Proximity-dependent Biotin Identification Research Articles

Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.

Introduction: The unique architecture of glomerular podocytes is integral to kidney filtration. Interdigitating foot processes extend from the podocyte cell body, wrap around fenestrated capillaries, and form specialized junctional complexes termed slit diaphragms to create a molecular sieve. However, the full complement of proteins which maintain foot process integrity, and how this localized proteome changes with disease, remain to be elucidated. Methods: Proximity-dependent biotin identification (BioID) enables the identification of spatially localized proteomes. To this end, we developed a novel in vivo BioID knock-in mouse model. We utilized the slit diaphragm protein podocin (Nphs2) to create a podocin-BioID fusion. Podocin-BioID localizes to the slit diaphragm, and biotin injection leads to podocyte-specific protein biotinylation. We isolated the biotinylated proteins and performed mass spectrometry to identify proximal interactors. Results and Discussion: Gene ontology analysis of 54 proteins specifically enriched in our podocin-BioID sample revealed 'cell junctions,' 'actin binding,' and 'cytoskeleton organization' as top terms. Known foot process components were identified, and we further uncovered two novel proteins: the tricellular junctional protein Ildr2 and the CDC42 and N-WASP interactor Fnbp1l. We confirmed that Ildr2 and Fnbp1l are expressed by podocytes and partially colocalize with podocin. Finally, we investigated how this proteome changes with age and uncovered a significant increase in Ildr2. This was confirmed by immunofluorescence on human kidney samples and suggests altered junctional composition may preserve podocyte integrity. Together, these assays have led to new insights into podocyte biology and support the efficacy of utilizing BioID in vivo to interrogate spatially localized proteomes in health, aging, and disease.

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 Using Proximity Labeling and Affinity Purification.

The DNA repair scaffold SLX4 has pivotal roles in cellular processes that maintain genome stability, most notably homologous recombination. Germline mutations in SLX4 are associated with Fanconi anemia, a disease characterized by chromosome instability and cancer susceptibility. The role of mammalian SLX4 in homologous recombination depends critically on binding and activating structure-selective endonucleases, namely SLX1, MUS81-EME1, and XPF-ERCC1. Increasing evidence indicates that cells rely on distinct SLX4-dependent complexes to remove DNA lesions in specific regions of the genome. Despite our understanding of SLX4 as a scaffold for DNA repair proteins, a detailed repertoire of SLX4 interactors has never been reported. Here, we provide a comprehensive map of the human SLX4 interactome using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS). We identified 221 unique high-confidence interactors, of which the vast majority represent novel SLX4-binding proteins. Network analysis of these hits revealed pathways with known involvement of SLX4, such as DNA repair, and several emerging pathways of interest, including RNA metabolism and chromatin remodeling. In summary, the comprehensive SLX4 interactome we report here provides a deeper understanding of how SLX4 functions in DNA repair while revealing new cellular processes that may involve SLX4.

Analysis of Ku70 S155 Phospho-Specific BioID2 Interactome Identifies Ku Association with TRIP12 in Response to DNA Damage.

The Ku heterodimer, composed of subunits Ku70 and Ku80, is known for its essential role in repairing double-stranded DNA breaks via non-homologous end joining (NHEJ). We previously identified Ku70 S155 as a novel phosphorylation site within the von Willebrand A-like (vWA) domain of Ku70 and documented an altered DNA damage response in cells expressing a Ku70 S155D phosphomimetic mutant. Here, we conducted proximity-dependent biotin identification (BioID2) screening using wild-type Ku70, Ku70 S155D mutant, and Ku70 with a phosphoablative substitution (S155A) to identify Ku70 S155D-specific candidate proteins that may rely on this phosphorylation event. Using the BioID2 screen with multiple filtering approaches, we compared the protein interactor candidate lists for Ku70 S155D and S155A. TRIP12 was exclusive to the Ku70 S155D list, considered a high confidence interactor based on SAINTexpress analysis, and appeared in all three biological replicates of the Ku70 S155D-BioID2 mass spectrometry results. Using proximity ligation assays (PLA), we demonstrated a significantly increased association between Ku70 S155D-HA and TRIP12 compared to wild-type Ku70-HA cells. In addition, we were able to demonstrate a robust PLA signal between endogenous Ku70 and TRIP12 in the presence of double-stranded DNA breaks. Finally, co-immunoprecipitation analyses showed an enhanced interaction between TRIP12 and Ku70 upon treatment with ionizing radiation, suggesting a direct or indirect association in response to DNA damage. Altogether, these results suggest an association between Ku70 phospho-S155 and TRIP12.

