a-comparative-approach-to-characterize-landscape-host-pathogen

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Significant efforts were gathered to generate  large-scale comprehensive protein-protein interaction network maps. This is  instrumental to understand the ...

Institut Pasteur 

Université Sorbonne Paris Cité

Benchmarking a luciferase complementation assay for detecting protein complexes.

Analyse comparative d&#39;une compl&eacute;mentation de luciferase pour la d&eacute;tection des complexes prot&eacute;iques.

Analisi comparativa di un&#39;analisi di complementazione di luciferase per la rilevazione di complessi della proteina.

Human Papillomaviruses (HPV) cause widespread infections in humans, resulting in latent infections or diseases ranging from benign hyperplasia to cancers. HPV-induced pathologies result from complex interplays between viral proteins and the host proteome. Given the major public health concern due to HPV-associated cancers, most studies have focused on the early proteins expressed by HPV genotypes with high oncogenic potential (designated high-risk HPV or HR-HPV). To advance the global understanding of HPV pathogenesis, we mapped the virus/host interaction networks of the E2 regulatory protein from 12 genotypes representative of the range of HPV pathogenicity. Large-scale identification of E2-interaction partners was performed by yeast two-hybrid screenings of a HaCaT cDNA library. Based on a high-confidence scoring scheme, a subset of these partners was then validated for pair-wise interaction in mammalian cells with the whole range of the 12 E2 proteins, allowing a comparative interaction analysis. Hierarchical clustering of E2-host interaction profiles mostly recapitulated HPV phylogeny and provides clues to the involvement of E2 in HPV infection. A set of cellular proteins could thus be identified discriminating, among the mucosal HPV, E2 proteins of HR-HPV 16 or 18 from the non-oncogenic genital HPV. The study of the interaction networks revealed a preferential hijacking of highly connected cellular proteins and the targeting of several functional families. These include transcription regulation, regulation of apoptosis, RNA processing, ubiquitination and intracellular trafficking. The present work provides an overview of E2 biological functions across multiple HPV genotypes.

Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions.

Virus du papillome humain (VPH) causent des infections tr&egrave;s r&eacute;pandues chez les humains, entra&icirc;nant des infections latentes ou maladies allant de l&#39;hyperplasie b&eacute;nigne de prostate aux cancers. Pathologies induites par les HPV r&eacute;sultent d&#39;interactions complexes entre les prot&eacute;ines virales et du prot&eacute;ome de l&#39;h&ocirc;te. Compte tenu de la pr&eacute;occupation de sant&eacute; publique majeur due aux cancers associ&eacute;es au VPH, la plupart des &eacute;tudes ont port&eacute; sur les d&eacute;but prot&eacute;ines exprim&eacute;es par les g&eacute;notypes de VPH &agrave; haut potentiel oncog&eacute;nique (d&eacute;sign&eacute; &agrave; haut risque de HPV ou VPH). Pour faire progresser la compr&eacute;hension globale de la pathogen&egrave;se de l&#39;HPV, nous avons cartographi&eacute; les r&eacute;seaux d&#39;interaction virus/h&ocirc;te de la prot&eacute;ine r&eacute;gulatrice E2 de 12 repr&eacute;sentant de g&eacute;notypes de la pathog&eacute;nicit&eacute; de la gamme de HPV. Identification &agrave; grande &eacute;chelle des partenaires E2-interaction a &eacute;t&eacute; r&eacute;alis&eacute;e par des projections de deux-hybride de levure d&#39;une banque d&#39;ADNc HaCaT. Bas&eacute; sur un sch&eacute;ma de score de haut-confiance, un sous-ensemble de ces partenaires a &eacute;t&eacute; ensuite valid&eacute; pour l&#39;interaction par paire dans les cellules de mammif&egrave;res avec toute la gamme des 12 prot&eacute;ines E2, ce qui permet une analyse comparative d&#39;interaction. Regroupement hi&eacute;rarchique d&#39;interaction h&ocirc;te-E2 profils surtout recapitulated phylog&eacute;nie HPV et fournit des indices sur l&#39;implication de E2 dans l&#39;infection &agrave; HPV. Un ensemble de prot&eacute;ines cellulaires puisse donc &ecirc;tre identifi&eacute; une discrimination, entre le VPH muqueux, E2 prot&eacute;ines du VPH 16 ou 18 du VPH g&eacute;nital non oncog&egrave;ne. L&#39;&eacute;tude des r&eacute;seaux d&#39;interactions r&eacute;v&egrave;le un d&eacute;tournement pr&eacute;f&eacute;rentiel des prot&eacute;ines cellulaires tr&egrave;s branch&eacute;s et le ciblage de plusieurs familles fonctionnelles. Il s&#39;agit de r&eacute;gulation de la transcription, r&eacute;gulation de l&#39;apoptose, ARN, ubiquitination et trafic intracellulaire. Ce travail donne un aper&ccedil;u des fonctions biologiques de E2 &agrave; travers plusieurs g&eacute;notypes de VPH.

