • NCI NIH HHS - R01 CA095641()

The Dietary Supplement Chondroitin-4-Sulfate Exhibits Oncogene-Specific Pro-tumor Effects on BRAF V600E Melanoma Cells.

  • Lin R
  • Mol. Cell
  • 2018 Mar 15

Literature context:


Abstract:

Dietary supplements such as vitamins and minerals are widely used in the hope of improving health but may have unidentified risks and side effects. In particular, a pathogenic link between dietary supplements and specific oncogenes remains unknown. Here we report that chondroitin-4-sulfate (CHSA), a natural glycosaminoglycan approved as a dietary supplement used for osteoarthritis, selectively promotes the tumor growth potential of BRAF V600E-expressing human melanoma cells in patient- and cell line-derived xenograft mice and confers resistance to BRAF inhibitors. Mechanistically, chondroitin sulfate glucuronyltransferase (CSGlcA-T) signals through its product CHSA to enhance casein kinase 2 (CK2)-PTEN binding and consequent phosphorylation and inhibition of PTEN, which requires CHSA chains and is essential to sustain AKT activation in BRAF V600E-expressing melanoma cells. However, this CHSA-dependent PTEN inhibition is dispensable in cancer cells expressing mutant NRAS or PI3KCA, which directly activate the PI3K-AKT pathway. These results suggest that dietary supplements may exhibit oncogene-dependent pro-tumor effects.

Funding information:
  • NCI NIH HHS - R01 CA140515()
  • NCI NIH HHS - R01 CA174786()
  • NCI NIH HHS - R01 CA183594()
  • Wellcome Trust - 090532(United Kingdom)

ORY-1001, a Potent and Selective Covalent KDM1A Inhibitor, for the Treatment of Acute Leukemia.

  • Maes T
  • Cancer Cell
  • 2018 Mar 12

Literature context:


Abstract:

The lysine-specific demethylase KDM1A is a key regulator of stem cell potential in acute myeloid leukemia (AML). ORY-1001 is a highly potent and selective KDM1A inhibitor that induces H3K4me2 accumulation on KDM1A target genes, blast differentiation, and reduction of leukemic stem cell capacity in AML. ORY-1001 exhibits potent synergy with standard-of-care drugs and selective epigenetic inhibitors, reduces growth of an AML xenograft model, and extends survival in a mouse PDX (patient-derived xenograft) model of T cell acute leukemia. Surrogate pharmacodynamic biomarkers developed based on expression changes in leukemia cell lines were translated to samples from patients treated with ORY-1001. ORY-1001 is a selective KDM1A inhibitor in clinical trials and is currently being evaluated in patients with leukemia and solid tumors.

Funding information:
  • NCI NIH HHS - 1 P50 CA121974(United States)

LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia.

  • Tarumoto Y
  • Mol. Cell
  • 2018 Mar 15

Literature context:


Abstract:

The lineage-specific transcription factor (TF) MEF2C is often deregulated in leukemia. However, strategies to target this TF have yet to be identified. Here, we used a domain-focused CRISPR screen to reveal an essential role for LKB1 and its Salt-Inducible Kinase effectors (SIK3, in a partially redundant manner with SIK2) to maintain MEF2C function in acute myeloid leukemia (AML). A key phosphorylation substrate of SIK3 in this context is HDAC4, a repressive cofactor of MEF2C. Consequently, targeting of LKB1 or SIK3 diminishes histone acetylation at MEF2C-bound enhancers and deprives leukemia cells of the output of this essential TF. We also found that MEF2C-dependent leukemias are sensitive to on-target chemical inhibition of SIK activity. This study reveals a chemical strategy to block MEF2C function in AML, highlighting how an oncogenic TF can be disabled by targeting of upstream kinases.

Funding information:
  • NCI NIH HHS - P01 CA013106()
  • NCI NIH HHS - R01 CA174793()
  • NIDDK NIH HHS - DK64540(United States)

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis.

  • Khajuria RK
  • Cell
  • 2018 Mar 22

Literature context:


Abstract:

Blood cell formation is classically thought to occur through a hierarchical differentiation process, although recent studies have shown that lineage commitment may occur earlier in hematopoietic stem and progenitor cells (HSPCs). The relevance to human blood diseases and the underlying regulation of these refined models remain poorly understood. By studying a genetic blood disorder, Diamond-Blackfan anemia (DBA), where the majority of mutations affect ribosomal proteins and the erythroid lineage is selectively perturbed, we are able to gain mechanistic insight into how lineage commitment is programmed normally and disrupted in disease. We show that in DBA, the pool of available ribosomes is limited, while ribosome composition remains constant. Surprisingly, this global reduction in ribosome levels more profoundly alters translation of a select subset of transcripts. We show how the reduced translation of select transcripts in HSPCs can impair erythroid lineage commitment, illuminating a regulatory role for ribosome levels in cellular differentiation.