Abstract 2620: TRIM4 is the E3 ubiquitin-ligase for TPL2/MAP3K8 and is modulated by oncogenic KRAS

Abstract TPL2 (tumor progression locus 2, a. k. a. Cot/MAP3K8) kinase becomes oncogenic via disruption of the C-terminus, which abrogates its proteasomal degradation. However, the mechanism underlying degradation of TPL2 remains unclear. Using proximity-dependent biotin identification (BioID), for the first time we have discovered that Tripartite Motif Containing 4 (TRIM4) is the E3-ligase that binds and degrades TPL2 via polyubiquitination of lysine 415 and 439. Notably, naturally-occurring oncogenic R442H and E188K mutations in TPL2 abrogated the binding and polyubiquitination by TRIM4. Furthermore, KRAS oncoprotein stabilizes TPL2 by promoting TRIM4 degradation. Using immunoprecipitation-mass spectrometry, we identified TRIM21 as a ligase that binds and stabilizes TRIM4, in part by reducing TRIM4 polyubiquitination. Therefore, oncogenic KRAS binds to and promotes TRIM21 degradation, destabilizing TRIM4 and prolonging the half-life of TPL2. Overall, we discovered novel mechanisms of TPL2 regulation which are influenced by oncogenic KRAS, providing opportunities for the development of novel therapies. Citation Format: Sapana Prakashrao Bansod. TRIM4 is the E3 ubiquitin-ligase for TPL2/MAP3K8 and is modulated by oncogenic KRAS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2620.

Putative Protein Interactome of the Rhomboid Protease RHBDL4.

The physiological functions of the rhomboid-related protein 4 (RHBDL4) are emerging, but their molecular details remain unclear. Because increased expression of RHBDL4 has been clinically linked to poorer outcomes in cancer patients, this association urgently demands a better understanding of RHBDL4. To elucidate the molecular interactions and pathways that RHBDL4 may be involved in, we conducted proximity-dependent biotin identification (BioID) assays. Our analyses corroborated several of the expected protein interactors such as the transitional endoplasmic reticulum (ER) ATPase VCP/p97 (TERA), but they also described novel putative interactors including IRS4, PGAM5, and GORS2. Using proximity-ligation assays, we validated VCP/p97, COPB, and VRK2 as proteins that are in proximity to RHBDL4. Overall, our results support the emerging functions of RHBDL4 in ER quality control and also point toward putative RHBDL4 functions in protein membrane insertion and membrane organization and trafficking.

Virotrap: Trapping Protein Complexes in Virus-Like Particles.

The discovery of protein-protein interactions can provide crucial information on protein function by linking proteins into known pathways or complexes within the cell. Mass spectrometry (MS)-based methods, such as affinity purification (AP)-MS and proximity-dependent biotin identification (BioID), allowed for a vast increase in the number of reported protein complexes. As a more recent addition to the arsenal of MS-based methods, Virotrap represents a unique technology that benefits from the specific properties of the human immunodeficiency virus-1 (HIV-1) Gag polyprotein. More specifically, Virotrap captures protein complexes in virus-like particles budded from human embryonic kidney (HEK293T) cells, bypassing the need for cell lysis and thus supporting identification of their content using MS. Being intrinsically different to its two main predecessors, affinity purification MS (AP-MS) and biotin-dependent identification (BioID), Virotrap was shown to complement data obtained with the existing MS-based toolkit. The proven complementarity of these MS-based strategies underlines the importance of using different techniques to enable comprehensive mapping of protein-protein interactions (PPIs). In this chapter, we provide a detailed overview of the Virotrap protocol to screen for PPIs using a bait protein of interest.