Comparaison de g&eacute;notype &agrave; grande &eacute;chelle du virus du papillome humain r&eacute;seaux d&#39;interactions h&ocirc;te-E2 fournit des nouvelles perspectives pour e2 fonctions mol&eacute;culaires.

Papillomavirus umano (HPV) provoca infezioni diffuse negli esseri umani, causando infezioni latenti o malattie che vanno da iperplasia benigna a tumori. Patologie indotte da HPV risultano di giochi complessi tra proteine virali e il proteoma host. Data la preoccupazione di salute pubblica a causa di tumori HPV-associati, maggior parte degli studi si sono concentrati sulle prime proteine espresse da HPV genotipi con alto potenziale oncogenico (designato ad alto rischio di HPV o HR-HPV). Per far avanzare la comprensione globale della patogenesi dell&#39;HPV, abbiamo mappato le reti di interazione virus/ospite della proteina E2 normativa da 12 rappresentante di genotipi di patogenicit&agrave; gamma di HPV. Identificazione su larga scala dei partner E2-interazione &egrave; stata eseguita da proiezioni di due-ibrido del lievito di una libreria di cDNA HaCaT. Basato su uno schema di punteggio alto-fiducia, un sottoinsieme di questi partner &egrave; stato poi convalidato per interazione pairwise in cellule di mammiferi con l&#39;intera gamma delle proteine E2 12, consentendo un&#39;analisi comparativa di interazione. Clustering gerarchico dell&#39;interazione ospite-E2 profili principalmente recapitulated filogenesi HPV e fornisce indizi per il coinvolgimento di E2 nell&#39;infezione da HPV. Una serie di proteine cellulari potrebbe essere identificata cos&igrave; discriminante, tra l&#39;HPV mucosali, proteine E2 di HR-HPV 16 o 18 dal non-oncogenica HPV genitale. Lo studio delle reti di interazione ha rivelato un dirottamento preferenziale delle proteine cellulari altamente connessi e la destinazione delle diverse famiglie funzionali. Questi includono la regolazione di trascrizione, regolazione del apoptosis, RNA processing, ubiquitination e traffico intracellulare. Il presente lavoro fornisce una panoramica delle funzioni biologiche E2 attraverso molteplici genotipi HPV.

Confronto genotipo su larga scala di papillomavirus umano reti di interazione E2-host fornisce nuove intuizioni per e2 funzioni molecolari.

Comparative interactomics is a strategy for inferring potential interactions among orthologous proteins or "interologs". Herein we focus, in contrast to standard homology-based inference, on the divergence of protein interaction profiles among closely related organisms, showing that the approach can correlate specific traits to phenotypic differences. As a model, this new comparative interactomic approach was applied at a large scale to human papillomaviruses (HPVs) proteins. The oncogenic potential of HPVs is mainly determined by the E6 and E7 early proteins. We have mapped and overlapped the virus-host protein interaction networks of E6 and E7 proteins from 11 distinct HPV genotypes, selected for their different tropisms and pathologies. We generated robust and comprehensive datasets by combining two orthogonal protein interaction assays: yeast two-hybrid (Y2H), and our recently described "high-throughput Gaussia princeps protein complementation assay" (HT-GPCA). HT-GPCA detects protein interaction by measuring the interaction-mediated reconstitution of activity of a split G. princeps luciferase. Hierarchical clustering of interaction profiles recapitulated HPV phylogeny and was used to correlate specific virus-host interaction profiles with pathological traits, reflecting the distinct carcinogenic potentials of different HPVs. This comparative interactomics constitutes a reliable and powerful strategy to decipher molecular relationships in virtually any combination of microorganism-host interactions.

Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase.

