A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations

“Mutation Assessor calls predicting the functional impact (medium to high) of somatic mutation (Reva et al., 2011) were obtained from cBioPortal (Cerami et al., 2012).”

“‘‘Tumor type corrected’’ survival p values denote significant correlation in model incorporating both the molecular feature and cancer type. p Values <0.05 correspond to an estimated false discovery rate (Storey and Tibshirani, 2003) of <10%.”

“Furthermore, AKT phosphorylates TSC2 at multiple sites, to inhibit the GTPase-activating protein function of the TSC protein complex (consisting of TSC1, TSC2, and TBC1D7) toward Rheb, a RAS family member (Dibble and Manning, 2013; Laplante and Sabatini, 2012).”

“AKT directly and indirectly phosphorylates many downstream proteins, including the GSKs, p27KIP1, FoxO transcription factors, MDM2, and BAD, to enhance cell survival and growth (Manning and Cantley, 2007).”

“A number of genes in the pathway were found significantly mutated or copy altered in pan-cancer analyses (Chang et al., 2016; Kandoth et al., 2013; Lawrence et al., 2014; Zack et al., 2013), including PIK3CA 4 Cancer Cell 31, 1–13, June 12, 2017 (14% mutated across all cancers; 6% amplified), PTEN…”

“Growth factor receptor tyrosine kinases (RTKs) activate PI3K through phosphorylation of adaptor proteins such as IRS1/IRS2 (Engelman et al., 2006).”

“A number of genes in the pathway were found significantly mutated or copy altered in pan-cancer analyses (Chang et al., 2016; Kandoth et al., 2013; Lawrence et al., 2014; Zack et al., 2013), including PIK3CA 4 Cancer Cell 31, 1–13, June 12, 2017 (14% mutated across all cancers; 6% amplified), PTEN…”

“(D) A gene expression signature of sensitivity to PI3K/AKT/mTOR inhibition in cancer cell lines, consisting of 146 genes (p < 0.01 by t test and p < 0.01 in regression model incorporating tumor type as a confounder), was derived using the dataset of Garnett et al. (2012).”

“The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway is one of the main growth regulatory pathways in both normal cells and cancer (Hennessy et al., 2005; Mayer and Arteaga, 2016).”

“For each gene considered, mutations were separated on the basis of whether or not a prediction ofmutation functionality could be made (by residue hotspot, by Mutation Assessor, by manual literature review, or by nonsense/ frameshift/indel involving PTEN or PIK3R1).”

“…pathway were found significantly mutated or copy altered in pan-cancer analyses (Chang et al., 2016; Kandoth et al., 2013; Lawrence et al., 2014; Zack et al., 2013), including PIK3CA 4 Cancer Cell 31, 1–13, June 12, 2017 (14% mutated across all cancers; 6% amplified), PTEN (9% mutated; 7%…”

“Features more strongly associated with an aggressive cancer type but having a survival association that was not independent of cancer type (PIK3CAmutation, for example, Hoadley et al., 2014) may show significance for the uncorrected but not the corrected survival test.”

“PIK3R1, and less commonly PIK3R2, which encode the p85a and p85b regulatory subunits of PI3K, are commonly mutated, resulting in reduced ability to inhibit PI3K p110a (Cheung et al., 2011; Thorpe et al., 2015).”

“AKT1 is occasionally activated by mutation at a single site, E17K (Carpten et al., 2007).”

“In addition, the RPPA proteomic platform would have potential for clinical applications to personalized therapy (Creighton and Huang, 2015), and transcriptional signatures associated with inhibitor sensitivity in cell lines may be defined (Singh et al., 2009).”

“The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway is one of the main growth regulatory pathways in both normal cells and cancer (Hennessy et al., 2005; Mayer and Arteaga, 2016).”

“Significantly altered genes (from Chang et al., 2016; Kandoth et al., 2013; Lawrence et al., 2014; Zack et al., 2013; percentages representing significant alterations are underlined) are bounded by orange lines.”

“Furthermore, AKT phosphorylates TSC2 at multiple sites, to inhibit the GTPase-activating protein function of the TSC protein complex (consisting of TSC1, TSC2, and TBC1D7) toward Rheb, a RAS family member (Dibble and Manning, 2013; Laplante and Sabatini, 2012).”

“Following previous studies (Akbani et al., 2014), we developed pathway signatures for both PI3K/AKT and mTOR components, based on member proteins selected by literature review, as a means of assessing the overall level of pathway activity given the variations of individual members.”

“PIK3R1, and less commonly PIK3R2, which encode the p85a and p85b regulatory subunits of PI3K, are commonly mutated, resulting in reduced ability to inhibit PI3K p110a (Cheung et al., 2011; Thorpe et al., 2015).”

