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Supplemental figure and table legends Supplementary Figure 1: KIAA1841 is well conserved among vertebrates. NCBI HomoloGene pairwise alignment scores of human KIAA1841 sequence compared to other vertebrate orthologs. Supplementary Figure 2: µ-germline transcripts (GLT) and AID mRNA expression are not affected by overexpression of KIAA1841. Splenic B cells were isolated from wild-type mice, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841. Levels of µ-GLT and AID mRNA were determined at 72h post-infection by RT-qPCR, and normalized to -actin mRNA and the pMIG control. The mean of three independent experiments +/- SD is shown. NS, p = not significant, p 0.05, two-tailed paired student’s t-test. Supplementary Figure 3: Overexpression of untagged and Xpress-tagged KIAA1841 does not affect cell proliferation. Splenic B cells were isolated from wild-type mice, stimulated with LPS+IL4, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841 or Xpress (Xp)-tagged KIAA1841. Cells are labeled with seminaphthorhodafluor (SNARF) cell tracking dye and SNARF intensity was measured at 0h, 24h, and 48h after retroviral infection. Histograms of transduced cells (GFP+) for pMIG control, KIAA1841 and Xp-KIAA1841 were superimposed at each time point. Three independent retroviral infection experiments are shown. Supplementary Figure 4: Sequence alignment of the putative SANT domain of KIAA1841 with the SANT domain of SWI3. Alignment was performed using ClustalOmega; *, conserved residue, :, strongly similar residues, ., weakly similar residues. Numbers indicate amino acid residues in each sequence. Helix 3, which has been reported to be important for the chromatin remodeling function of SWI3 (Boyer et. al., 2002), is well conserved in KIAA1841. Supplementary Table 1: Negative regulators of CSR recovered by the shRNA screen. Genes with shRNAs showing at least 2-fold enrichment in IgA+ compared to IgA- samples, i.e. log2(Cy3/Cy5)>1, and FDR less than 10 were identified as negative regulators. The novel gene of interest, NM_027860, which encodes for the protein KIAA1841, is highlighted in yellow. Supplementary Table 2: Positive regulators of CSR recovered by the shRNA screen. Genes with shRNAs showing at least 2-fold enrichment in IgA- compared to IgA+ samples, i.e. log2(Cy3/Cy5)<-1, and FDR less than 10, were identified as positive regulators. Known positive regulator, activation-induced cytidine deaminase (Aicda), is highlighted in green. Supplementary Figure 1 2.5 NS NS 2 pMIG KIAA1841 expression 1.5 1 0.5 Relative mRNA mRNA Relative 0 µ-GLT AID Supplementary Figure 2 GFP+ gated Exp 1 Exp 2 Exp 3 pMIG KIAA1841 Xp-KIAA1841 0 hr 24 hr 48 hr SNARF Supplementary Figure 3 KIAA1841 MVLDMILYPLIGI-PQTINWETVARLVPGLTPKECVKRFDELKS------ 60 SWI3 WSKEDLQKLLKGIQEFGADWYKVAKNVGNKSPEQCILRFLQLPIEDKFLY 576 : : * ** :* .