Interactomique comparative est une strat&eacute;gie pour inf&eacute;rer les interactions potentielles entre les prot&eacute;ines orthologues ou &laquo; interologs &raquo;. Ici nous nous concentrons, contrairement &agrave; l&#39;inf&eacute;rence standard bas&eacute;e sur l&#39;homologie, sur la divergence des profils d&#39;interaction de prot&eacute;ines parmi les organismes apparent&eacute;s, montrant que l&#39;approche peut corr&eacute;ler des traits sp&eacute;cifiques aux diff&eacute;rences ph&eacute;notypiques. Comme un mod&egrave;le, cette nouvelle approche comparative interactomic a &eacute;t&eacute; appliqu&eacute;e &agrave; grande &eacute;chelle aux prot&eacute;ines de virus du papillome humain (HPV). Le potentiel oncog&egrave;ne du HPV est principalement d&eacute;termin&eacute; par les prot&eacute;ines pr&eacute;coces E6 et E7. Nous avons cartographi&eacute; et chevauchent les r&eacute;seaux d&#39;interactions prot&eacute;iques virus-h&ocirc;te de prot&eacute;ines E6 et E7 11 g&eacute;notypes de VPH distinctes, s&eacute;lectionn&eacute;s pour leurs diff&eacute;rents Tropismes et les pathologies. Nous avons g&eacute;n&eacute;r&eacute; des ensembles de donn&eacute;es robuste et complet en combinant deux essais d&#39;interaction de prot&eacute;ine orthogonale : levure-hybride (Y2H) et notre r&eacute;cemment d&eacute;crite &laquo; high-throughput Gaussia princeps prot&eacute;ine analyse de compl&eacute;mentation &raquo; (HT-ACPP). HT-ACPP d&eacute;tecte l&#39;interaction de la prot&eacute;ine en mesurant la reconstitution induite par l&#39;interaction de l&#39;activit&eacute; d&#39;un split g. princeps lucif&eacute;rase. Regroupement hi&eacute;rarchique des profils d&#39;interaction r&eacute;capitul&eacute; phylog&eacute;nie HPV et a &eacute;t&eacute; utilis&eacute; pour corr&eacute;ler les profils d&#39;interaction virus-h&ocirc;te sp&eacute;cifique avec des traits pathologiques, refl&eacute;tant les potentiels canc&eacute;rog&egrave;nes distinctes des diff&eacute;rents HPV. Ce comparatif interactomique constitue une strat&eacute;gie fiable et puissante pour d&eacute;chiffrer les relations mol&eacute;culaires dans pratiquement n&#39;importe quelle combinaison des interactions microorganismes-h&ocirc;te.

Analyse comparative d&#39;interactomes virus-h&ocirc;te avec un dosage de compl&eacute;mentation de mammif&egrave;res prot&eacute;ine haut d&eacute;bit bas&eacute;e sur Gaussia princeps lucif&eacute;rase.

Interattomica comparativa &egrave; una strategia per la deduzione di potenziali interazioni tra proteine orthologous o &quot;interologs&quot;. Qui ci concentriamo, in contrasto con standard inferenza basata su omologia, sulla divergenza dei profili di interazione della proteina tra organismi strettamente correlati, mostrando che l&#39;approccio pu&ograve; correlare specifici tratti di differenze fenotipiche. Come un modello, questo nuovo approccio comparativo interactomic &egrave; stato applicato a larga scala di proteine di papillomavirus umano (HPV). Il potenziale oncogenico del HPV &egrave; determinato principalmente dalle proteine E6 ed E7 precoce. Abbiamo mappato e le reti di interazione della proteina virus-ospite delle proteine E6 ed E7 da 11 diversi genotipi HPV, selezionati per la loro diverse tropismi e patologie si sovrappongono. Abbiamo generato robusto e completo set di dati dalla combinazione di due analisi di interazione proteina ortogonale: lievito due-ibrido (Y2H) e il nostro recentemente descritto &quot;high-throughput Gaussia princeps complementazione analisi della proteina&quot; (HT-GPCA). HT-GPCA rileva interazione proteina misurando la ricostituzione dell&#39;attivit&agrave; di un split g. princeps luciferase interazione mediata. Clustering gerarchico dei profili di interazione ricapitolate filogenesi HPV e fu utilizzato per correlare i profili di interazione virus-ospite specifico con tratti patologici, riflettendo i potenziali cancerogeni distinti di HPV diverso. Questo interattomica comparativa costituisce una strategia potente e affidabile per decifrare i rapporti molecolari in praticamente qualsiasi combinazione delle interazioni microrganismo-ospite.

Analisi comparativa dei virus-host interactomes con un dosaggio di complementazione dei mammiferi high-throughput di proteine basato su Gaussia princeps luciferasi.

Over 100 genotypes of human papillomaviruses (HPVs) have been identified as being responsible for unapparent infections or for lesions ranging from benign skin or genital warts to cancer. The pathogenesis of HPV results from complex relationships between viral and host factors, driven in particular by the interplay between the host proteome and the early viral proteins. The E2 protein regulates the transcription, the replication as well as the mitotic segregation of the viral genome through the recruitment of host cell factors to the HPV regulatory region. It is thereby a pivotal factor for the productive viral life cycle and for viral persistence, a major risk factor for cancer development. In addition, the E2 proteins have been shown to engage numerous interactions through which they play important roles in modulating the host cell. Such E2 activities are probably contributing to create cell conditions appropriate for the successive stages of the viral life cycle, and some of these activities have been demonstrated only for the oncogenic high-risk HPV. The recent mapping of E2-host protein-protein interactions with 12 genotypes representative of HPV diversity has shed some light on the large complexity of the host cell hijacking and on its diversity according to viral genotypes. This article reviews the functions of E2 as they emerge from the E2/host proteome interplay, taking into account the large-scale comparative interactomic study.

