DYSREGULATION OF WT1 (-KTS) IS ASSOCIATED WITH THE KIDNEY-SPECIFIC EFFECTS OF THE LMX1B R246Q MUTATION
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1 DYSREGULATION OF WT1 (-KTS) IS ASSOCIATED WITH THE KIDNEY-SPECIFIC EFFECTS OF THE LMX1B R246Q MUTATION Gentzon Hall 1,2#, Brandon Lane 1,3#, Megan Chryst-Ladd 1,3, Guanghong Wu 1,3, Jen-Jar Lin 4, XueJun Qin 1, Elizabeth R. Hauser 1, Rasheed Gbadegesin 1,3* 1 Duke Molecular Physiology Institute, 2 Division of Nephrology, Duke University Medical Center, Durham, NC 3 Department of Pediatrics, Duke University Medical Center, Durham, NC 4 Department of Pediatrics, Wake Forest Baptist Medical Center, Winston Salem, NC # These authors contributed equally to this manuscript *To whom correspondence should be addressed: rasheed.gbadegesin@duke.edu
2 Supplementary material Supplementary Figure 1: Genome wide linkage studies showing suggestive locus on chromosome 9q (dark arrow) in (a) DUK35705 and in (b) DUK34319.
3 Supplementary Figure 2: Renal specific R246Q LMX1B mutations in two families with FSGS. (a) Genome-wide linkage studies in two families with SRNS yielded a minimal candidate region on chromosome 9q (black arrow). Chromosome numbers are shown on the X axis and LOD scores are on the Y axis. LMX1B is located in the chromosome 9q peak. (b) Segregating missense heterozygous mutation c.737g>a p.r246q is found in LMX1B gene in families and Mutant sequence on the left and wild-type sequence on the right.
4 Supplementary Figure 3. RQ values for LMX1B expression in control, myc-lmx1bwt, and myc-lmx1br246q podocyte cells. Expression was quantified relative to control cells which have an RQ value of 1.
5 Supplementary Figure 4: Immunofluorescence staining of myc-lmx1bwt and myc- LMX1BR246Q cell lines for F-actin showed structurally normal F-actin cytoskeleton in both cell lines and similar subcellular localization of nephrin, CD2AP, and WT1.
6 Supplementary Figure 5: Expression of COL4A4 and TRPC6, in myc-lmx1bwt and myc- LMX1BR246Q-overexpressing podocytes (n=3, *p value <0.05).
7 Supplementary Figure 6. Unedited blots shown in the paper. a. Figure 2a, b. Figure 2b, c. Figure 3 a.
8 b.
9 c.
10 Supplementary Table 1: 68 rare variants shared by three affected individuals in Family VARIANT ID RS ID REF ALLELE GENOTYPE ExAC ALL MAF GENE FUNCTION 1 20_ _T rs C het E-05 ZMYND8 NON SYNONYMOUS 2 20_ _A rs G het FRG1B NON SYNONYMOUS 3 10_ _T rs C het ANKRD2 NON SYNONYMOUS 4 3_ _A rs G het LPP NON SYNONYMOUS 5 13_ _G rs A het IRG1 NON SYNONYMOUS 6 1_ _T rs C het NA IGSF3 NON SYNONYMOUS 7 3_ _A rs G het NA FRG2C NON SYNONYMOUS 8 20_ _C rs A het NCOA3 NON SYNONYMOUS 9 22_ _T rs C het NAGA NON SYNONYMOUS 10 20_ _A rs G het BPIFB3 NON SYNONYMOUS 11 9_ _G rs A het NA ANKRD20A4 NON SYNONYMOUS 12 9_ _A NA G het NA LMX1B NON SYNONYMOUS 13 10_ _A NA G het NA GFRA1 NON SYNONYMOUS 14 16_ _G rs C het NA HYDIN NON SYNONYMOUS 15 16_ _C rs T het NA HYDIN NON SYNONYMOUS 16 16_ _T rs C het NA HYDIN NON SYNONYMOUS 17 16_ _T rs C het NA HYDIN NON SYNONYMOUS 18 21_ _G rs A het NA POTED NON SYNONYMOUS 19 22_ _G rs A het NA KIAA1671 NON SYNONYMOUS 20 1_ _A rs G het E-06 IGSF3 STOP_GAINED 21 2_ _T rs C het ANO7 STOP_GAINED 22 3_ _ _DEL_G rs TG het NA FRG2C FRAME_SHIFT 23 3_ _ _INS_G rs A het NA ZNF717 FRAME_SHIFT 24 16_ _ _DEL_A rs GA het NA HYDIN FRAME_SHIFT 25 19_ _T rs C het NA PLK5 SPLICE_SITE_REGION 26 1_ _T NA C het NA FAM43B START_GAINED 27 3_ _A rs G het NA DNAJB8 START_GAINED 28 3_ _G rs12011 A het NA MAGEF1 START_GAINED 29 4_ _T rs G het NA CISD2 START_GAINED 30 22_ _T rs C het NA CSDC2 START_GAINED 31 22_ _G rs A het NA LDOC1L START_GAINED 32 1_ _T rs C het NA IGSF3 STOP_GAINED 33 X_ _C rs T het 0 FAM104B NON SYNONYMOUS 34 1_ _G rs A het E-05 IGSF3 NON SYNONYMOUS 35 11_ _T NA G het E-06 LDHAL6A NON SYNONYMOUS 36 1_ _C rs T het E-06 IGSF3 NON SYNONYMOUS 37 3_ _C NA T het E-05 LMOD3 NON SYNONYMOUS 38 3_ _G NA T het E-05 GPR149 NON SYNONYMOUS