**: * . :*::*: ** :* Helix 3 Supplementary Figure 4 Supplementary Table 1: Negative regulators of CSR recovered by the shRNA screen Gene.Name log2.ratio q.value... Hit? Codex_hai Codex_97mCodex_19mCodex_Accession Codex_gene.name Codex_gene.symbol OB_ReleasOB_Plate OB_Well_ROB_Well_C 092308m1_V2MM_141890 3.829646 3.004939 TRUE HP_36260 TGCTGTTGGCTTTATC XM_157111 Mus musculus LOC212310 (LOC212310), mR. 2.4 SM2050 h 12 mPool2_V2MM_133332 3.684535 3.004939 TRUE HP_35407 TGCTGTTGGATTCTCT XM_149195 RIKEN cDNA E230025N21 gene E230025N21Rik 2.11 SM2373 e 7 mPool2_V2MM_2305 3.67322 2.205692 TRUE HP_22592 TGCTGTTGCTCCTAAAXM_132611 similar to variable region of immunoglobulin kappa light chain 2.11 SM2381 h 4 mPool7_V2MM_141895 3.615101 3.004939 TRUE HP_36260 TGCTGTTGCGCTTTAT XM_157111 Mus musculus LOC212310 (LOC212310), mRNA. 2.1 SM2329 a 8 mPool7_V2MM_88676 3.592123 2.205692 TRUE HP_31011 TGCTGTTGGTACAGATNM_175463 RIKEN cDNA A930012O16 gene A930012O16Rik 2.9 SM2257 e 8 mPool7_V2MM_88676 3.592123 2.205692 TRUE HP_31011 TGCTGTTGGTACAGATNM_175463 RIKEN cD A930012O16 gene A930012O16Rik 2.9 SM2257 e 8 mPool2_V2MM_145554 3.486776 3.004939 TRUE HP_36626 TGCTGTTGCATTCTTATXM_161053 Mus musculus LOC230170 (LOC230170), mR. 2.4 SM2040 e 9 mPool2_V2MM_145554 3.486776 3.004939 TRUE HP_36626 TGCTGTTGCATTCTTATXM_161053 Mus musculus LOC230170 (LOC230170), mRNA. 2.4 SM2040 e 9 mPool2_V2MM_92494 3.390594 3.004939 TRUE HP_31384 TGCTGTTGGTTGGAATNM_178720 RIKEN cDNA 9430016A21 gene 9430016A21Rik 2.6 SM2137 a 5 mPool2_V2MM_138848 3.381957 2.205692 TRUE HP_35956 TGCTGTTGGACATTAAXM_154566 Mus musculus LOC238925 (LOC238925), mR. 2.4 SM2030 d 11 mPool2_V2MM_138848 3.381957 2.205692 TRUE HP_35956 TGCTGTTGGACATTAAXM_154566 Mus musculus LOC238925 (LOC238925), mRNA. 2.4 SM2030 d 11 mPool2_V2MM_134275 3.329965 2.205692 TRUE HP_35500 TGCTGTTGGGCTAGTTXM_357654 hypothetical LOC384452 2.11 SM2368 f 8 mPool7_V2MM_199459 3.328607 2.205692 TRUE HP_41750 TGCTGTTGCCATTTAA XM_289192 Mus musculus LOC332813 (LOC332813), mRNA. 2.9 SM2276 c 3 mPool2_V2MM_17530 3.318772 2.205692 TRUE HP_240804TGCTGTTGGATACTTT NM_134054 RIKEN cDNA 1110002B05 gene 1110002B05Rik 2.11 SM2378 g 1 092308m1_V2MM_171708 3.314424 1.959154 TRUE HP_39219 TGCTGTTGCATGTTAGXM_286679 Mus musculus hypothetical gene supported by AK039985 (LOC328540), mR. 2.5 SM2074 b 9 mPool2_V2MM_36734 3.311664 3.004939 TRUE HP_25950 TGCTGTTGCTTGTACANM_023816 RIKEN cDNA 1700012M14 gene 1700012M14Rik 2.11 SM2392 a 9 mPool2_V2MM_84705 3.309396 3.004939 TRUE HP_14696 TGCTGTTGCTAATCAT NM_028930 transmembrane channel‐like gene family 5 Tmc5 2.6 SM2137 b 10 092308m1_V2MM_121144 3.273188 3.004939 TRUE HP_34202 TGCTGTTGCGGCATCTXM_141454 Mus musculus similar to lactate dehydrogese [Mus musculus] (LOC228430), mR. 2.6 SM2106 g 6 092308m1_V2MM_124008 3.268085 2.205692 TRUE HP_34486 TGCTGTTGGTCTGGAAXM_143251 Mus musculus similar to hypothetical protein [Macaca fascicularis] (LOC242043), 2.6 SM2102 b 7 mPool7_V2MM_113184 3.252594 2.205692 TRUE HP_334174TGCTGTTGCTACATTC XM_136853 Mus musculus LOC241181 (LOC241181), mRNA. 2.1 SM2304 d 4 mPool2_V2MM_120733 3.242869 2.205692 