The HPV E2-Host Protein-Protein Interactions: A Complex Hijacking of the Cellular Network.

Plus de 100 g&eacute;notypes du virus du papillome humain (HPV) ont &eacute;t&eacute; identifi&eacute;s comme &eacute;tant responsable des infections inapparente ou de l&eacute;sions allant de b&eacute;nignes de la peau ou des verrues g&eacute;nitales au cancer. La pathog&eacute;nie du VPH r&eacute;sultant des relations complexes entre viral and host factors, pilot&eacute;es notamment par l&#39;interaction entre le prot&eacute;ome de l&#39;h&ocirc;te et les prot&eacute;ines virales pr&eacute;coces. La prot&eacute;ine E2 r&eacute;gule la transcription, la reproduction ainsi que la s&eacute;gr&eacute;gation mitotique du g&eacute;nome viral par le recrutement des facteurs cellule h&ocirc;te &agrave; la r&eacute;gion r&eacute;gulatrice de HPV. C&#39;est donc un facteur crucial pour le cycle de vie viral productif et &agrave; la persistance virale, un facteur de risque majeur pour le d&eacute;veloppement du cancer. En outre, les prot&eacute;ines E2 montrent &agrave; s&#39;engager de nombreuses interactions &agrave; travers lequel ils jouent un r&ocirc;le important dans la modulation de la cellule h&ocirc;te. Ces activit&eacute;s de E2 contribuent probablement pour cr&eacute;er les conditions de la cellule appropri&eacute;e pour les &eacute;tapes successives du cycle de vie viral, et certaines de ces activit&eacute;s ont &eacute;t&eacute; d&eacute;montr&eacute;s que pour le HPV &agrave; haut risque oncog&egrave;ne. La cartographie r&eacute;cente d&#39;interactions prot&eacute;ine-prot&eacute;ine E2-h&ocirc;te avec 12 g&eacute;notypes repr&eacute;sentatifs de la diversit&eacute; de l&#39;HPV a faire la lumi&egrave;re sur la grande complexit&eacute; du d&eacute;tournement de cellule h&ocirc;te et sur sa diversit&eacute; selon les g&eacute;notypes viraux. Cet article passe en revue les fonctions de E2 tels qu&#39;ils ressortent de l&#39;interaction du prot&eacute;ome E2/h&ocirc;te, en tenant compte de l&#39;&eacute;tude &agrave; grande &eacute;chelle interactomic comparative.

Les Interactions de prot&eacute;ine-prot&eacute;ine E2-h&ocirc;te contre le VPH : Un d&eacute;tournement Complex du r&eacute;seau cellulaire.

Pi&ugrave; di 100 genotipi di papillomavirus umano (HPV) sono state identificate come responsabili assenti infezioni o lesioni che vanno dalla pelle benigna o verruche genitali al cancro. La patogenesi dell&#39;HPV deriva da complesse relazioni tra virale e ospitare fattori, guidate in particolare dall&#39;interazione tra il proteoma host e le prime proteine virali. La proteina E2 regola la trascrizione, la replica, nonch&eacute; la segregazione mitotica del genoma virale attraverso l&#39;assunzione di fattori cellula ospite alla regione normativa HPV. &Egrave; quindi un fattore cruciale per il ciclo di vita virale produttivo e per la persistenza virale, un importante fattore di rischio per lo sviluppo del cancro. Inoltre, le proteine E2 hanno dimostrate di impegnarsi numerose interazioni attraverso cui giocano ruoli importanti nel modulare la cellula ospite. Tali attivit&agrave; E2 sono probabilmente contribuendo a creare condizioni di cella appropriata per le fasi successive del ciclo di vita virale, e alcune di queste attivit&agrave; sono state dimostrate solo per l&#39;HPV ad alto rischio oncogenico. La recente mappatura delle interazioni della proteina-proteina E2-host con 12 genotipi rappresentativi della diversit&agrave; HPV ha fatto qualche luce sulla grande complessit&agrave; del dirottamento della cellula ospite e sulla sua diversit&agrave; secondo genotipi virali. Questo articolo recensisce le funzioni di E2 che emergono dall&#39;interazione proteome E2/host, prendendo in considerazione lo studio su grande scala comparativa interactomic.

Article	Year
Benchmarking a luciferase complementation assay for detecting protein complexes. Nature methods\| PubMed ID: 22127214	2011
Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions. PLoS pathogens\| PubMed ID: 22761572	2012
Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase. Methods (San Diego, Calif.)\| PubMed ID: 22898364	2012
The HPV E2-Host Protein-Protein Interactions: A Complex Hijacking of the Cellular Network. The open virology journal\| PubMed ID: 23341853	2012

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