A systematic atlas of chaperome deregulation topologies across the human cancer landscape
[['Eukaryotic proteomes comprise a complex repertoire of diverse protein species that are organized in a modular interactome network in order to execute native function in support of proteostasis and a healthy cellular phenotype .', 'Proteome balance is safeguarded by the proteostasis network ( PN ) , an intricately regulated network of conserved processes that have evolved to safeguard the healthy folded proteome [1] .', 'Cellular proteostasis capacity is limited within the constraints of each cell’s proteostasis boundary [2] .', 'Proteostasis imbalances , deficiency and functional collapse are implicated in a broad and increasing spectrum of protein conformational diseases with loss of native function or gain of toxic function , ranging from metabolic and neurodegenerative diseases to cancer [3 , 4] .', 'Increasing awareness of the fundamental role of the PN in cellular health , its relevance in diseases and potential as a therapeutic target of proteostasis regulator ( PR ) drugs call for a systematic and systems-level assessment of PN deregulation throughout the human diseasome , towards improved understanding of diseases of proteostasis deficiency and rationalized network-informed approaches to therapeutic proteostasis re-adjustment .', 'Important progress has been made in our understanding of proteostasis biology , building on fundamental insights on conserved proteostasis processes and their role in disease , such as chaperone-assisted protein folding and quality control [5–8] , clearance through autophagy [9–13] and the ubiquitin-proteasome system ( UPS ) [14–16] , followed by the appreciation of their concerted action within a conserved tightly regulated PN [1 , 17] .', 'The identification , development and first clinical evaluations of small molecule PR drugs for therapeutic re-adjustment of proteostasis diseases such as cystic fibrosis represents a novel and powerful therapeutic paradigm [1 , 2 , 18–23] .', 'First investigations have started to explore systems-level quantitative and functional approaches to assess the implications of PN functional arms such as the chaperome in human tissue aging and disease [4 , 24–26] .', 'A precise understanding of the molecular mechanisms by which PN alterations contribute to disease could open novel therapeutic intervention strategies in a wide spectrum of proteostasis-related diseases .', 'Still , to date , there has been no systematic study addressing the characteristics and extent of PN alterations in human diseases at a systems-level .', 'The folding functional arm , the human chaperome , is highly conserved and of central importance in the PN , responsible for maintaining the native folded proteome .', 'In cancers , mutations and genomic instability inevitably entail alterations of proteome composition and balance that are far less well explored than the consequences of nucleic acid sequence alterations .', 'Post-translational alterations at the proteomic level are beyond the reach of DNA repair mechanisms and cancer cells are constantly challenged by the need to accommodate large amounts of proteotoxic stress in consequence of increased translational flux and proliferation as well as proteotoxic stressors .', 'Proteome instability and pathological alterations in the abundance of key signalling or housekeeping molecules such as kinases , metabolic enzymes or molecular transporters have to be buffered by the PN to ensure cellular survival .', 'The cancerous state poses characteristic requirements on the PN , such as high chaperone levels and elevated proteasome activity in order to ensure for sufficient correction or elimination of aberrant protein species in light of increased translational flux and metabolic stress [27] .', 'This chronic challenge ultimately drives cancer cells into a dependency on quality control and stress response mechanisms , a phenomenon previously described as non-oncogene addiction [28 , 29] .', 'Several individual chaperones and heat shock proteins such as HSP90 have consistently been found upregulated in cancers [27] .', 'However , the profile and extent of chaperome differential expression has not been assessed systematically across the human cancer landscape .', 'Challenged by the genetic complexity and heterogeneity , collective prevalence and unmet medical need of the wide spectrum of human cancers as well as the lack of a systems-level understanding of proteostasis alterations during carcinogenic transformation , we developed a novel integrated analytical pipeline and software toolkit for the quantitative profiling