TRUE HP_34162 TGCTGTTGGAAATTTCXM_141156 Mus musculus similar to olfactory receptor MOR264‐19 [Mus musculus] (LOC228 2.11 SM2359 f 5 mPool7_V2MM_79723 3.198836 3.004939 TRUE HP_30137 TGCTGTTGGCCAGGATNM_009828 cyclin A2 Ccna2 2.8 SM2227 d 7 092308m1_V2MM_159994 3.196066 2.205692 TRUE HP_38058 TGCTGTTGCATCTAACAK048916 cD sequence BC052055 BC052055 2.6 SM2115 f 1 mPool2_V2MM_14135 3.188079 2.205692 TRUE HP_23748 TGCTGTTGCCCTGAAANM_007672 cerebellar degeneration‐related 2 Cdr2 2.11 SM2379 d 10 mPool2_V2MM_212177 3.187273 1.959154 TRUE HP_42985 TGCTGTTGCTTCTATCCXM_148779 RIKEN cDNA 4930541O19 gene 4930541O19Rik 2.11 SM2365 f 7 mPool2_V2MM_17214 3.164486 2.205692 TRUE HP_240494TGCTGTTGGAGCTAAANM_011623 topoisomerase (DNA) II alpha Top2a 2.11 SM2387 h 6 mPool7_V2MM_67258 3.157407 2.205692 TRUE HP_28924 TGCTGTTGCCGTTTGCNM_021546 amyloid beta (A4) precursor protein‐binding, family A, m Apba2bp 2.8 SM2237 d 7 mPool2_V2MM_208999 3.152098 3.004939 TRUE HP_42677 TGCTGTTGCTCAGGAAXM_157672 similar to Suppressor of G2 allele of SKP1 homolog (Sgt1) (Putative 40‐6‐3 protein 2.1 SM2338 a 5 mPool2_V2MM_94467 3.148552 2.205692 TRUE HP_31575 TGCTGTTGCAGCATGTBC052532 cDNA sequence BC006779 BC006779 2.6 SM2142 a 7 mPool7_V2MM_202647 3.143102 2.205692 TRUE HP_42064 TGCTGTTGGTATGATTAK045028 histone deacetylase 10 Hdac10 2.1 SM2317 h 10 mPool2_V2MM_1433 3.143072 2.205692 TRUE HP_225074TGCTGTTGCCGCATACNM_007855 twist homolog 2 (Drosophila) Twist2 2.11 SM2386 g 12 mPool2_V2MM_134121 3.135473 3.004939 TRUE HP_35484 TGCTGTTGCTGTCTTTANM_177582 hypothetical protein B930074I24 2.1 SM2349 h 4 092308m1_V2MM_180277 3.099315 2.205692 TRUE HP_40075 TGCTGTTGCTTTAGAT XM_288480 Mus musculus LOC331828 (LOC331828), mRNA. 2.5 SM2072 h 3 092308m1_V2MM_180277 3.099315 2.205692 TRUE HP_40075 TGCTGTTGCTTTAGAT XM_288480 Mus musculus LOC331828 (LOC331828), mR. 2.5 SM2072 h 3 092308m1_V2MM_156420 3.091247 2.205692 TRUE HP_37705 TGCTGTTGCTGCTTTA NM_027860 RIKEN cD 0610010F05 gene 0610010F05Rik 2.6 SM2115 e 4 092308m1_V2MM_70303 3.088266 3.004939 TRUE HP_29221 TGCTGTTGCAACCAATNM_028911 RIKEN cD 4933414I15 gene 4933414I15Rik 2.3 SM2006 e 3 mPool7_V2MM_197834 3.086251 2.205692 TRUE HP_41589 TGCTGTTGGATGATAAXM_111554 similar to Aspartate aminotransferase, mitochondrial precursor (Transamise A) (G 2.9 SM2266 b 12 mPool7_V2MM_197834 3.086251 2.205692 TRUE HP_41589 TGCTGTTGGATGATAAXM_111554 similar to Aspartate aminotransferase, mitochondrial precursor (Transaminase A) 2.9 SM2266 b 12 mPool7_V2MM_205300 3.075308 2.205692 TRUE HP_42316 TGCTGTTGCAAAGTTCXM_138746 Mus musculus similar to thymine D glycosylase [Mus musculus] (LOC238743), mR 2.1 SM2306 d 1 mPool7_V2MM_205300 3.075308 2.205692 TRUE HP_42316 TGCTGTTGCAAAGTTCXM_138746 Mus musculus similar to thymine DNA glycosylase [Mus musculus] (LOC238743), 2.1 SM2306 d 1 092308m1_V2MM_135215 3.072112 1.959154 TRUE HP_35593 TGCTGTTGCTTTATTTCXM_489372 similar to RIKEN cD 6720401G13 gene 2.5 SM2057 a 3 mPool2_V2MM_212145 3.039733 3.004939 TRUE HP_42982 TGCTGTTGCCCTTTAA AK017143 RIKEN cDNA 5031425E22 gene 5031425E22Rik 2.11 SM2362 d 9 mPool7_V2MM_144853 3.031093 2.205692 TRUE HP_365564TGCTGTTGGAGCTTATXM_160377 Mus musculus LOC229769 (LOC229769), mRNA. 2.1 SM2331 f 2 092308m1_V2MM_155240 3.030417 2.205692 TRUE HP_37588 TGCTGTTGGCCTGAAAXM_197286 Mus musculus LOC271407 (LOC271407), mR. 2.6 SM2114 g 7 mPool2_V2MM_106531 3.008607 3.004939 TRUE HP_32763 TGCTGTTGGAAACATCNM_001002927 preproenkephalin 1 Penk1 2.1 SM2316 h 4 mPool2_V2MM_210729 3.001055 2.205692 TRUE HP_42846 TGCTGTTGCGCAGTTAXM_359191 gene model 1773, (NCBI) Gm1773 2.11 SM2363 b 5 mPool2_V2MM_123973
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    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
  • Macropinocytosis Requires Gal-3 in a Subset of Patient-Derived Glioblastoma Stem Cells

    Macropinocytosis Requires Gal-3 in a Subset of Patient-Derived Glioblastoma Stem Cells

    ARTICLE https://doi.org/10.1038/s42003-021-02258-z OPEN Macropinocytosis requires Gal-3 in a subset of patient-derived glioblastoma stem cells Laetitia Seguin1,8, Soline Odouard2,8, Francesca Corlazzoli 2,8, Sarah Al Haddad2, Laurine Moindrot2, Marta Calvo Tardón3, Mayra Yebra4, Alexey Koval5, Eliana Marinari2, Viviane Bes3, Alexandre Guérin 6, Mathilde Allard2, Sten Ilmjärv6, Vladimir L. Katanaev 5, Paul R. Walker3, Karl-Heinz Krause6, Valérie Dutoit2, ✉ Jann N. Sarkaria 7, Pierre-Yves Dietrich2 & Érika Cosset 2 Recently, we involved the carbohydrate-binding protein Galectin-3 (Gal-3) as a druggable target for KRAS-mutant-addicted lung and pancreatic cancers. Here, using glioblastoma patient-derived stem cells (GSCs), we identify and characterize a subset of Gal-3high glio- 1234567890():,; blastoma (GBM) tumors mainly within the mesenchymal subtype that are addicted to Gal-3- mediated macropinocytosis. Using both genetic and pharmacologic inhibition of Gal-3, we showed a significant decrease of GSC macropinocytosis activity, cell survival and invasion, in vitro and in vivo. Mechanistically, we demonstrate that Gal-3 binds to RAB10, a member of the RAS superfamily of small GTPases, and β1 integrin, which are both required for macro- pinocytosis activity and cell survival. Finally, by defining a Gal-3/macropinocytosis molecular signature, we could predict sensitivity to this dependency pathway and provide proof-of- principle for innovative therapeutic strategies to exploit this Achilles’ heel for a significant and unique subset of GBM patients. 1 University Côte d’Azur, CNRS UMR7284, INSERM U1081, Institute for Research on Cancer and Aging (IRCAN), Nice, France. 2 Laboratory of Tumor Immunology, Department of Oncology, Center for Translational Research in Onco-Hematology, Swiss Cancer Center Léman (SCCL), Geneva University Hospitals, University of Geneva, Geneva, Switzerland.
  • Análise Integrativa De Perfis Transcricionais De Pacientes Com

    Análise Integrativa De Perfis Transcricionais De Pacientes Com

    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.