Periostin Protects Against Alcohol-related Liver Disease by Activating Autophagy by Interacting With Protein Disulfide Isomerase

The matricellular protein periostin plays a critical role in liver inflammation, fibrosis, and even carcinoma. Here, the biological function of periostin in alcohol-related liver disease (ALD) was investigated. We used wild-type (WT), Postn-null (Postn-/-) mice and Postn-/- mice with periostin recovery to investigate the biological function of periostin in ALD. Proximity-dependent biotin identification analysis identified the protein that interacted with periostin, and coimmunoprecipitation analysis validated the interaction between protein disulfide isomerase (PDI) and periostin. Pharmacological intervention and genetic knockdown of PDI were used to investigate the functional correlation between periostin and PDI in ALD development. Periostin was markedly upregulated in the livers of mice that were fed ethanol. Interestingly, periostin deficiency severely aggravated ALD in mice, whereas the recovery of periostin in the livers of Postn-/- mice significantly ameliorated ALD. Mechanistic studies showed that the upregulation of periostin alleviated ALD by activating autophagy through inhibition of the mechanistic target of rapamycin complex 1 (mTORC1) pathway, which was verified in murine models treated with the mTOR inhibitor rapamycin and the autophagy inhibitor MHY1485. Furthermore, a protein interaction map of periostin was generated by proximity-dependent biotin identification analysis. Interaction profile analysis identified PDI as a key protein that interacted with periostin. Intriguingly, periostin-mediated enhancement of autophagy by inhibiting the mTORC1 pathway in ALD depended on its interaction with PDI. Moreover, alcohol-induced periostin overexpression was regulated by transcription factor EB. Collectively, these findings clarify a novel biological function and mechanism of periostin in ALD and the periostin-PDI-mTORC1 axis is a critical determinant of ALD.

Proximity-dependent biotin labeling in testicular germ cells identified TESMIN-associated proteins

Characterization of protein–protein interactions (PPI) is a key to understanding the functions of proteins of interest. Recently developed proximity-dependent biotin identification (BioID) has been actively investigated as an alternative PPI mapping method because of its usefulness in uncovering transient PPI. Here, as an example of proximity labeling proteomics application in the testis, we generated two transgenic mouse lines expressing two biotin ligases (BioID2 or TurboID) fused with TESMIN, which translocates from the cytosol to the nucleus during meiotic progression and is required for reproduction. The BioID2 transgene, albeit not the TurboID transgene, rescued fertility defects of the Tesmin KO male mice, indicating that the TESMIN-BioID2 fusion can physiologically replace TESMIN. Furthermore, biotinylated protein pull-down and affinity-purification followed by mass spectrometry using the TESMIN-BioID2 transgenic mice captured components of the MYBL1–MuvB complex that regulate cell-cycle gene expression. Thus, our study shows that proximity labeling proteomics can be applied in male germ cells, although the choice of biotin ligase needs to be carefully tested.