“, 1999), as well as activating mutations inMTOR (Grabiner et al., 2014).”

“(E) Diagram of interactions involving PI3K/AKT/MTOR pathway represented by selected features from (C) and (D) (Carbonneau et al., 2016; Dodd et al., 2015; Guo et al., 2016; Weiler et al., 2014), with differential protein expression patterns represented, comparing tumors in HIGH P-AKT group with…”

“PTEN is subject to both genomic deletion and small point mutations that inactivate its function, and is one of the most commonly mutated cancer genes overall (Keniry and Parsons, 2008).”

“Genomic rearrangements were detected in all tumor and normal genomes by Meerkat (Yang et al., 2013).”

“We applied this signature to the Library of Integrated Networkbased Cellular Signatures (LINCS) database (Duan et al., 2014) of perturbational expression profiles across multiple cell and perturbation types.”

“Cancer Cell 31, 1–13, June 12, 2017 7 (A) A previously defined gene transcription signature of PI3K/AKT/mTOR (Creighton et al., 2010) (originally derived using the Connectivity Map, or CMAP, dataset) was re-examined in the LINCS database of perturbational expression profiles, with the PI3K/AKT/mTOR…”

“These mutations and proteins would suggest a model (Figure 7E) whereby mutant IDH1 may lead to high phosphoERK (Chaturvedi et al., 2013) and SRC can activate PI3K (Chen et al., 2015; Su et al., 2016), andwhere activatedmTOR signaling may activate transcription targets of hypoxia via HIF-1a…”

“Notably, VHL was recently found to directly suppress AKT activity (Guo et al., 2016), and generation of Cancer Cell 31, 1–13, June 12, 2017 9 (A) Tumor cases were separated into distinct groups on the basis of genetic or genomic alteration and of protein expression: (1) cases with nonsilent somatic…”

“RPPA methodology and quality control procedures have been described previously (Akbani et al., 2014; Li et al., 2017).”

“…involving PI3K/AKT/MTOR pathway represented by selected features from (C) and (D) (Carbonneau et al., 2016; Dodd et al., 2015; Guo et al., 2016; Weiler et al., 2014), with differential protein expression patterns represented, comparing tumors in HIGH P-AKT group with tumors harboring PI3K/ RTK…”

“2-hydroxyglutarate by mutated IDH1/2 was also recently found to lead to the activation of mTOR (Carbonneau et al., 2016); our data here would highlight the importance of both of the above relationships in the setting of human cancer.”

“A large proportion of mutations identified in driver genes that activate PI3K/AKT/mTOR are of low occurrence, highlighting the need to functionally annotate the long tail of infrequent mutations present in heterogeneous cancers (Dogruluk et al., 2015).”

“…SRC can activate PI3K (Chen et al., 2015; Su et al., 2016), andwhere activatedmTOR signaling may activate transcription targets of hypoxia via HIF-1a (particularly in the absence of VHL), including NDRG1 and growth factors that may lead to a further increase ERK and PI3K signaling (Clark, 2009).”

“Inactivating mutations in both TSC1 and TSC2 have been identified in cancer at low frequency (Hornigold et al., 1999), as well as activating mutations inMTOR (Grabiner et al.”

“In addition, the RPPA proteomic platform would have potential for clinical applications to personalized therapy (Creighton and Huang, 2015), and transcriptional signatures associated with inhibitor sensitivity in cell lines may be defined (Singh et al., 2009).”

“MYC signatures (Coller and Bild) and the Bild Ras signature were from ref (Creighton, 2008), and the Settleman k-ras sensitivity signature were from ref (Singh et al., 2009).”

“, 2013) and SRC can activate PI3K (Chen et al., 2015; Su et al., 2016), andwhere activatedmTOR signaling may activate transcription targets of hypoxia via HIF-1a (particularly in the absence of VHL), including NDRG1 and growth factors that may lead to a further increase ERK and PI3K signaling (Clark, 2009).”

“, 2013) and SRC can activate PI3K (Chen et al., 2015; Su et al., 2016), andwhere activatedmTOR signaling may activate transcription targets of hypoxia via HIF-1a (particularly in the absence of VHL), including NDRG1 and growth factors that may lead to a further increase ERK and PI3K signaling (Clark, 2009).”

“Several pathways are featured in more detail as separate publications, including: (1) PI3K pathway (Zhang et al., 2017): aberrations in the PI3K pathway were found predominantly as activating events in PIK3CA (less commonly in PIK3CB) and inactivating events in PTEN or PIK3R1withPIK3CA and PTEN…”