of chaperome changes across the human cancer landscape ( Fig 1 ) .', 'We utilized an expert-curated functional chaperome ontology comprising the ensemble of 332 human chaperone and co-chaperone genes [4] ( Fig 1A ) .', 'In order to apply our analytical workflow on a recent and comprehensive cancer gene expression dataset with clinical relevance , we turned to The Cancer Genome Atlas ( TCGA ) compendium [30] .', 'We started with a customized genomic analysis pipeline in order to map chaperome functional family expression changes across TCGA solid cancers compared to matching normal tissue ( Fig 1B ) .', 'The resulting top-level view on cancer chaperome deregulation revealed a broad chaperome upregulation throughout the majority of cancers .', 'This consistent and high overall chaperome upregulation prompted us to zoom in on functional sub-families .', 'This analysis surfaced clusters of chaperome functional family up- and downregulation signatures that enabled further stratification of cancers .', 'In summary , our analysis of the 10 major chaperome functional families reveals pronounced tissue differences of cancer chaperome deregulation .', 'The preferential upregulation of ATP-dependent chaperone families such as HSP90s and HSP60s , while ATP-independent chaperones , co-chaperones , and small heat shock proteins ( sHSPs ) are consistently downregulated , is opposed to chaperome alteration patterns observed in brain tissues during aging and in neurodegenerative diseases [4] .', 'These characteristic chaperome-wide differences further justify our approach and need for systematic maps of PN deregulation across the human diseasome .', 'In order to enable comprehensive , contextual , and quantitative representations of the complexity of chaperome alterations across a large number of patient biopsy disease datasets , we developed a new custom data dimensionality reduction and visualisation approach .', 'Combining Meta-PCA , a novel principal component analysis ( PCA ) based two-step dimension reduction algorithm and its resulting quantitative M-scores of chaperome functional family disease alteration of gene expression with contextual polar plot visualisations , we provide intuitive quantitative maps of cancer chaperome gene expression changes ( Fig 1B ) .', 'The mechanistic understanding of genotype-phenotype relationships in complex genetically heterogeneous diseases such as cancers requires the consideration of the cellular interactome network [31] .', 'To reduce complexity and to highlight contextual changes of chaperome functional families , we first generated a custom curated high-confidence physical protein-protein interaction ( PPI ) chaperome network .', 'We then collapsed proteins ( nodes ) and physical PPIs ( edges ) into a meta-network , where meta-nodes represent respective functional family members and meta-edges bundle the interactions between families ( Fig 1C ) .', 'This curated high-quality chaperome meta-network base-grid enabled the contextual projection of cancer-specific chaperome functional family differential gene expression ( M-scores ) onto the underlying interactome .', 'We integrated these dimensions into interactome-guided , three-dimensional topographic maps visualising chaperome functional family cancer differential gene expression changes in the context of interactome network proximity , intuitively providing quantitative views of cancer chaperome deregulation ( Fig 1D ) .', 'To make these resources easily available to the community , we developed Proteostasis Profiler ( Pro2 ) , an integrated web-based suite of applications enabling intuitive quantitative analyses and comparative visualisation of differential expression of complex PN alterations across large disease dataset compendia such as the TCGA .', 'Visualisation and analysis features include heat map clustering and polar plot display .', 'Integrated meta-networks and interactome-guided 3D topographic maps ease comparative exploration of cancer chaperome deregulation in the context of interactome network wiring .', 'Pro2 is designed to serve the scientific community as a user-friendly application for systems-level exploration of PN disease alterations , at reduced complexity .', 'Overall , this study represents a systematically derived systems-level atlas of chaperome deregulation maps in cancers and neurodegenerative diseases , with a detailed focus on chaperome functional family alterations .', 'The integrated genomic analysis workflow , built into the Pro2 suite of visualisation tools , provides a resource and analytical platform for future characterisation and exploration of PN deregulation patterns