Breaking the Pump: Targeting the Sodium-Potassium Pump As a Therapeutic Strategy in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a heterogenous hematologic malignancy with poor overall survival despite intensive cytotoxic chemotherapy and newer targeted agents. With a 5-year survival rate of only 30% in adults with AML, new therapeutic strategies are needed. Tissue-specific differences in the expression of paralog genes, which are not essential in most cell types due to the buffering effect of the partner pair, could make for highly selective gene dependencies. To identify novel, selective paralogous targets for AML, we integrated the Cancer Dependency Map, which provides genome-scale CRISPR/Cas9 depletion screening data in hundreds of cancer cell lines, with numerous databases characterizing protein-protein interactions, paralog relationships, and gene expression in cancer models. Here, we identified ATP1B3 as a context-specific, paralog related dependency in AML. ATP1B3 is the smaller glycoprotein beta subunit of the sodium-potassium pump (Na/K-ATP pump). Together with the catalytic alpha subunit ATP1A1, it forms a heterodimer located in the plasma membrane, regulating the electrochemical gradient through the transport of Na and K ions across the membrane. The Na/K-ATP pump is of vital importance in the maintenance of cellular homeostasis and membrane potential. While ATP1A1 carries out the ion transport and enzymatic activity, making it a common essential gene (a gene which ranks among the most depleted genes in at least 90% of screened cell lines), ATP1B3 is not essential in most cancer cells. The beta subunit is important for intracellular transport and stabilization of the alpha subunit in the membrane, but it has three paralogs: ATP1B3 showing similar expression patterns across tissues, ATP1B2 exclusively expressed in brain and retina, and ATP1B1 showing differential expression across tissues. ATP1B1 has uniformly low expression in hematological malignancies and low ATP1B1 expression is the strongest predictor of ATP1B3 dependency (Figure 1). Using CRISPR/Cas9 knockout and competitive growth assays, we showed that knockout of ATP1B3 in ATP1B1 low-expressing AML cells indeed leads to synthetic lethality. Knockout of ATP1B3 significantly decreased number and size of colonies in a patient-derived xenograft (PDX) model of AML to a similar degree as the knockout of the common essential gene ATP1A1. Moreover, in these AML models, the absence of both paralogs of the beta subunit resulted in the destabilization of their binding partner ATP1A1. In contrast, expression of ATP1B1 stabilized ATP1A1 despite ATP1B3 knockout in solid tumors and in ATP1B1-overexpressing AML cells. In vivo, using an orthotopic AML cell line mouse model and an AML PDX model, ATP1B3 knockout resulted in lower leukemia burden in comparison to ATP1B1 knockout or a non-targeting control guide. To determine if ATP1B1 and ATP1B3 share primarily redundant functions, we utilized BioID (proximity-dependent biotin identification) to identify their interaction partners. We discovered that in AML, there is significant overlap of the ATP1B1 and ATP1B3 binding partners, and ATP1A1 is among the strongest. Enrichment of gene sets involved in protein folding in the endoplasmic reticulum are also consistent with the important role of the beta subunits in proper ATP1A1 folding and stabilization. Taken together, we identified ATP1B3 as a selective dependency in AML. We propose that when ATP1B1 is poorly expressed, elimination of ATP1B3 leads to the destabilization of the sodium-potassium pump including ATP1A1. ATP1B3 is a potential tumor-selective therapeutic target for AML and other hematologic malignancies with low expression of ATP1B1. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Establishment of in vivo proximity labeling with biotin using TurboID in the filamentous fungus Sordariamacrospora

Proximity-dependent biotin identification (BioID) has emerged as a powerful methodology to identify proteins co-localizing with a given bait protein in vivo. The approach has been established in animal cells, plants and yeast but not yet in filamentous fungi. BioID relies on promiscuous biotin ligases fused to bait proteins to covalently label neighboring proteins with biotin. Biotinylated proteins are specifically enriched through biotin affinity capture from denatured cell lysates and subsequently identified and quantified with liquid chromatography-mass spectrometry (LC–MS). In contrast to many other affinity capture approaches for studying protein–protein interactions, BioID does not rely on physical protein–protein binding within native cell lysates. This feature allows the identification of protein proximities of weak or transient and dynamic nature. Here, we demonstrate the application of BioID for the fungal model organism Sordariamacrospora (Sm) using the example of the STRIPAK complex interactor 1 (SCI1) of the well-characterized striatin-interacting phosphatase and kinase (SmSTRIPAK) complex as proof of concept. For the establishment of BioID in S.macrospora, a codon-optimized TurboID biotin ligase was fused to SCI1. Biotin capture of the known SmSTRIPAK components PRO11, SmMOB3, PRO22 and SmPP2Ac1 demonstrates the successful BioID application in S.macrospora. BioID proximity labeling approaches will provide a powerful proteomics tool for fungal biologists.

