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Supplementary Text. Retinal Disease Genes for Next-Generation Sequencing in the Panels

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Supplementary Text. Retinal Disease Genes for Next-Generation Sequencing in the Panels Supplementary Text. Retinal disease genes for next-generation sequencing in the panels. Panel 1. The list of 256 genes of targeted panel sequencing. ABCA4 BBS2 CEP290 DHDDS GPR125 INVS ABCC6 BBS4 CERKL DHX38 GPR143 IQCB1 ABHD12 BBS5 CFH DMD GPR179 ITM2B ACBD5 BBS7 CHM DTHD1 GRK1 JAG1 ADAM9 BBS9 CIB2 EFEMP1 GRM6 KCNJ13 ADAMTS18 BEST1 CLN3 ELOVL4 GUCA1A KCNV2 ADGRV1 C10orf11 CLRN1 EMC1 GUCA1B KIAA1549 ADIPOR1 C12orf65 CLUAP1 ERCC6 GUCY2D KIF11 AGBL5 C1QTNF5 CNGA1 EXOSC2 HARS KIZ AHI1 C21orf2 CNGA3 EYS HGSNAT KLHL7 AIPL1 C2orf71 CNGB1 FAM161A HK1 LAMA1 ALMS1 C8orf37 CNGB3 FBLN5 HMCN1 LCA5 APOB CABP4 CNNM4 FBN1 HMX1 LART ARL2BP CACNA1F COL11A1 FLVCR1 IDH3B LRIT3 ARL3 CACNA2D4 COL2A1 FRMD7 IFT140 LRP5 ARL6 CAPN5 COL9A1 FSCN2 IFT172 LZTFL1 ATF6 CC2D2A CRB1 FZD4 IFT27 MAK ATXN7 CDH23 CRX GDF6 IFT81 MAPKAPK3 BBIP1 CDH3 CSPP1 GNAT1 IMPDH1 MERTK BBS1 CDHR1 CWC27 GNAT2 IMPG1 MFN2 BBS10 CEP164 CYP4V2 GNB3 IMPG2 MFRP BBS12 CEP250 DFNB31 GNPTG INPP5E MFSD8 MIR204 OPN1LW PLK4 RDH5 SLC24A1 TUBGCP4 MKKS OPN1MW PNPLA6 REEP6 SLC25A46 TUBGCP6 MKS1 OPN1SW POC1B RGR SLC7A14 TULP1 MTTP OTX2 POMGNT1 RGS9 SNRNP200 UNC119 MVK PANK2 PRCD RGS9BP SPATA7 USH1C MYO7A PAX2 PRDM13 RHO SPP2 USH1G NBAS PCDH15 PROM1 RIMS1 TEAD1 USH2A NDP PCYT1A PRPF3 RLBP1 TIMM8A VCAN NEK2 PDE6A PRPF31 ROM1 TIMP3 WDPCP NEUROD1 PDE6B PRPF4 RP1 TMEM126A WDR19 NMNAT1 PDE6C PRPF6 RP1L1 TMEM216 WFS1 NPHP1 PDE6G PRPF8 RP2 TMEM237 ZNF408 NPHP3 PDE6H PRPH2 RP9 TOPORS ZBF423 NPHP4 PDZD7 PRPS1 RPE65 TREX1 ZNF513 NR2E3 PEX1 RAB28 RPGR TRIM32 NR2F1 PEX2 RAX2 RPGRIP1 TRNT1 NRL PEX7 RB1 RPGRIP1L TRPM1 NYX PGK1 RBP3 RS1 TSPAN12 OAT PHYH RBP4 RTN4IP1 TTC8 OFD1 PITPNM3 RD3 SAG TTLL5 OPA1 PLA2G5 RDH11 SDCCAG8 TTPA OPA3 PLA2G6 RDH12 SEMA4A TUB Panel 2. The list of 1651 genes of clinical exome