Funding information:
  • NHLBI NIH HHS - R33 HL120791()
  • NHLBI NIH HHS - T32 HL007574()
  • NIDDK NIH HHS - R01 DK103794()
  • NIGMS NIH HHS - R01 GM062917-06(United States)

A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response.

  • Hoshii T
  • Cell
  • 2018 Feb 22

Literature context:


Abstract:

MLL/SET methyltransferases catalyze methylation of histone 3 lysine 4 and play critical roles in development and cancer. We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. Mutagenesis studies and CRISPR-Cas9 domain screening show the enzymatic SET domain is not necessary for AML cell survival but that a newly identified region termed the "FLOS" (functional location on SETD1A) domain is indispensable. FLOS disruption suppresses DNA damage response genes and induces p53-dependent apoptosis. The FLOS domain acts as a cyclin-K-binding site that is required for chromosomal recruitment of cyclin K and for DNA-repair-associated gene expression in S phase. These data identify a connection between the chromatin regulator SETD1A and the DNA damage response that is independent of histone methylation and suggests that targeting SETD1A and cyclin K complexes may represent a therapeutic opportunity for AML and, potentially, for other cancers.

Funding information:
  • NICHD NIH HHS - R01 HD070056-01(United States)

Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions.

  • Kim J
  • Mol. Cell
  • 2018 Jan 4

Literature context:


Abstract:

Recent integrative epigenome analyses highlight the importance of functionally distinct chromatin states for accurate cell function. How these states are established and maintained is a matter of intense investigation. Here, we present evidence for DNA damage as an unexpected means to shape a protective chromatin environment at regions of recurrent replication stress (RS). Upon aberrant fork stalling, DNA damage signaling and concomitant H2AX phosphorylation coordinate the FACT-dependent deposition of macroH2A1.2, a histone variant that promotes DNA repair by homologous recombination (HR). MacroH2A1.2, in turn, facilitates the accumulation of the tumor suppressor and HR effector BRCA1 at replication forks to protect from RS-induced DNA damage. Consequently, replicating primary cells steadily accrue macroH2A1.2 at fragile regions, whereas macroH2A1.2 loss in these cells triggers DNA damage signaling-dependent senescence, a hallmark of RS. Altogether, our findings demonstrate that recurrent DNA damage contributes to the chromatin landscape to ensure the epigenomic integrity of dividing cells.

Funding information:
  • Intramural NIH HHS - ZIA BC011282-01()
  • NIGMS NIH HHS - R01 GM073046(United States)

Abnormal Cell Sorting Underlies the Unique X-Linked Inheritance of PCDH19 Epilepsy.

  • Pederick DT
  • Neuron
  • 2018 Jan 3

Literature context:


Abstract:

X-linked diseases typically exhibit more severe phenotypes in males than females. In contrast, protocadherin 19 (PCDH19) mutations cause epilepsy in heterozygous females but spare hemizygous males. The cellular mechanism responsible for this unique pattern of X-linked inheritance is unknown. We show that PCDH19 contributes to adhesion specificity in a combinatorial manner such that mosaic expression of Pcdh19 in heterozygous female mice leads to striking sorting between cells expressing wild-type (WT) PCDH19 and null PCDH19 in the developing cortex, correlating with altered network activity. Complete deletion of PCDH19 in heterozygous mice abolishes abnormal cell sorting and restores normal network activity. Furthermore, we identify variable cortical malformations in PCDH19 epilepsy patients. Our results highlight the role of PCDH19 in determining cell adhesion affinities during cortical development and the way segregation of WT and null PCDH19 cells is associated with the unique X-linked inheritance of PCDH19 epilepsy.

Synthesis and anticancer activity of novel quinazolinone-based rhodanines.