DCAF7 regulates cell proliferation through IRS1-FOXO1 signaling

SummaryCell proliferation is dependent on growth factors insulin and IGF1. We sought to identify interactors of IRS1, the most proximal mediator of insulin/IGF1 signaling, that regulate cell proliferation. Using proximity-dependent biotin identification (BioID), we detected 40 proteins displaying proximal interactions with IRS1, including DCAF7 and its interacting partners DYRK1A and DYRK1B. In HepG2 cells, DCAF7 knockdown attenuated cell proliferation by inducing cell cycle arrest at G2. DCAF7 expression was required for insulin-stimulated AKT phosphorylation, and its absence promoted nuclear localization of the transcription factor FOXO1. DCAF7 knockdown induced expression of FOXO1-target genes implicated in G2 cell cycle inhibition, correlating with G2 cell cycle arrest. In Drosophila melanogaster, wing-specific knockdown of DCAF7/wap caused smaller wing size and lower wing cell number; the latter recovered upon double knockdown of wap and dfoxo. We propose that DCAF7 regulates cell proliferation and cell cycle via IRS1-FOXO1 signaling, of relevance to whole organism growth.

Proximity‐dependent biotinylation identifies a suite of candidate effector proteins from Fusarium graminearum

Fusarium graminearum is a fungal pathogen that causes Fusarium head blight in cereal crops. The identification of proteins secreted from pathogens to overcome plant defenses and cause disease, collectively known as effectors, can reveal the etiology of a disease process. Proximity-dependent biotin identification (BioID) was used to identify potential effector proteins secreted in planta by F. graminearum during the infection of Arabidopsis. Mass spectrometry analysis of streptavidin affinity-purified proteins revealed over 300 proteins from F. graminearum, of which 62 were candidate effector proteins (CEPs). An independent analysis of secreted proteins from axenic cultures of F. graminearum showed a 42% overlap with CEPs, thereby assuring confidence in the BioID methodology. The analysis also revealed that 19 out of 62 CEPs (approx. 30%) had been previously characterized with virulence function in fungi. The functional characterization of additional CEPs was undertaken through deletion analysis by the CRISPR/Cas9 method, and by overexpression into Triticum aestivum (wheat) leaves by the Ustilago hordei delivery system. Deletion studies of 12 CEPs confirmed the effector function of three previously characterized CEPs and validated the function of another four CEPs on wheat inflorescence or vegetative tissues. Lastly, overexpression in wheat showed that all seven CEPs enhanced resistance against the bacterial pathogen Pseudomonas syringae DC3000.

Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells

Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein, and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions. Proximity-dependent biotin identification (Bio-ID) mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3 and a strong pathway relationship to interleukin-2 regulated genes, which are known to govern cytotoxicity pathways. Chromatin immunoprecipitation and DNA sequencing analysis defined a canonical EBF4 binding motif, 5'-CCCNNGG/AG-3', closely related to the EBF1 binding site; using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted assay for transposase-accessible chromatin sequencing in EBF4-overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together, our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.

Plasmodium falciparum S-Adenosylmethionine Synthetase Is Essential for Parasite Survival through a Complex Interaction Network with Cytoplasmic and Nuclear Proteins.

S-adenosylmethionine synthetase (SAMS) is a key enzyme for the synthesis of the lone methyl donor S-adenosyl methionine (SAM), which is involved in transmethylation reactions and hence required for cellular processes such as DNA, RNA, and histone methylation, but also polyamine biosynthesis and proteostasis. In the human malaria parasite Plasmodium falciparum, PfSAMS is encoded by a single gene and has been suggested to be crucial for malaria pathogenesis and transmission; however, to date, PfSAMS has not been fully characterized. To gain deeper insight into the function of PfSAMS, we generated a conditional gene knockdown (KD) using the glmS ribozyme system. We show that PfSAMS localizes to the cytoplasm and the nucleus of blood-stage parasites. PfSAMS-KD results in reduced histone methylation and leads to impaired intraerythrocytic growth and gametocyte development. To further determine the interaction network of PfSAMS, we performed a proximity-dependent biotin identification analysis. We identified a complex network of 1114 proteins involved in biological processes such as cell cycle control and DNA replication, or transcription, but also in phosphatidylcholine and polyamine biosynthesis and proteasome regulation. Our findings highlight the diverse roles of PfSAMS during intraerythrocytic growth and sexual stage development and emphasize that PfSAMS is a potential drug target.

