Figure 1 Large consanguineous pedigree from Northern Pakistan

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Figure 1 Large consanguineous pedigree from Northern Pakistan Figure 1 Large consanguineous pedigree from Northern Pakistan. Affected members of the family present with a complex ... Figure 1 Large consanguineous pedigree from Northern Pakistan. Affected members of the family present with a complex developmental disorder affecting multiple tissues segregating as an autosomal recessive condition. Two affected individuals (Patients NA and AA) from two separate branches of the family were selected for exome sequencing. Cells derived from an unaffected healthy sibling (Subject RG) and an affected individual (Patient AA) were used in the functional studies. Individuals NA, RG and AA are indicated with arrows. The cG745A mutation reported in this family was confirmed by Sanger sequencing (Fig. 3) in 10 family members marked with an asterisk. Their corresponding genotypes (G/G, G/A, A/A) are given. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Brain, Volume 142, Issue 5, 10 April 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2 Skeletal and neurological abnormalities in patients Figure 2 Skeletal and neurological abnormalities in patients. (A–C) Patient AA, aged 43 years, and Patient NA (D–I), ... Figure 2 Skeletal and neurological abnormalities in patients. (A–C) Patient AA, aged 43 years, and Patient NA (D–I), aged 45 years, show a range of clinical abnormalities, including clinodactyly, overlapping of fifth toes, increased thoracic kyphosis, thumb hypoplasia and enlarged ventricles in the brain. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Brain, Volume 142, Issue 5, 10 April 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3 Genomic structure and mutation in WIPI2 gene Figure 3 Genomic structure and mutation in WIPI2 gene. (A) The exon-intron structure of the WIPI2 gene is depicted, ... Figure 3 Genomic structure and mutation in WIPI2 gene. (A) The exon-intron structure of the WIPI2 gene is depicted, highlighting the pV249M mutation. (B) Phylogenetic analysis demonstrates the cG745A mutation is in a region that is highly conserved across multiple species. (C) Model of WIPI2 (Wilson et al., 2014) based on the structure of Hsv2 (Baskaran et al., 2012). WIPI2 is a 7-bladed propeller protein capable of interacting with PI(3)P and PI(3,5)P2 at sites 1 and 2. The WIPI2 pV249M mutation resides within site 2 in blade 6. (D) Sanger sequencing confirms the cG745A mutation correctly segregates with the phenotype in 10 family members (Fig. 1). Representative sequence traces from affected (−/−), unaffected (+/−) and control (+/+) individuals are presented, corresponding to genotypes AA, AG and GG, respectively. (E) Sequence alignment of PROPPIN family members. The boxed region highlights the position of the pV249M residue and its comparison across PROPPIN family members. Figure adapted from Baskaran et al. (2012). Residues involved in binding PI(3)P and PI(3,5)P2, including R243, which is an essential requirement for binding to occur, are highlighted in yellow. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Brain, Volume 142, Issue 5, 10 April 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4 WIPI2 puncta formation is inhibited in human fibroblasts isolated from patients carrying a WIPI2 mutation. ... Figure 4 WIPI2 puncta formation is inhibited in human fibroblasts isolated from patients carrying a WIPI2 mutation. (A) Control (RG) and mutant (AA) human fibroblasts were incubated in either full medium (FM), or treated with 100 nM Bafilomycin A1 in full-nutrient medium (FB), or amino acid starvation medium (SM), or 100 nM Bafilomycin A1 in starvation medium (SB) for 2 h and then fixed. Cells were stained with antibodies against WIPI2 and LC3. Scale bar = 10 μm. (B and C) WIPI2 and LC3 puncta were quantified in 10 fields per condition. Statistical analysis was performed by one-way ANOVA with Tukey’s post-test. ****P < 0.0001. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Brain, Volume 142, Issue 5, 10 April 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5 Analysis of WIPI2 interaction with ATG16L1 Figure 5 Analysis of WIPI2 interaction with ATG16L1. (A) GFP-WIPI2b WT or GFP-WIPI2b V231M were transiently expressed ... Figure 5 Analysis of WIPI2 interaction with ATG16L1. (A) GFP-WIPI2b WT or GFP-WIPI2b V231M were transiently expressed in HEK293A cells. The cells were lysed and subjected to immunoprecipitation using GFP-TRAP beads. ATG16L1, ATG12 and GFP (alone or GFP-WIPI2b), in the input, unbound and bound to the GFP-TRAP beads, were detected using the specific antibodies against ATG16L1, ATG12 and GFP. Note data are from same western blot but shown in pieces to aid interpretation. (B) Total cell lysate from the unaffected control (RG) and the patient (AA) were analysed for levels of FIP200, ATG16L1 and WIPI2. (C) Cell lysates from the control (RG) or the patient (AA) were prepared after the treatment of the respective cell lines with a crosslinker on ice. WIPI2 was immunoprecipitated with an antibody against WIPI2, and the input, unbound and immunoprecipitates were analysed by western blot, using antibodies against ATG16L1 and WIPI2. The WIPI2 immunoprecipitation was done with antibody plus protein A beads (beads + Ab) or antibody alone (Ab). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Brain, Volume 142, Issue 5, 10 April 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075 The content of this slide may be subject to copyright: please see the slide notes for details.