across the human diseasome , and as a readout interface for network shifts induced by therapeutic regulation .'], ['Homeostasis of the cellular proteome , or proteostasis , is fine-tuned by the proteostasis network ( PN ) , an intricately regulated network of conserved processes that have evolved to safeguard the native functional proteome and cellular health .', 'The human chaperome , an ensemble of 332 chaperones and co-chaperones , represents a central functional arm within the PN in charge of maintaining the cellular folding landscape ( S1A Table ) [4] .', 'Motivated by the genetic heterogeneity of cancers , their prevalence and associated medical need as well as the lack of a systems-level understanding of the role of proteostasis genomic alterations during carcinogenesis , we systematically assessed chaperome gene expression changes across the diverse spectrum of human cancers .', 'We focused on an established resource of human cancer patient biopsy RNA-seq datasets provided through The Cancer Genome Atlas ( TCGA ) [30 , 32] .', 'We considered 22 human solid cancers with available corresponding healthy counterpart tissue biopsy data .', 'To obtain global views on chaperome commonalities or differences between cancers , we applied Gene Set Analysis ( GSA ) in order to quantify gene expression changes of the chaperome and its functional families .', 'GSA is an advanced derivative of Gene Set Enrichment Analysis ( GSEA ) that methodologically differs primarily through its use of the maxmean statistic , the mean of the positive or negative gene scores in each gene set , whichever is larger in absolute value , that has proven superior to the modified Kolmogorov-Smirnov statistic used in GSEA [33] .', 'Secondly , GSA uses a different null distribution for false discovery rate ( FDR ) estimations , through a restandardization of genes in addition to sample permutation in GSEA .', 'This step is crucial , as it allows assessing statistical robustness of the expert-curated chaperome functional ontology gene family groups .', 'We obtained the GSA derived probability ( p values ) for each functional gene group to be significantly up- or downregulated in cancer as ∆GSA values in the interval [-1 , +1] according to ( ( 1—upregulation p value ) — ( 1—downregulation p value ) ) .', 'Notably , the human chaperome is predominantly upregulated across the majority of TCGA solid cancers with a ∆GSA group mean change of +0 . 50 as compared to 100 random sets of non-chaperome genes ( Fig 2A ) .', 'This overall chaperome upregulation highlights cellular non-oncogene addiction to chaperone-assisted folding and protein quality control mechanisms in consequence of increased client load , further challenging cellular proteostasis and driving “proteostasis addiction” in cancers [34] .', 'Despite the diverse established knowledge about the role of chaperone upregulation in cancer , the deregulation of the human chaperome has not been assessed at a systems-level throughout the human cancer landscape .', 'To functionally resolve the general chaperome upregulation across cancers , we zoomed in on functional family gene expression alterations .', 'GSA followed by Euclidean clustering of chaperome functional families revealed characteristic cancer differences .', 'We found the key ATP-dependent HSP90 and HSP60 families , of which selected members have previously been shown to be upregulated in cancers , amongst the most highly upregulated functional families with ∆GSA group mean changes of +0 . 55 and +0 . 51 , respectively , alongside ER-specific chaperone factors ( +0 . 53 ) , followed by Prefoldins ( PFDs , +0 . 40 ) , HSP100 AAA+ ATPases ( +0 . 32 ) , and mitochondria-specific chaperones ( MITOs , +0 . 09 ) ( Fig 2B ) .', 'These six functional families of predominantly ATP-dependent chaperones represent an upregulation cluster with an overall group mean change of +0 . 40 .', 'Intriguingly , the HSP70-HSP40 system and the large family of TPR-domain containing co-chaperones are overall repressed , with less consistent and largely cancer-specific alterations .', 'HSP40 co-chaperones ( -0 . 09 ) cluster closest with HSP70s ( -0 . 10 ) , indicative of the functional relationship they engage in during the HSP70 chaperone cycle .', 'While HSP40 co-chaperones are overall weakly downregulated ( -0 . 09 ) , also the second group of co-chaperones , the TPR-domain containing proteins , clustered with the HSP70-HSP40 system and were overall downregulated ( -0 . 18 ) .', 'Strikingly , sHSPs ( -0 . 74 ) were overall very consistently and strongly downregulated .', 'Overall , sHSPs , TPRs , and the HSP70-HSP40 system clustered in a downregulation cluster with an overall group mean change of -0 . 28 across cancers .', 'Besides marked differences in the pattern of cancer functional family changes , Euclidean clustering of cancer groups ( rows ) revealed two major clusters ( Fig 2B ) ( with a p-value equal to 0 . 016 via multiscale bootstrap resampling ) .', 'The vast majority of cancers is characterised by the consistent upregulation of HSP90s , ER-specific chaperones , HSP60s , PFDs , HSP100s and MITOs , opposed by a very consistent downregulation of sHSPs and a more cancer-specific overall downregulation of the HSP70-HSP40 system an TPR-domain co-chaperones .', 'This group comprises Cluster I , representing ~91% of cancers , while Cluster II comprises ~9% of cancers with largely opposed chaperome deregulation signatures , in this set namely skin cutaneous melanoma ( SKCM ) , and pheochromocytoma and paraganglioma ( PCPG ) .', 'In summary , systematically assessing gene expression data derived from a total of 10 , 456 patient samples uncovers broad differences in chaperome-scale deregulation across the variety of human solid cancers .', 'While the vast majority of cancers shows consistent and strong upregulation of chaperome genes , this analysis reveals marked clusters of chaperome functional family expression signatures that further stratify cancers by differential chaperome expression .', 'The major ATP-dependent chaperone functional families are consistently upregulated across a majority of cancers , while co-chaperones and sHSPs are consistently repressed ( Fig 2B ) .', 'In order to quantify this trend , we assessed the 22 differentially regulated cancer chaperomes for functional characteristics .', 'First , we compared expression of 88 chaperones against 244 co-chaperones represented in the human chaperome [4] .', 'Projecting TCGA cancer groups by their chaperone and co-chaperone differential expression highlights a significant preponderance of cancer chaperome upregulation , including both chaperones and co-chaperones , while only a minor fraction of each is downregulated ( S2A and S2B Fig ) .', 'Overall , chaperones tend to be more upregulated than co-chaperones ( S2B Fig ) .', 'Consistently , within the group of chaperones , we find an overall preponderance of upregulation of both ATP-dependent and ATP-independent chaperones , while only small fractions each are downregulated ( S2C and S2D Fig ) .', 'The 50 ATP-dependent chaperones are more upregulated than the 38 ATP-independent chaperones , while ATP-independent chaperones are more downregulated than ATP-dependent chaperones ( S2D Fig ) .', 'This analysis exposes a sub-group of cancers as notable exceptions to these trends , suggesting fundamental differences in chaperome deregulation .', 'Projection of TCGA cancer groups by chaperone and co-chaperone up- and downregulation lends support for two groups of cancers , Group 1 and Group 2 ( Fig 3A ) .', 'These groups are recapitulated when projecting cancers by up- and downregulation of ATP-dependent versus ATP-independent chaperones ( Fig 3C ) .', 'K-means clustering confirms the significant separation of the Group 2 cancers pheochromocytoma and paraganglioma ( PCPG ) , thyroid carcinoma ( THCA ) , and the three kidney cancers kidney chromophobe ( KICH ) , kidney renal papillary cell carcinoma ( KIRP ) , and kidney renal clear cell carcinoma ( KIRC ) from Group 1 cancers , with a median silhouette width of s = 0 . 63 ( Fig 3A ) and s = 0 . 68 ( Fig 3C ) .', 'Group 1 cancers ( red ) represent the majority of cancers , characterized by strong overall chaperome upregulation , with low chaperone and co-chaperone repression , and a trend for upregulation of ATP-dependent chaperones ( Fig 3B and 3D ) .', 'Five Group 2 cancers however partition more distantly , with a lack of chaperome upregulation ( Fig 3A and 3C ) .', 'These cancers include three different kidney cancers , KICH , KIRP , and KIRC , which consistently lack chaperome upregulation ( Fig 3A and 3B ) .', 'Also , ATP-dependent chaperones are not preferentially upregulated in kidney cancers .', 'Rather , an inverse trend is observed with increased downregulation of ATP-dependent chaperones ( Fig 3C and 3D ) .', 'Notably also , pheochromocytoma and paraganglioma ( PCPG ) , rare related tumors of orthosympathetic origin , similarly show an even more prominent inverse alteration , with a preponderance of overall chaperome downregulation and preferential downregulation of ATP-dependent chaperones .', 'Pheochromocytomas originate in the adrenal medulla , with close spatial association to the kidney , whose cancers are also Group 2 cancers .', 'THCA is similar to PCPG , with a preferential downregulation of the chaperome and both PCPG and THCA represent tumors forming from cells of neuroendocrine origin .', 'Collectively , the data point to a preferential upregulation of ATP-dependent chaperones in the majority of cancers , which we refer to as Group 1 cancers , with general differences in chaperome deregulation in Group 2 cancers , comprising kidney cancers and cancers of neuroendocrine origin , such as PCPG and THCA .', 'Human embryonic stem cells ( hESCs ) are characterized by their capacity to replicate infinitely in culture , while maintaining a pluripotent state [35] .', 'This immortal , undifferentiated phenotype resembles hallmark features of cancer cells such as an elevated global translational rate [36] and is expected to demand increased PN capacity capable of buffering imbalances to maintain proteostasis .', 'Given the “stemness” phenotype of cancer cells and their resemblances with pluripotent stem cells we hypothesized that the consistent chaperome upregulation in cancers acts to mimic an enhanced stem cell PN setup .', 'Increased proteasome activity [37] and elevated overall levels of the TRiC/CCT complex [38] , representatives of the clearance and folding functional arms of the PN , respectively , have recently been associated with the intrinsic PN of pluripotent stem cells that acts to support their identity and immortality .', 'It can be hypothesized that increased levels of central PN processes in stem cells exemplify characteristics of an enhanced PN setup .', 'We thus assessed to which extent this stem cell PN setup is recapitulated in cancers .', 'First , we assessed differential changes of the proteasome across TCGA cancers and observed an overall consistent upregulation of the 43 proteasomal genes ( HGNC Family ID 690 ) in > 70% of cancers ( Fig 4A , S1B Table ) [39] , matching the role of increased proteasomal activity for proteome maintenance in stem cells [37] .', 'Notably , Group 1 and Group 2 cancers , which are specifically defined based on chaperome differential expression signatures ( Fig 3 ) , do not co-partition with cancer clusters obtained by proteasome differential expression ( Fig 4A ) .', 'Next , we assessed cancer differential expression of the eukaryotic chaperonin TRiC/CCT , a hetero-oligomeric complex of two stacked rings with each eight paralogous subunits representing the cytoplasmic ATP-driven HSP60 chaperones in charge of folding approximately 10% of the proteome [40] .', 'TRiC/CCT is highly conserved and essential for cell viability [40] .', 'Loss of complex subunits induces cell death and a decline of pluripotency of hESCs and induced pluripotent stem cells ( iPSCs ) [38] .', 'Within the PN , TRiC/CCT mediated folding and autophagic clearance act in concert to prevent aggregation [41] .', 'TRiC/CCT levels decline during stem cell differentiation , and CCT8 acts as complex assembly factor [38] .', 'Intrigued by the finding that CCT8 is the most highly elevated subunit in stem cells and likely acting as assembly factor [38] , we assessed differential expression of individual TRiC/CCT subunits across cancers .', 'Hierarchical clustering of subunit expression across solid cancers highlighted CCT8 as highly consistently upregulated across all cancers ( mean change = 0 . 76 , t test ) , and as overall second most highly upregulated subunit besides CCT6A ( mean change = 0 . 786 , t test ) ( Fig 4B ) .', 'Consistent with the overall preferential downregulation of ATP-dependent chaperones observed in Group 2 cancers ( Fig 3 ) , we found these cancers to cluster together with overall lowest TRiC/CCT expression , where PCPG stands out with a consistent downregulation of all subunits ( Fig 4B ) .', 'Together these findings suggest that proteostasis shifts in cancer cells add to an altered , enhanced PN state that mimics the immortal and resilient stem cell phenotype , buffering genome instability and ensuing proteomic imbalances in support of sustained and increased cellular proliferation throughout cancerogenesis .', 'Overall chaperome upregulation in cancers , with preferential enrichment for upregulation of ATP-dependent chaperones , alongside consistent downregulation of sHSPs , is diametrically opposed to chaperome deregulation trends previously observed in a study of chaperome alterations in human aging brains and in patient brains with age-onset neurodegenerative diseases [4] .', 'While sHSPs were the only chaperome family found significantly induced in brain aging and the age-onset neurodegenerative diseases Alzheimer’s ( AD ) , Huntington’s ( HD ) , and Parkinson’s ( PD ) disease , this family is consistently downregulated across cancers ( Fig 2B ) .', 'This opposed chaperome deregulation points towards characteristic and fundamental differences in PN deregulation between disease families .', 'To investigate this disease group difference further , we applied the analysis outlined for cancers above also on the gene expression datasets that had earlier revealed global chaperome repression in AD , HD , and PD [4] .', 'Our analysis reproduced the human chaperome as overall downregulated across AD , HD , and PD as compared to random permutations of non-chaperome genes ( -0 . 20 ∆GSA group mean change , Fig 5A ) .', 'Delving deeper into chaperome functional subfamilies , we reproduce earlier findings reporting broad repression of the major chaperome functional families except for sHSPs , the only family found strongly upregulated ( +0 . 76 ) accompanied by slight upregulation of ER-specific chaperones ( +0 . 21 ) and TPRs ( +0 . 13 ) ( Fig 5B ) .', 'Thereby , our analytical workflow reproduces previously observed trends obtained in independent analyses , with different methods .', 'With strong sHSP repression and upregulation of the HSP90 , ER , HSP60 , PFD , HSP100 and MITO chaperone families , cancers and neurodegenerative diseases display markedly diametrically opposed chaperome deregulation , not only at the overall chaperome-level ( Fig 5C ) , but also with respect to alteration trends of chaperome functional families , where 70% of functional groups are altered in opposite directions ( Fig 5D ) .', 'These opposing chaperome deregulation signatures are in line with differing implications of proteostasis alterations in these diseases .', 'While broad chaperome repression and proteostasis functional collapse is associated with aggregation and cytotoxicity of chronically expressed misfolding-prone proteins in neurodegenerative diseases [4] , enhanced proteostasis buffering capacity is associated with “stemness” , immortality and proliferative potential of both stem and cancer cells [27] .', 'Indeed , epidemiological evidence suggests an inverse correlation between cancers and neurodegenerative diseases [45–48] , supportive of a potential mechanistic link between opposed chaperome deregulation and the molecular underpinnings of the two disease groups .', 'These global differences in chaperome deregulation call for a systematic and quantitative assessment of PN deregulation dynamics in human diseases .', 'In light of the diverse signatures of differential chaperome deregulation observed across cancers ( Fig 2 ) , and motivated by the increasing amount of genomics datasets available for cancers and other human diseases , we aimed at reducing data complexity by extracting quantitative indicators of chaperome differential cancer gene expression alterations , in order to gain insights through reduced complexity while retaining maximum information content .', 'We devised Meta-PCA , a novel principal component analysis ( PCA ) based semi-supervised two-step dimension reduction approach that facilitates stratification of cancer patient and normal control samples within heterogeneous gene expression datasets ( Fig 1B ) .', 'Based on previous work on dimensionality reduction of heterogeneous gene expression datasets [49 , 50] , we hypothesized that the underlying information contained in each chaperome functional group has a low dimensionality ( meaning the functionality of each chaperome group can be quantified using only few , possibly one , variable ) and could be surfaced using PCA , if there were sufficient samples available to represent the complete heterogeneity of chaperome alterations in cancers .', 'Compared to conventional PCA , our method can deal with the effect of different group sizes , which as a confounder would negatively affect PCA results .', 'Compared to simply calculating mean expression values of each functional group’s genes , Meta-PCA considers a wider range of gene expression information inherent to each functional group , resulting in scores with higher resolution .', 'This could also be achieved by fully supervised methods such as Linear Discriminant Analysis .', 'However , this case requires use of a method , which is blind to sample annotations so that these can later be used for validation , such as the unsupervised classification of cancer tissue type .', 'Meta-PCA first uses tissue-wise PCA analyses to separate cancerous from control samples for individual tissues and maps functional family group gene expression changes to the global , or “meta” , mean expression change across cancers in order to obtain M-scores as quantitative indices of relative disease gene expression change ( Eq 1 ) .', 'Inherent to the Meta-PCA method , patient-specific genomic variability is averaged out through the use of Meta-PCs derived from the TCGA collection of cancer biopsy samples , yielding mean reference boundaries .', 'Assessing quantitative M-scores obtained through Meta-PCA against differential gene expression ( ∆GSA ) obtained via GSA ( Fig 2 ) , we observed an overall significant Pearson correlation of 0 . 61 ( S1 Fig ) .', 'In addition to general comparability between results obtained through both methods , Meta-PCA analysis reduces complexity while retaining genomic information .', 'Therefore , we focus on Meta-PCA for quantitative representation of proteostasis alterations in human diseases .', 'We plot differential chaperome changes as M-scores for all cancer samples and chaperome functional families simultaneously using polar plots , such that axes represent functional families or sub-groups ( Fig 2B ) .', 'We obtain the mean of all biopsy samples as reference boundaries for healthy ( blue line ) and cancer groups ( red line ) and include the 90% confidence interval ( CI ) ( red and blue halos ) ( Fig 6 ) .', 'This quantitative visualisation reduces complexity and highlights relativity of disease gene expression changes at a chaperome-scale .', 'The polar maps recapitulate characteristic chaperome deregulation signatures in GSA-derived clusters of functional family upregulation and downregulation signatures , for instance in Cluster I cancers such as lung adenocarcinoma ( LUAD ) ( Figs 2 and 6A ) , or the inverse trend with overall chaperome downregulation in Cluster II cancers such as pheochromocytoma and paraganglioma ( PCPG ) ( Figs 2 and 6B ) .', 'Concordantly , chaperome polar maps reveal characteristic patterns of cancer groups stratified based on differential expression of ATP-dependent chaperones versus ATP-independent co-chaperones , Group 1 versus Group 2 cancers ( Figs 3 and 6 ) .', 'In LUAD , representative of Group 1 cancers , most functional chaperome families , with a preferential enrichment of ATP-dependent chaperones , are upregulated , while sHSPs are reduced ( Fig 6A ) .', 'On the contrary , in Group 2 cancers such as PCPG , gene expression of most chaperome functional families is downregulated ( Fig 6B ) .', 'Inconsistencies between these broad clusters exist , suggesting differences in tissue of origin and molecular underpinnings of respective cancers .', 'However , broad commonalities between distinct cancers originating from the same organ are revealed .', 'For instance , lung adenocarcinoma ( LUAD ) and lung squamous cell carcinoma ( LUSC ) share overall similarity , revealing only subtle differences , for instance in HSP40 expression ( Figs 2 and S3 ) .', 'The kidney cancers KICH , KIRP , and KIRC also show similar patterns .', 'As Group 2 cancers , they share and stand out against other cancers with a lack of preferential upregulation of ATP-dependent chaperones ( Fig 3 ) , and overall reduced upregulation , or downregulation , of HSP60s ( Figs 2 , 3 , 4B and S3 ) .', 'A recent study indeed implicated HSP60 downregulation in tumorigenesis and progression of clear cell renal cell carcinoma ( KIRC ) by disrupting mitochondrial proteostasis [51] .', 'Overall , these contextual quantitative representations enable an appreciation of the complex chaperome shifts in different cancer tissues derived from > 10 , 000 patient biopsy samples .', 'The resulting compendium of differential cancer chaperome polar plots ( S3 Fig ) is also available online through the Proteostasis Profiler ( Pro2 ) tool associated to this study .', 'The integration of disease-related differential transcriptomic changes with the cellular protein interactome network , or the edgotype , is instrumental to our understanding of genotype—phenotype relationships [31] .', 'Towards integrated quantitative views of cancer chaperome deregulation , we curated a high-confidence physical chaperome protein-protein interactome network ( CHAP-PPI ) to serve as coordinate base grid layout for the analysis of differential chaperome topographies ( Fig 1C ) .', 'We started with 328 , 244 unique human PPIs ( edges ) between 16 , 995 proteins ( nodes ) downloaded from the BioGRID , IntAct , DIP , and MINT databases [52] , [53] , [54] , [55] .', 'Zooming in on cancer chaperome alterations in the context of physical interactome wiring , we extracted the CHAP-PPI considering the 332 human chaperome genes as previously described [4] .', "Considering edges with the PSI-MI annotation 'physical association' we obtained 272 , 367 unique physical edges , of which 666 unique edges connect 220 chaperome nodes .", 'We developed a custom script to curate the high-confidence physical CHAP-PPI , considering edges with multiple p
['Introduction', 'Results', 'Discussion', 'Materials and methods']
['Proteome balance is safeguarded by the proteostasis network ( PN ) , an intricately regulated network of conserved processes that evolved to maintain native function of the diverse ensemble of protein species , ensuring cellular and organismal health .', 'Proteostasis imbalances and collapse are implicated in a spectrum of human diseases , from neurodegeneration to cancer .', 'The characteristics of PN disease alterations however have not been assessed in a systematic way .', 'Since the chaperome is among the central components of the PN , we focused on the chaperome in our study by utilizing a curated functional ontology of the human chaperome that we connect in a high-confidence physical protein-protein interaction network .', 'Challenged by the lack of a systems-level understanding of proteostasis alterations in the heterogeneous spectrum of human cancers , we assessed gene expression across more than 10 , 000 patient biopsies covering 22 solid cancers .', 'We derived a novel customized Meta-PCA dimension reduction approach yielding M-scores as quantitative indicators of disease expression changes to condense the complexity of cancer transcriptomics datasets into quantitative functional network topographies .', 'We confirm upregulation of the HSP90 family and also highlight HSP60s , Prefoldins , HSP100s , ER- and mitochondria-specific chaperones as pan-cancer enriched .', 'Our analysis also reveals a surprisingly consistent strong downregulation of small heat shock proteins ( sHSPs ) and we stratify two cancer groups based on the preferential upregulation of ATP-dependent chaperones .', 'Strikingly , our analyses highlight similarities between stem cell and cancer proteostasis , and diametrically opposed chaperome deregulation between cancers and neurodegenerative diseases .', 'We developed a web-based Proteostasis Profiler tool ( Pro2 ) enabling intuitive analysis and visual exploration of proteostasis disease alterations using gene expression data .', 'Our study showcases a comprehensive profiling of chaperome shifts in human cancers and sets the stage for a systematic global analysis of PN alterations across the human diseasome towards novel hypotheses for therapeutic network re-adjustment in proteostasis disorders .']
['Protein homeostasis , or proteostasis , is maintained by the proteostasis network ( PN ) , an intricately regulated modular network of interacting processes that evolved to balance the native proteome , supporting cellular and organismal health throughout lifespan .', 'Imbalances and collapse of cellular proteostasis capacity , the capacity to buffer against cytotoxic damage and stress , is increasingly implicated in some of the most challenging diseases of our time , including neurodegeneration and cancers .', 'The systems-level PN alterations in these diseases are not understood to date .', 'Here , we address this challenge , focussing on the human chaperome , the ensemble of chaperones and co-chaperones , which represents a central conserved PN functional arm .', 'We devised a novel data dimensionality reduction approach enabling quantitative contextual visualization of chaperome alterations in the heterogeneous spectrum of cancers based on gene expression data from thousands of patient biopsies .', 'We developed Proteostasis Profiler ( Pro2 ) , a new web-tool enabling intuitive visualisation of cancer chaperome deregulation maps .', 'We stratify two cancer groups based on diverging chaperome deregulation and highlight similarities between cancer and stem cell proteostasis .', 'Our study also exposes drastically opposed shifts between cancers and neurodegenerative diseases .', 'Collectively , this study sets the stage for a systematic global analysis of PN alterations across the human diseasome .']
['medicine and health sciences', 'biopsy', 'neurodegenerative diseases', 'protein interaction networks', 'topographic maps', 'surgical and invasive medical procedures', 'multivariate analysis', 'mathematics', 'statistics (mathematics)', 'network analysis', 'genome analysis', 'research and analysis methods', 'computer and information sciences', 'geography', 'genomics', 'proteins', 'mathematical and statistical techniques', 'gene expression', 'principal component analysis', 'cartography', 'proteomics', 'biochemistry', 'proteomes', 'neurology', 'earth sciences', 'genetics', 'biology and life sciences', 'physical sciences', 'computational biology', 'statistical methods']