P455: BREAKING THE PUMP: TARGETING THE SODIUM-POTASSIUM PUMP AS A THERAPEUTIC STRATEGY IN ACUTE MYELOID LEUKEMIA

Background: Acute myeloid leukemia (AML) is a heterogenous hematologic malignancy with poor overall survival despite intensive cytotoxic chemotherapy and newer targeted agents. With a 5-year survival rate of only 29% in adults with AML, new therapeutic strategies are needed. Aims: In order to identify novel, selective targets for AML, we used the Cancer Dependency Map, which provides genome-scale CRISPR/Cas9 depletion screen data in hundreds of cancer cell lines. Here, we identified ATP1B3 as a context-specific dependency that could be therapeutically exploited. ATP1B3 is the smaller glycoprotein subunit (beta) of the sodium-potassium pump (Na/K-ATP pump). Together with the catalytic alpha subunit ATP1A1, it forms a heterodimer located in the plasma membrane, regulating the electrochemical gradient through the transport of Na and K ions across the membrane. The Na/K-ATP pump is of vital importance in the maintenance of cellular homeostasis and membrane potential and because of its function as a receptor and signal transducer. While the ATP1A1 carries out ion transport and enzymatic activity, making it a common essential gene (a gene which ranks among the most depleted genes in at least 90% of screened cell lines), ATP1B3 is not essential in all cancer cells. This beta subunit seems to be crucial for intracellular transport and stabilization of the alpha subunit in the membrane. The beta subunit has 4 paralogs, showing similar expression patterns among tissues, with one exception, ATP1B1. Methods: We used a diverse panel of functional genomic based assays, validating our finding using CRISPR/Cas9 knockout and overexpression constructs for the Na/K-ATP pump beta subunit paralogs. In an approach to analyze protein-protein interactions we generated BioID constructs for a mass spectrometry-based analysis. For an in vivo study we used a bioluminescent imaging (BLI)-based orthotopic mouse model of AML, carrying non-targeting, ATP1B1 or ATP1B3 knockout guides. Results: By using CRISPR/Cas9 knockout we could validate ATP1B3 as a selective dependency and performing competitive growth assays we showed that loss of ATP1B3 in ATP1B1 low expressing AML cells leads to synthetic lethality. The absence of both paralogs of the beta subunit results in the loss of their common essential binding partner ATP1A1 in hematologic malignancies, while higher expression of ATP1B1 can stabilize ATP1A1 under the loss of ATP1B3 in solid tumors or in ATP1B1 overexpressing AML cells. Next, we validated our findings in vivo. In a BLI-based orthotopic mouse model of AML, we found that the AML model with ATP1B3 knockout showed lower leukemia burden and normal spleen weight in comparison to a non-targeting or ATP1B1 knockout control. To understand the specific role of ATP1B3 we produced BioID (proximity-dependent biotin identification) constructs for ATP1B1 and ATP1B3. In ongoing studies, through this mass spectrometry-based analysis of protein-protein interactions, we will gain a greater insight into the protein partners of the Na/K-ATP pump. Summary/Conclusion: Taken together, we identified ATP1B3 as a selective dependency in AML. We propose that the elimination of ATP1B3 leads to the destabilization of the sodium-potassium pump when ATP1B1 levels are low, making it a potential tumor-selective therapeutic target for AML and other hematologic malignancies with low expression of ATP1B1.