  • El-Sayed S
  • Chem Cent J
  • 2017 Oct 13

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Abstract:

BACKGROUND: Rhodanines and quinazolinones have been reported to possess various pharmacological activities. RESULTS: A novel series of twenty quinazolinone-based rhodanines were synthesized via Knoevenagel condensation between 4-[3-(substitutedphenyl)-3,4-dihydro-4-oxoquinazolin-2-yl)methoxy]substituted-benzaldehydes and rhodanine. Elemental and spectral analysis were used to confirm structures of the newly synthesized compounds. The newly synthesized compounds were biologically evaluated for in vitro cytotoxic activity against the human fibrosarcoma cell line HT-1080 as a preliminary screen using the MTT assay. CONCLUSIONS: All the target compounds were active, displaying IC50 values roughly in the range of 10-60 µM. Structure-activity relationship study revealed that bulky, hydrophobic, and electron withdrawing substituents at the para-position of the quinazolinone 3-phenyl ring as well as methoxy substitution on the central benzene ring, enhance cytotoxic activity. The four most cytotoxic compounds namely, 45, 43, 47, and 37 were further tested against two human leukemia cell lines namely, HL-60 and K-562 and showed cytotoxic activity in the low micromolar range with compound 45 being the most active, having IC50 values of 1.2 and 1.5 μM, respectively. Interestingly, all four compounds were devoid of cytotoxicity against normal human fibroblasts strain AG01523, indicating that the synthesized rhodanines may be selectively toxic against cancer cells. Mechanistic studies revealed that the most cytotoxic target compounds exhibit pro-apoptotic activity and trigger oxidative stress in cancer cells.

Prostaglandin E1 and Its Analog Misoprostol Inhibit Human CML Stem Cell Self-Renewal via EP4 Receptor Activation and Repression of AP-1.

  • Li F
  • Cell Stem Cell
  • 2017 Sep 7

Literature context:


Abstract:

Effective treatment of chronic myelogenous leukemia (CML) largely depends on the eradication of CML leukemic stem cells (LSCs). We recently showed that CML LSCs depend on Tcf1 and Lef1 factors for self-renewal. Using a connectivity map, we identified prostaglandin E1 (PGE1) as a small molecule that partly elicited the gene expression changes in LSCs caused by Tcf1/Lef1 deficiency. Although it has little impact on normal hematopoiesis, we found that PGE1 treatment impaired the persistence and activity of LSCs in a pre-clinical murine CML model and a xenograft model of transplanted CML patient CD34+ stem/progenitor cells. Mechanistically, PGE1 acted on the EP4 receptor and repressed Fosb and Fos AP-1 factors in a β-catenin-independent manner. Misoprostol, an FDA-approved EP4 agonist, conferred similar protection against CML. These findings suggest that activation of this PGE1-EP4 pathway specifically targets CML LSCs and that the combination of PGE1/misoprostol with conventional tyrosine-kinase inhibitors could provide effective therapy for CML.

In Situ Capture of Chromatin Interactions by Biotinylated dCas9.

  • Liu X
  • Cell
  • 2017 Aug 24

Literature context:


Abstract:

Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here, we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single-copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally regulated super-enhancers reveals spatial features that causally control gene transcription. Thus, comprehensive and unbiased analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

New library construction method for single-cell genomes.

  • Xi L
  • PLoS ONE
  • 2017 Jul 20

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Abstract:

A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments. The library is then amplified by a carefully optimized PCR protocol in a uniform and synchronized fashion for next-generation sequencing. Each step of the protocol can be quantitatively characterized. Our shallow sequencing data show that the library is tightly distributed and is useful for the determination of copy number variations.

Funding information:
  • Biotechnology and Biological Sciences Research Council - BB/L010496/1(United Kingdom)

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells.

  • Pott S
  • Elife
  • 2017 Jun 27

Literature context:


Abstract:

Gaining insights into the regulatory mechanisms that underlie the transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization in single cells. Here I adapted Nucleosome Occupancy and Methylome-sequencing (NOMe-seq) to measure chromatin accessibility and endogenous DNA methylation in single cells (scNOMe-seq). scNOMe-seq recovered characteristic accessibility and DNA methylation patterns at DNase hypersensitive sites (DHSs). An advantage of scNOMe-seq is that sequencing reads are sampled independently of the accessibility measurement. scNOMe-seq therefore controlled for fragment loss, which enabled direct estimation of the fraction of accessible DHSs within individual cells. In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding events and to estimate the average nucleosome phasing distances in single cells. scNOMe-seq is therefore well-suited to characterize the chromatin organization of single cells in heterogeneous cellular mixtures.

Replication Study: Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia.

  • Shan X
  • Elife
  • 2017 Jun 27

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Abstract:

In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Fung et al., 2015), that described how we intended to replicate selected experiments from the paper "Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia" (Dawson et al., 2011). Here, we report the results of those experiments. We found treatment of MLL-fusion leukaemia cells (MV4;11 cell line) with the BET bromodomain inhibitor I-BET151 resulted in selective growth inhibition, whereas treatment of leukaemia cells harboring a different oncogenic driver (K-562 cell line) did not result in selective growth inhibition; this is similar to the findings reported in the original study (Figure 2A and Supplementary Figure 11A,B; Dawson et al., 2011). Further, I-BET151 resulted in a statistically significant decrease in BCL2 expression in MV4;11 cells, but not in K-562 cells; again this is similar to the findings reported in the original study (Figure 3D; Dawson et al., 2011). We did not find a statistically significant difference in survival when testing I-BET151 efficacy in a disseminated xenograft MLL mouse model, whereas the original study reported increased survival in I-BET151 treated mice compared to vehicle control (Figure 4B,D; Dawson et al., 2011). Differences between the original study and this replication attempt, such as different conditioning regimens and I-BET151 doses, are factors that might have influenced the outcome. We also found I-BET151 treatment resulted in a lower median disease burden compared to vehicle control in all tissues analyzed, similar to the example reported in the original study (Supplementary Figure 16A; Dawson et al., 2011). Finally, we report meta-analyses for each result.

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors.

  • Blanco-Melo D
  • Elife
  • 2017 Apr 11

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Abstract:

Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a near-complete catalog of HERV-T fossils in primate genomes allowed us to estimate a ~32 MY old ancestral sequence and reconstruct a functional envelope protein (ancHTenv) that could support infection of a pseudotyped modern gammaretrovirus. Using ancHTenv, we identify monocarboxylate transporter-1 (MCT-1) as a receptor used by HERV-T for attachment and infection. A single HERV-T provirus in hominid genomes includes an env gene (hsaHTenv) that has been uniquely preserved. This apparently exapted HERV-T env could not support virion infection but could block ancHTenv mediated infection, by causing MCT-1 depletion from cell surfaces. Thus, hsaHTenv may have contributed to HERV-T extinction, and could also potentially regulate cellular metabolism.

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.

  • Xie S
  • Mol. Cell
  • 2017 Apr 20

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Abstract:

The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population and their contribution to expression in these cells. Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a manner greatly exceeding repression of individual constituents.

Modified mRNA Vaccines Protect against Zika Virus Infection.

  • Richner JM
  • Cell
  • 2017 Mar 9

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Abstract:

The emergence of ZIKV infection has prompted a global effort to develop safe and effective vaccines. We engineered a lipid nanoparticle (LNP) encapsulated modified mRNA vaccine encoding wild-type or variant ZIKV structural genes and tested immunogenicity and protection in mice. Two doses of modified mRNA LNPs encoding prM-E genes that produced virus-like particles resulted in high neutralizing antibody titers (∼1/100,000) that protected against ZIKV infection and conferred sterilizing immunity. To offset a theoretical concern of ZIKV vaccines inducing antibodies that cross-react with the related dengue virus (DENV), we designed modified prM-E RNA encoding mutations destroying the conserved fusion-loop epitope in the E protein. This variant protected against ZIKV and diminished production of antibodies enhancing DENV infection in cells or mice. A modified mRNA vaccine can prevent ZIKV disease and be adapted to reduce the risk of sensitizing individuals to subsequent exposure to DENV, should this become a clinically relevant concern.

Funding information:
  • NIAID NIH HHS - P01 AI106695()
  • NIAID NIH HHS - R01 AI073755()
  • NIAID NIH HHS - R01 AI104972()
  • NIAID NIH HHS - R01 AI116813()

Ligand and Target Discovery by Fragment-Based Screening in Human Cells.

  • Parker CG
  • Cell
  • 2017 Jan 26

Literature context:


Abstract:

Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.

Funding information:
  • NCI NIH HHS - R01 CA132630()
  • NIDDK NIH HHS - R24 DK099810()
  • NIH HHS - S10 OD016357()

γ-Protocadherin structural diversity and functional implications.

  • Goodman KM
  • Elife
  • 2016 Oct 26

Literature context:


Abstract:

Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire γ-Pcdh ectodomain. The trans-dimer structures reveal determinants of γ-Pcdh isoform-specific homophilic recognition. We identified and structurally mapped cis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formed cis dimers, whereas γA isoforms did not, but both γA and γB isoforms could interact in cis with α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdh trans interface, and suggest that subfamily- or isoform-specific cis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code.

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.

  • Horlbeck MA
  • Elife
  • 2016 Sep 23

Literature context:


Abstract:

We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen for essential genes in K562 cells demonstrates that the large majority of sgRNAs are highly active. We also find CRISPRi does not exhibit any detectable non-specific toxicity recently observed with CRISPR nuclease approaches. Precision-recall analysis shows that we detect over 90% of essential genes with minimal false positives using a compact 5 sgRNA/gene library. Our results establish CRISPRi and CRISPRa as premier tools for loss- or gain-of-function studies and provide a general strategy for identifying Cas9 target sites.

Funding information:
  • NINDS NIH HHS - R01 NS073981(United States)