sequencing. AAAS, AARS, AARS2, ABCA3, ABCA4, ABCB6, ABCB7, ABCC6, ABCC8, ABCD3, ABHD12, ABHD5, ACBD5, ACO2, ACOX1, ACTA2, ACTB, ACTG1, ACVR1C, ADAM9, ADAMTS10, ADAMTS17, ADAMTS18, ADAMTS2, ADAMTSL3, ADAMTSL4, ADAR, ADCK3, ADGRG1, ADSL, AFF4, AFG3L2, AGA, AGBL1, AGK, AGPS, AGXT, AHI1, AIPL1, AKT1, ALDH18A1, ALDH1A3, ALG13, ALG2, ALG3, ALMS1, ALX1, ALX3, ALX4, AMPD2, ANO10, ANO5, ANO7, ANTXR1, AP1S1, AP3B1, AP4E1, APOE, APOPT1, APP, APTX, ARHGAP31, ARL13B, ARL2BP, ARL6, ARMS2, ARSA, ARSB, ARSE, ARX, ASB10, ASIP, ASPA, ASPM, ASXL1, ATCAY, ATF6, ATIC, ATM, ATN1, ATOH7, ATP1A2, ATP1A3, ATP2B3, ATP5A1, ATP6V0A2, ATRX, ATXN1, ATXN10, ATXN2, ATXN3, ATXN7, ATXN8, ATXN8OS, AUH, B3GALNT2, B3GALT6, B3GALTL, B3GAT3, B3GLCT, B3GNT1, B4GALNT1, B9D1, BAG3, BBIP1, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, BCAP31, BCOR, BCS1L, BDNF, BEAN1, BEST1, BFSP1, BFSP2, BLOC1S3, BLOC1S6, BMP2K, BMP4, BRAF, BRAT1, BRIP1, BTAF1, BTD, BUB1B, C10orf11, C10orf2, C12orf57, C12orf65, C19orf12, C2, C21orf2, C2orf71, C3, C5, C5AR2, C5orf42, C8orf37, C9, CA4, CABP4, CACNA1A, CACNA1F, CACNA2D4, CACNB4, CANT1, CAPN5, CASK, CAV1, CBS, CC2D2A, CCBE1, CCDC28B, CD5, CDH23, CDH3, CDHR1, CDKN2B, CECR1, CEP104, CEP164, CEP250, CEP290, CEP41, CERKL, CETP, CFB, CFH, CFHR1, CFHR2, CFHR3, CFHR5,CFI, CHD7, CHM, CHMP1A, CHMP4B, CHN1, CHRDL1, CHST14, CHST6, CHSY1, CIB2, CISD2, CKAP2L, CLCN5, CLDN16, CLDN19, CLN3, CLN5, CLP1, CLPB, CLRN1, CLUL1, CNBP, CNGA1, CNGA3, CNGB1, CNGB3, CNNM4, CNOT3, CNTN4, COG4, COL11A1, COL11A2, COL18A1, COL1A1, COL25A1, COL2A1, COL3A1, COL4A1, COL4A2, COL4A3, COL4A4, COL4A5, COL5A1, COL5A2, COL7A1, COL8A2, COL9A1, COL9A2, COL9A3, COLEC11, COQ2, COX10, COX14, COX15, COX20, COX6B1, COX7B, CP, CPT2, CRB1, CREBBP, CRX, CRYAA, CRYAB, CRYBA1, CRYBA2, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGB, CRYGC, CRYGD, CRYGS, CSNK2A2, CSPP1, CST3, CTC1, CTDP1, CX3CR1, CYP1B1, CYP27A1, CYP2U1, CYP46A1, CYP4V2, CYP51A1, CYP7B1, DAG1, DARS, DARS2, DCN, DCX, DDHD2, DDX58, DES, BFNB31, DGUOK, DHCR24, DHCR7, DHDDS, DIAPH1, DISP1, DKC1, DLAT, DMPK, DMXL1, DNA2, DNAJC19, DNM1L, DNM2, DNMT1, DOCK6, DPAGT1, DPM1, DPM2, DPYD, DRAM2, DTHD1, DTNBP1, EARS2, EBP, ECHS1, EDA, EDN3, EDNRB, EEF2, EFEMP1, EFNB1, EGR2, EIF2B1, EIF2B2, EIF2B3, EIF2B4, EIF2B5, ELOVL4, ELOVL5, ELP4, EMC1, ENTPD1, EPG5, EPHA2, ERBB3, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, ESCO2, ETFA, ETFB, ETFDH, EXO5, EXOSC3, EYA1, EYS, F13B, FA2H, FAH, FA M 111A , FA M 111B , FA M 120A , FA M 126A , FA M 161A , FA N C A , FA N C C , FA N C D 2, FA N C E , FA N C G , FA N C L , FA R 1, FA R S2, FA ST K D 2, FBLN5, FBN1, FBN2, FBXL4, FGF10, FGF14, FGF5, FGF8, FGFR2, FGFR3, FH, FIG4, FKBP14, FKRP, FKTN, FLNB, FLNC, FLVCR1, FMR1, FNBP4, FOXC1, FOXD3, FOXE3, FOXH1, FOXL2, FOXRED1, FRAS1, FREM1, FREM2, FRMD7, FSCN2, FTL, FXN, FYCO1, FZD4, GAL3ST3, GALC, GALE, GALK1, GALT, GAN, GATA6, GBA, GBA2, GCM2, GCNT2, GDF3, GDF6, GEMIN4, GFER, GFM1, GGCX, GJA1, GJA3, GJA8, GJB1, GJB6, GJC2, GLA, GLB1, GLI2, GLI3, GLIS3, GMPPA, GMPPB, GNAL, GNAQ, GNAS, GNAT1, GNAT2, GNB5, GNPAT, GNPTG, GPR12, GPR125, GPR143, GRP98, GRID2, GRIP1, GRK1, GRM1, GRM6, GRN, GSN, GSTM1, GSTT1, GTF2H5, GUCA1A, GUCA1B, GUCY2D, GYG2, HARS, HCCS, HDAC6, HDAC8, HESX1, HEY1, HF1, HIBCH, HK1, HMCN1, HMGB3, HMX1, HNRNPDL, HPD, HPS1, HPS3, HPS4, HPS5, HPS6, HSD17B4, HSD17B4, HSF4, HSPD1, HSPG2, HTRA1, HYLS1, IARS2, IBA57, IDH3B, IDO1, IDUA, IFIH1, IFT122, IFT140, IFT172, IFT27, IKBKAP, IKBKG, IL1A, IMMT, IMPDH1, IMPG1, IMPG2, INPP5E, INVS, IQCB1, IRF4, IRX5, ISCA2, ISPD, ITM2B, ITPR1, JAG1, JAM3, KAL1, KANK1, KANSL1, KAT6B, KATNIP, KCNA1, KCNC3, KCND3, KCNH1, KCNJ13, KCNV2, KCTD1, KDM5C, KDM6A, KIAA0586, KIAA1549, KIF11, KIF1A, KIF1B, KIF1C, KIF21A, KIF2A, KIF7, KIZ, KLHL7, KMT2D, KRAS, KRT12, KRT2, L2HGDH, LAMA1, LAMB1, LAMB2, LAMTOR2, LCA5, LCAT, LDB3, LEPREL1, LIM2, LIPC, LIPT1, LMNB1, LMX1B, LONP1, LOXHD1, LOXL1, LRAT, LRIT3, LRP2, LRP5, LRPAP1, LRPPRC, LRRC4, LSS, LTBP2, LUM, LYST, LZTFL1, MAB21L2, MAF, MAGEL2, MAK, MAN2B1, MAP2, MAP2K1, MAP2K2, MAP6, MARS2, MASP1, MATP, MBD5, MBTPS2, MC1R, MCOLN1, MED12, MED13, MED25, MERTK, MFN2, MFRP, MFSD8, MICU1, MIP, MIR184, MIR96, MITF, MKKS, MKS1, MLPH, MMACHC, MMADHC, MMP3, MMP9, MOCS1, MOCS2, MOGS, MPC1, MPDU1, MPDZ, MPLKIP, MPV17, MPZ, MRE11A, MTAP, MTFMT, MTHFR, MTO1, MTPAP, MTR, MTRR, MUTYH, MVK, MYH11, MYH3, MYH9, MYLK, MYO15A, MYO5A, MYO7A, MYOC, MYOT, NAA10, NADK2, NAGA, NALCN, NBAS, NDN, NDP, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NEK2, NEI1, NEUROD1, NF1, NF2, NHS, NIPBL, NMNAT1, NOD2, NODAL, NOP56, NOS3, NPHP1, NPHP3, NPHP4, NR2E3, NR2F1, NRAS, NRL, NSD1, NT5C1B, NT5C2, NTF4, NUBPL, NUP62, NXNL1, NYX, OAT, OCA2, OCLN, OCRL, ODZ3, OFD1, OGG1, OLFM2, OPA1, OPA3, OPHN1, OPN1LW, OPN1SW, OPTC, OPTN, OR2W3, OSMR, OSTM1, OTX2, P3H2, PAH, PAK7, PANK2, PAX2, PAX3, PAX6, PCDH15, PCK1, PCLO, PCYT1A, PDE6A, PDE6B, PDE6C, PDE6D, PDE6G, PDE6H, PDGFRB, PDHX, PDP1, PDSS1, PDSS2, PDZD7, PET100, PEX1, PEX10, PEX11B, PEX16, PEX2, PEX26, PEX5, PEX7, PGAM5, PHF6, PHGDH, PHIP, PHOX2A, PHYH, PIEZO2, PIGN, PIGT, PIK3CA, PIK3R1, PIK3R5, PIKFYVE, PITPNM3, PITX2, PITX3, PLA2G6, PLCG2, PLDN, PLK4, PLOD1, PLOD3, PLP1, PMM2, PMP22, PNPLA6, PCO1B, POLG, POLG2, POLR1C, POLR1D, POLR3A, POLR3B, POMGNT1, POMGNT2, POMK, POMT1, POMT2, PON1, PORCN, PPARGC1A, PPP2R5D, PPT1, PQBP1, PRCD, PRDM13, PRDM5, PRICKLE2, PRIMPOL, PRKAR1A, PRKCG, PRNP, PROM1, PRPF3, PRPF31, PRPF4, PRPF6, PRPF8, PRPH, PRPH2, PRPS1, PRRT2, PRSS12, PRSS56, PRX, PSAP, PTCH1, PTCH2, PTEN, PTH, PTPN11, PURA, PVRL3, PXDN, PYCR1, RAB18, RAB23, RAB27A, RAB28, RAB3GAP1, RAB3GAP2, RAD54B, RAG1, RARB, RARS, RAX, RAX2, RAXL1, RB1, RBBP8, RBM10, RBP3, RBP4, RD3, RDH11, RDH12, RDH5, RECQL4, RELN, RET, RGR, RHO, RIMS1, RIPK4, RLBP1, RNASEH2C, RNASET2, RNLS, ROM1, RP1, RP1L1, RP2, RP9, RPE65, RPGR, RPGRIP1, RPGRIP1L, RPIA, RPL11, RPL15, RPL26, RPL35A, RPL5, RPS10, RPS17, RPS19, RPS24, RPS26, RPS27A, RPS28, RPS29, RPS7, RPTOR, RRM2B, RS1, RUBCN, RYR1, SACS, SAG, SALL1, SALL4, SBF2, SC5D, SCARB1, SCARF2, SCN1A, SCN2A, SCN8A, SCO1, SCO2, SDCCAG8, SDHA, SDHAF1, SDHB, SDHD, SEC23A, SEMA3E, SEMA4A, SEPSECS, SERAC1, SERPINF1, SERPING1, SERPINI1, SETX, SH3PXD2B, SH3TC2, SHH, SIL1, SIX3, SIX5, SIX6, SKI, SKIV2L, SLC16A12, SLC16A2, SLC17A5, SLC19A2, SLC19A3, SLC1A3, SLC24A1, SLC24A4, SLC24A5, SLC25A4, SLC25A46, SLC2A10, SLC33A1, SLC35A2, SLC38A8, SLC39A5, SLC45A2, SLC4A11, SLC4A3, SLC4A4, SLC52A2, SLC7A14, SLC9A1, SLC9A6, SLITRK6, SLURP1, SMAD3, SMAD4, SMARCAL1, SMC3, SMOC1, SMS, SNAI2, SNIP1, SNRNP200, SNRPN, SNX10, SNX14, SNX3, SOD2, SOST, SOX10, SOX2, SPAST, SPATA5, SPATA7, SPG11, SPG7, SPP2, SPRTN, SPTBN2, SRD5A3, SRPX, ST3GAL5, STAMBP, STK11, STRA6, STS, STT3B, STUB1, SUCLA2, SUCLG1, SUFU, SURF1, SYNE1, SYT14, TACO1, TACSTD2, TAF2, TAL1, TAT, TBC1D20, TBC1D24, TBC1D7, TBK1, TBP, TBX15, TCF4, TCF7L1, TCF7L2, TCIRG1, TCOF1, TCTN1, TCTN2, TCTN3, TDRD7, TEAD1, TECTA, TEBN3, TF, TFAP2A, TFG, TGFB1, TGFB2, TGFBI, TGFBR1, TGFBR2, TGIF1, THOC6, TIMM8A, TIMP3, TINF2, TLR4, TMCO1, TMEM114, TMEM126A, TMEM138, TMEM216, TMEM231, TMEM237, TMEM240, TMEM67, TMEM70, TMEM98, TNF, TNFRSF10A, TNFRSF11A, TNFSF11, TNXB, TOPORS, TO53, TPCN2, TPP1, TRAF3IP1, TRAPPC11, TREX1, TRIM32, TRPM1, TSFM, TSPAN12, TTBK2, TTC19, TTC21B, TTC8, TTLL5, TTPA, TTR, TUB, TUBA1A, TUBB, TUBB3, TUBB4A, TUBG1, TUBGCP4, TUBGCP6, TUFM, TULP1, TULP3, TWIST1, TYR, TYRP1, UBE3A, UBE3B, UBE3E, UBIAD1, UCHL1, UNC119, UNC45B, UQCRQ, UROC1, USH1C, USH1E, USH1G, USH1H, USH1K, USH2A, VAX1, VCAN, VHL, VIM, VLDLR, VPS13B, VPS37A, VSX1, VSX2, WDPCP, WDR19, WDR36, WDR73, WFS1, WNT3, WRN, WT1, WWOX, XKR4, XRCC1, XYLT2, YAP1, YARS2, ZBTZ20, ZEB1, ZFYVE26, ZIC2, ZNF335, ZNF408, ZNF423, ZNF469, ZNF513, ZNF592, ZNF644, ZNRF1, ZSWIM6, AASS, ABAT, ABCA1, ABCA12, ABCC9, ABCD1,
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  • Key Pathways Involved in Prostate Cancer Based on Gene Set Enrichment Analysis and Meta Analysis
    Key pathways involved in prostate cancer based on gene set enrichment analysis and meta analysis Q.Y. Ning1, J.Z. Wu1, N. Zang2, J. Liang3, Y.L. Hu2 and Z.N. Mo4 1Department of Infection, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China 2The Medical Scientific Research Centre, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China 3Department of Biology Technology, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China 4Department of Urology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China Corresponding authors: Y.L. Hu / Z.N. Mo E-mail: [email protected] / [email protected] Genet. Mol. Res. 10 (4): 3856-3887 (2011) Received June 7, 2011 Accepted October 14, 2011 Published December 14, 2011 DOI http://dx.doi.org/10.4238/2011.December.14.10 ABSTRACT. Prostate cancer is one of the most common male malignant neoplasms; however, its causes are not completely understood. A few recent studies have used gene expression profiling of prostate cancer to identify differentially expressed genes and possible relevant pathways. However, few studies have examined the genetic mechanics of prostate cancer at the pathway level to search for such pathways. We used gene set enrichment analysis and a meta-analysis of six independent studies after standardized microarray preprocessing, which increased concordance between these gene datasets. Based on gene set enrichment analysis, there were 12 down- and 25 up-regulated mixing pathways in more than two tissue datasets, while there were two down- and two up-regulated mixing pathways in three cell datasets.
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  • Alternating Hypoglycemia and Hyperglycemia in a Toddler with a Homozygous P.R1419H ABCC8 Mutation: an Unusual Clinical Picture
    J Pediatr Endocr Met 2015; 28(3-4): 345–351 Patient report Open Access Shira Harel, Ana S.A. Cohen, Khalid Hussain, Sarah E. Flanagan, Kamilla Schlade-Bartusiak, Millan Patel, Jaques Courtade, Jenny B.W. Li, Clara Van Karnebeek, Harley Kurata, Sian Ellard, Jean-Pierre Chanoine and William T. Gibson* Alternating hypoglycemia and hyperglycemia in a toddler with a homozygous p.R1419H ABCC8 mutation: an unusual clinical picture Abstract Results: A 16-month-old girl of consanguineous descent manifested hypoglycemia. She had dysregulation of Background: Inheritance of two pathogenic ABCC8 alleles insulin secretion, with postprandial hyperglycemia fol- typically causes severe congenital hyperinsulinism. We lowed by hypoglycemia. Microarray revealed homozygo- describe a girl and her father, both homozygous for the sity for the regions encompassing KCNJ11 and ABCC8. Her same ABCC8 mutation, who presented with unusual father had developed diabetes at 28 years of age. Sequenc- phenotypes. ing of ABCC8 identified a homozygous missense mutation, Methods: Single nucleotide polymorphism microarray p.R1419H, in both individuals. Functional studies showed and Sanger sequencing were performed. Western blot, absence of working KATP channels. rubidium efflux, and patch clamp recordings interrogated Conclusion: This is the first description of a homozygous the expression and activity of the mutant protein. p.R1419H mutation. Our findings highlight that homozy- gous loss-of-function mutations of ABCC8 do not neces- sarily translate into early-onset severe hyperinsulinemia. *Corresponding author: William T. Gibson, Child and Family Research Institute, Department of Medical Genetics, British Keywords: ABCC8; diabetes; hyperglycemia; hyperinsu- Columbia Children’s Hospital, 950 West 28th Avenue, Vancouver, linism; hypoglycemia. BC, V5Z 4H4, Canada, Phone: +1-604-875-2000 ext.
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  • A New Model for X-Linked Tremor/Ataxia
    © 2016. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2016) 9, 553-562 doi:10.1242/dmm.022848 RESEARCH ARTICLE Spontaneous shaker rat mutant – a new model for X-linked tremor/ ataxia Karla P. Figueroa1, Sharan Paul1, Tito Calì2, Raffaele Lopreiato2, Sukanya Karan1, Martina Frizzarin2, Darren Ames3, Ginevra Zanni4, Marisa Brini5, Warunee Dansithong1, Brett Milash3, Daniel R. Scoles1, Ernesto Carafoli6 and Stefan M. Pulst1,* ABSTRACT mode of inheritance. Here, we describe the genetic analysis of the The shaker rat is an X-linked recessive spontaneous model of shaker rat, a model of Purkinje cell (PC) degeneration. This mutant progressive Purkinje cell (PC) degeneration exhibiting a shaking arose spontaneously and was observed in Sprague Dawley (SD) ataxia and wide stance. Generation of Wistar Furth (WF)/Brown outbred stock in 1991 at Saint Louis University, first described by Norwegian (BN) F1 hybrids and genetic mapping of F2 sib-sib La Regina et al. (1992), and the phenotype of whole-body tremor, ‘ ’ offspring using polymorphic markers narrowed the candidate gene ataxia and wide stance designated as shaker . The shaker trait was region to 26 Mbp denoted by the last recombinant genetic marker reported as an X-linked recessive trait. DXRat21 at 133 Mbp to qter (the end of the long arm). In the WF Various animal models of spontaneously occurring mutants that background, the shaker mutation has complete penetrance, results in parallel some aspects of human hereditary ataxia have been a stereotypic phenotype and there is a narrow window for age of reported; for example, weaver, lurcher, stumbler, tottering and disease onset; by contrast, the F2 hybrid phenotype was more varied, teetering mice (Chou et al., 1991; Frankel et al., 1994; Green and with a later age of onset and likely non-penetrance of the mutation.
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  • Yan Et Al. Supplementary Material
    SUPPLEMENTARY MATERIAL FOR: CELL ATLAS OF THE HUMAN FOVEA AND PERIPHERAL RETINA Wenjun Yan*, Yi-Rong Peng*, Tavé van Zyl*, Aviv Regev, Karthik Shekhar, Dejan Juric, and Joshua R, Sanes^ *Co-First authors ^Author for correspondence, [email protected] Figure S1 tSNE visualization showing contributions to cell types by batch for photoreceptors (a), horizontal cells (b), bipolar cells (c), amacrine cells (d), retinal ganglion cells (e) and non-neuronal cells (f). Each dot represents one cell. Colors distinguish retina samples. Source of each sample is shown in Table S1. Overall, batch eFFects were minimal. Figure S2 Violin and superimposed box plots showing expression of OPN4 in RGC clusters Figure S3 Heat maps showing expression patterns of disease genes by cell classes in the Fovea and periphery. Only genes expressed by more than 20% of cells in any individual class in either Fovea or peripheral cells are plotted. Table S1 Information on donors from whom retinal cells were obtained for scRNA-seq proFiling. Table S2 Publications reporting single cell or single nucleus profiling on cells from human retina. 1 Figure S1 a b c PR HC BP H1 H2F1 H2F2 H3 tSNE1 tSNE1 H4 tSNE1 H5 H9 H11 tSNE2 tSNE2 tSNE2 e AC f RGC g Non-neuronal tSNE1 tSNE1 tSNE1 tSNE2 tSNE2 tSNE2 Figure S2 OPN4 4 2 log Expression 0 MG-ON MG-OFF PG-OFF PG-ON hRGC5 hRGC6 hRGC7 hRGC8 hRGC9 hRGC10 hRGC11 hRGC12 Figure S3 Fovea Fovea Peripheral Peripheral Rods Cones BP HC AC RGC Muller Astro MicG Endo Rods Cones BP HC AC RGC Muller Astro MicG Endo ARL13B MAPK8IP3 EXOC6 LSM4 Expression
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  • Somatic and Inherited Mutations in Primary Aldosteronism
    59 1 F L FERNANDES-ROSA, S BOULKROUN Genetic basis of 59: 1 R47–R63 Review and others primary aldosteronism Somatic and inherited mutations in primary aldosteronism Fabio Luiz Fernandes-Rosa1,2,3,*, Sheerazed Boulkroun1,2,* and Maria-Christina Zennaro1,2,3 Correspondence should be addressed 1 INSERM, UMRS_970, Paris Cardiovascular Research Center, Paris, France to F L Fernandes-Rosa or 2 University Paris Descartes, Sorbonne Paris Cité, Paris, France S Boulkroun 3 Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique, Email Paris, France fabio.fernandes-rosa@ *(F L Fernandes-Rosa and S Boulkroun contributed equally to this work) inserm.fr or sheerazed. [email protected] Abstract Primary aldosteronism (PA), the most common form of secondary hypertension, is caused Key Words in the majority of cases by unilateral aldosterone-producing adenoma (APA) or bilateral f primary aldosteronism adrenal hyperplasia. Over the past few years, somatic mutations in KCNJ5, CACNA1D, f aldosterone-producing ATP1A1 and ATP2B3 have been proven to be associated with APA development, adenoma representing more than 50% of sporadic APA. The identification of these mutations has f familial allowed the development of a model for APA involving modification on the intracellular hyperaldosteronism ionic equilibrium and regulation of cell membrane potential, leading to autonomous f somatic mutations aldosterone overproduction. Furthermore, somatic CTNNB1 mutations have also been f germline mutations identified in APA, but the link between these mutations and APA development remains f potassium channels unknown. The sequence of events responsible for APA formation is not completely f calcium channels understood, in particular, whether a single hit or a double hit is responsible for both f ATPase Journal of Molecular Endocrinology aldosterone overproduction and cell proliferation.
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  • ABCB7 Gene ATP Binding Cassette Subfamily B Member 7
    ABCB7 gene ATP binding cassette subfamily B member 7 Normal Function The ABCB7 gene provides instructions for making a protein known as an ATP-binding cassette (ABC) transporter. ABC transporter proteins carry many types of molecules across membranes in cells. The ABCB7 protein is located in the inner membrane of cell structures called mitochondria. Mitochondria are involved in a wide variety of cellular activities, including energy production, chemical signaling, and regulation of cell growth and division. In the mitochondria of developing red blood cells (erythroblasts), the ABCB7 protein plays a critical role in the production of heme. Heme contains iron and is a component of hemoglobin, the protein that carries oxygen in the blood. The ABCB7 protein is also involved in the formation of certain proteins containing clusters of iron and sulfur atoms (Fe-S clusters). Researchers suspect that the ABCB7 protein transports Fe-S clusters from mitochondria, where they are formed, to the surrounding cellular fluid (cytosol), where they can be incorporated into proteins. Overall, researchers believe that the ABCB7 protein helps maintain an appropriate balance of iron (iron homeostasis) in developing red blood cells. Health Conditions Related to Genetic Changes X-linked sideroblastic anemia and ataxia At least three mutations in the ABCB7 gene have been identified in people with X-linked sideroblastic anemia with ataxia. Each of these mutations changes a single protein building block (amino acid) in the ABCB7 protein, slightly altering its structure. These changes disrupt the protein's usual role in heme production and iron homeostasis. Anemia results when heme cannot be produced normally, and therefore not enough hemoglobin is made.
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  • Structures and Functions of Mitochondrial ABC Transporters
    ATP-binding cassette transporters: from mechanism to organism 943 Structures and functions of mitochondrial ABC transporters Theresia A. Schaedler*, Belinda Faust†, Chitra A. Shintre†, Elisabeth P. Carpenter†, Vasundara Srinivasan‡, Hendrik W. van Veen§ and Janneke Balk1 *Department of Biological Chemistry and Crop Protection, Rothamsted Research, West Common, Harpenden, AL5 2JQ, U.K. †Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, U.K. ‡LOEWE center for synthetic microbiology (SYNMIKRO) and Philipps University, D-35043 Marburg, Germany §Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, U.K. John Innes Centre and University of East Anglia, Colney Lane, Norwich, NR4 7UH, U.K. Abstract A small number of physiologically important ATP-binding cassette (ABC) transporters are found in mitochondria. Most are half transporters of the B group forming homodimers and their topology suggests they function as exporters. The results of mutant studies point towards involvement in iron cofactor biosynthesis. In particular, ABC subfamily B member 7 (ABCB7) and its homologues in yeast and plants are required for iron-sulfur (Fe-S) cluster biosynthesis outside of the mitochondria, whereas ABCB10 is involved in haem biosynthesis. They also play a role in preventing oxidative stress. Mutations in ABCB6 and ABCB7 have been linked to human disease. Recent crystal structures of yeast Atm1 and human ABCB10 have been key to identifying substrate-binding sites and transport mechanisms. Combined with in vitro and in vivo studies, progress is being made to find the physiological substrates of the different mitochondrial ABC transporters. Sequence analysis of mitochondrial ABC The ABCB7 group, which includes the ABC transporters transporters of the mitochondria Atm1 in yeast and ATM3 in Arabidopsis, Mitochondria of most eukaryote species harbour 2–4 can be found in virtually all eukaryotic species.
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