P1408: MONOALLELIC AND BIALLELIC GERMLINE MUTATIONS AFFECTING THE TRANSCRIPTION FACTOR HELIOS CAUSE PLEIOTROPIC DEFECTS OF IMMUNITY

Background: Helios, encoded by IKZF2, is a member of the Ikaros family of transcription factors with pivotal roles in T-follicular helper, NK- and T-regulatory cell physiology. Somatic IKZF2 mutations are frequently found in lymphoid malignancies. Aims: Although germline mutations in IKZF1 and IKZF3, encoding Ikaros and Aiolos, have recently been identified in patients with phenotypically similar immunodeficiency syndromes, the effect of germline mutations in IKZF2 on human hematopoiesis and immunity remains to be elucidated. Methods: We performed whole exome sequencing in six patients with immune dysregulation and their family members. We then applied Co-immunoprecipitation, electrophoretic mobility shift assay and immunofluorescence microscopy techniques to assess dimerization and DNA binding capabilities of the mutations. Proteomic analysis by proximity-dependent Biotin Identification (BioID) was used to assess affinity of mutant Helios to its interaction partners, while single-cell RNA sequencing was applied to peripheral blood mononuclear cells (PBMCs) of two patients to study the transcriptional effect of the truncating and biallelic IKZF2 mutations. Results: We identified six patients with monoallelic germline IKZF2 mutations (one nonsense (p.R291X)- and 4 distinct missense variants) and one patient with a biallelic germline IKZF2 mutation (p.I325V). While patients with heterozygous variants were affected by immune dysregulation (systemic lupus erythematosus, immune thrombocytopenia or EBV-associated hemophagocytic lymphohistiocytosis), the patient with the homozygous variant suffered from recurrent respiratory tract infections complicated by bronchiectasis. Immunophenotype analysis revealed reduced propensities of NK cells, CD4+ T-cells with an inverted CD4/CD8 ratio, T-follicular helper cells and hypogammaglobulinemia across patients, while the p.I325V patient also had a reduction in relative and absolute B-cells and low relative proportions of Treg, MAIT and iNKT populations. Single-cell RNA sequencing of PBMCs from the patients carrying the monoallelic R291X truncating variant or the biallelic I325V variant revealed upregulation of pro-inflammatory genes associated with T-cell receptor activation and T-cell exhaustion. Our biochemical and proteomic analysis has revealed that only the truncating R291X mutation results in loss of Helios DNA binding and dimerization properties. However, BioID analysis revealed aberrant interaction of 4/6 Helios mutants with core components of the Nucleosome Remodeling histone Deacetylase (NuRD) complex conveying Helios-mediated epigenetic and transcriptional dysregulation. Summary/Conclusion: Thus, germline mutations in IKZF2 cause a novel syndrome associating immunodeficiency and profound immune dysregulation and disrupt interaction with the NuRD complex.

Cell tension controlling pathways and nutrient availability regulate plasma membrane ATP synthase trafficking

Introduction: The interplay between mechanical stress and cell metabolism is an emerging topic. However, the mechanotransduction pathways coordinating cell metabolism to the tensional status of the cell are poorly understood. Here, we provide several evidences suggesting that caveolae – mechanosensitive plasma membrane invaginations-, nutrient availability and cell tension controlling conditions are important for the biology of mitochondrial ATP synthase. Material and Methods: For achieving the caveolar interactome, plasma membrane biotinylation and co-localization experiments, we have used human retinal pigment epithelial-1 (RPE-1) cells, murine vascular aortic smooth muscle (MOVAS) cells and mouse embryonic fibroblasts (MEF). We used proximity-dependent biotin identification (BioID) and mass spectrometry to obtain the different interactomes of caveolar components. For plasma membrane (PM) localization of the ATP synthase we used PM biotinylation under different metabolic and mechanical conditions (nutrient starving, cell confluence). To study co-localization, we performed Proximity Ligation Assays (PLAs) in combination with mitochondrial and caveolar markers. Results: First, we have identified the interactome of all core caveolar components. Among the interactors, we identified subunits α and β of the mitochondrial ATP synthase, which interact with most of the caveolar components. Apart from its main localization at the inner mitochondrial membrane, the ATP synthase has also been detected in the PM, facing the extracellular space; this pool is known as ecto-ATP synthase. We show that the interaction with Caveolin-1 (Cav1), one of the main components of caveolae, occurs outside caveolae and mitochondria. In addition, the presence of ecto- ATP synthase at the PM is dependent on Cav1. Furthermore, conditions regulating cell tension, and metabolic challenges that promote autophagy, impinge on ecto-ATP synthase trafficking Conclusions: This study has characterized the interactome of caveolar components and has focused on the subunits α and β of the ATP synthase, which are also present at the PM. These subunits interact with Cav-1, but this interaction seems to occur in intracellular trafficking vesicles. Moreover, this process could be altered by mechanical cues and nutrient deprivation. Thus, our study suggests that trafficking routes regulating PM residents, and regulated by several caveolar components, are linked to nutrient starvation and mitochondrial biology.