11 VARIANT ID RS ID REF ALLELE GENOTYPE ExAC ALL MAF GENE FUNCTION 39 3_ _A rs G het FNDC3B NON SYNONYMOUS 40 20_ _T rs C het AURKA NON SYNONYMOUS 41 16_ _C rs T het HYDIN NON SYNONYMOUS 42 1_ _G rs A het IGSF3 NON SYNONYMOUS 43 1_ _C rs T het USP48 NON SYNONYMOUS 44 16_ _G rs C het HYDIN NON SYNONYMOUS 45 4_ _C rs G het NEUROG2 NON SYNONYMOUS 46 1_ _C rs G het OR2T5 NON SYNONYMOUS 47 17_ _T rs C het RTN4RL1 NON SYNONYMOUS 48 9_ _A rs G het FAM205A NON SYNONYMOUS 49 22_ _C rs A het XKR3 NON SYNONYMOUS 50 12_ _A rs G het PWP1 NON SYNONYMOUS 51 1_ _T rs C het PIGR NON SYNONYMOUS 52 1_ _T rs C het PADI3 NON SYNONYMOUS 53 3_ _C rs T het NA FRG2C NON SYNONYMOUS 54 3_ _G rs A het NA FRG2C NON SYNONYMOUS 55 3_ _G rs T het NA FRG2C NON SYNONYMOUS 56 3_ _G rs A het NA FRG2C NON SYNONYMOUS 57 3_ _T rs C het NA FRG2C NON SYNONYMOUS 58 3_ _A rs G het NA FRG2C NON SYNONYMOUS 59 3_ _A rs G het NA FRG2C NON SYNONYMOUS 60 3_ _A rs G het NA FRG2C NON SYNONYMOUS 61 3_ _G rs A het NA FRG2C NON SYNONYMOUS 62 3_ _A rs T het NA FRG2C NON SYNONYMOUS 63 8_ _T NA A het NA SLC7A2 NON SYNONYMOUS 64 9_ _C rs G het NA ANKRD20A4 NON SYNONYMOUS 65 9_ _T rs A het NA ANKRD20A4 NON SYNONYMOUS 66 16_ _G rs A het NA HYDIN NON SYNONYMOUS 67 22_ _T rs G het NA XKR3 NON SYNONYMOUS 68 22_ _T rs C het NA RIMBP3B NON SYNONYMOUS
12 Supplementary Table 2: Filtering algorithm for Whole exome sequencing data Remove all variants with MAF >1% in dbgap Remove all synonymous and non-coding variants except those in the obligatory splice site and promoter regions Remove all homozygous variants Remove all variants that are not shared by affected individuals 68 shared variants in DUK35705
13 Supplementary Table 3. Sequences and ABI identification numbers for the qpcr probes used in this analysis. Probe ID Target Sequence Hs _g1 Hs _m1 INF2 CD2AP ggaccactacaagacggtgtgcagccagcagtaccgcttcagcattgtcatgaacgagctctccggcag cgacaacgtgccctacgtggtcaccctgcttag tttttattgaaacttgtattatttttaaagagatctatactataaatatggtgatatatttacaagtaatctgt taagatatactatttgagagggacagattagccttttagtaactatagtcactactttttccataatgcat Hs _s1 SYNPO ggtggccagtgaggaggaagaggtaccactggtggtttatctaaaggagaatgcagcactgctgacagcc Hs _m1 NPHS2 ccaaatcctccggcttaggggcctgtgagtggcttcttgtcctcatttccctgctcttcatcatcatgac Hs _m1 NPHS1 aggtctccaccagccttctggagaacctgaagaccagctgcccacagagccaccttcaggaccctcg Hs _m1 COL4A4 ctggcagggtcttgccttcccgtatttagcacgctgccctttgcctactgcaacatccaccaggtgtgccactat Hs _m1 COL4A3 tcacaagtgcaggttctgagggcaccgggcaagcactggcctcccctggctcctgcctggaagaattccg Hs _m1 PTPRO (GLEPP1) Hs _m1 Hs _m1 LMX1B TRPC6 gtacatttttatccatcagtgtgtgcaactgatgtggatgaagaagaagcagcagttctgcatcagtgatg tcatatacgagaatgttagc agctcttcgcggccaagtgcagcggctgcatggagaagatcgcccccaccgagttcgtgatgcgggcgct ggagtgcgtgtaccacctgggctgcttct ggcatgatatgggctgaatgtaaagaaatctggactcagggccccaaggaatatttgtttgagttgtggaa catgcttgattttggtatgttagcaattttcgcagcatcattca Hs _g1 ACTB ggcgtgatggtgggcatgggtcagaaggattcctatgtgggcgacgaggcccagagcaagaga Hs _m1 WT1 aatttataccaaatgacatcccagcttgaatgcatgacctggaatcagatgaacttaggagccaccttaaag WT1 Hs _m1 (+KTS isoforms only) agcccttcagctgtcggtggccaagttgtcagaaaaagtttgcccggtcagatgaat
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