Heat shock protein Grp78/BiP/HspA5 binds directly to TDP-43 and mitigates toxicity associated with disease pathology

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure or effective treatment in which TAR DNA Binding Protein of 43 kDa (TDP-43) abnormally accumulates into misfolded protein aggregates in affected neurons. It is widely accepted that protein misfolding and aggregation promotes proteotoxic stress. The molecular chaperones are a primary line of defense against proteotoxic stress, and there has been long-standing interest in understanding the relationship between chaperones and aggregated protein in ALS. Of particular interest are the heat shock protein of 70 kDa (Hsp70) family of chaperones. However, defining which of the 13 human Hsp70 isoforms is critical for ALS has presented many challenges. To gain insight into the specific Hsp70 that modulates TDP-43, we investigated the relationship between TDP-43 and the Hsp70s using proximity-dependent biotin identification (BioID) and discovered several Hsp70 isoforms associated with TDP-43 in the nucleus, raising the possibility of an interaction with native TDP-43. We further found that HspA5 bound specifically to the RNA-binding domain of TDP-43 using recombinantly expressed proteins. Moreover, in a Drosophila strain that mimics ALS upon TDP-43 expression, the mRNA levels of the HspA5 homologue (Hsc70.3) were significantly increased. Similarly we observed upregulation of HspA5 in prefrontal cortex neurons from human ALS patients. Finally, overexpression of HspA5 in Drosophila rescued TDP-43-induced toxicity, suggesting that upregulation of HspA5 may have a compensatory role in ALS pathobiology.

New insights into the molecular mechanisms of ROR1, ROR2, and PTK7 signaling from the proteomics and pharmacological modulation of ROR1 interactome

ROR1, ROR2, and PTK7 are Wnt ligand-binding members of the receptor tyrosine kinase family. Despite their lack of catalytic activity, these receptors regulate skeletal, cardiorespiratory, and neurological development during embryonic and fetal stages. However, their overexpression in adult tissue is strongly connected to tumor development and metastasis, suggesting a strong pharmacological potential for these molecules. Wnt5a ligand can activate these receptors, but lead to divergent signaling and functional outcomes through mechanisms that remain largely unknown. Here, we developed a cellular model by stably expressing ROR1, ROR2, and PTK7 in BaF3 cells that allowed us to readily investigate side-by-side their signaling capability and functional outcome. We applied proteomic profiling to BaF3 clones and identified distinctive roles for ROR1, ROR2, and PTK7 pseudokinases in modulating the expression of proteins involved in cytoskeleton dynamics, apoptotic, and metabolic signaling. Functionally, we show that ROR1 expression enhances cell survival and Wnt-mediated cell proliferation, while ROR2 and PTK7 expression is linked to cell migration. We also demonstrate that the distal C-terminal regions of ROR1 and ROR2 are required for receptors stability and downstream signaling. To probe the pharmacological modulation of ROR1 oncogenic signaling, we used affinity purification coupled to mass spectrometry (AP-MS) and proximity-dependent biotin identification (BioID) to map its interactome before and after binding of GZD824, a small molecule inhibitor previously shown to bind to the ROR1 pseudokinase domain. Our findings bring new insight into the molecular mechanisms of ROR1, ROR2, and PTK7, and highlight the therapeutic potential of targeting ROR1 with small molecule inhibitors binding to its vestigial ATP-binding site.

Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins.

Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication.