Additional file 1: of Novel targeted therapies and immunotherapy for advanced thyroid cancers

Table S1. Ongoing clinical trials mentioned. (DOCX 16 kb

Basal kinomic activity profiles.

<p>Unsupervised hierarchical clustering of basal (untreated) tyrosine kinomic profiles displaying log transformed slope-exposure for (<b>A</b>) all 144 peptides and (<b>B</b>) as change from sample mean and filtered for variance >1. Red in (A) indicates relative increased signal and in (B) indicates an increase from sample mean. Blue indicates the opposite. Blue arrowhead points to red line denoting dendrogram separation. (<b>C</b>) Western blotting of GAPDH and Actin is shown with sample concentration indicated for each patient.</p

Kinomic platform and Electromagnetic Navigation Bronchoscopy.

<p>(A) Overall experimental flow with a (B) Representative in-procedure display of ENB and a schematic of PamChip assay used to measure basal kinomic activity displayed as (C) raw array picture of the 144 phosphorylatable peptides and (D) phosphorylation changes with drug treatment displayed with illustration of comparative fluorescent detection below.</p

CONSORT diagram on patient enrollment.

<p>CONSORT diagram on patient enrollment.</p

<i>Ex vivo</i> drug response profile.

<p>Displays <i>ex</i><i>vivo</i> drug response profiles as (A) a heatmap of kinase activity (log signal values) change from untreated, clustered by row, of altered phosphopeptides per patient, per dose at 20 nM, 0.5 µM or 20 µM. (B) <i>Ex vivo</i> prewash kinetic peptide phosphorylation (y axis per cell) over time (x axis per cell) of selected peptides in the selected samples, in response to indicated drugs at 20 µM. Blue lines denote untreated, and green lines indicate treated phosphorylation curves.</p

Patient characteristics and tumor evaluation.

<p>M-male; F-female; NSCLC-non small cell lung cancer; MD-PD-moderately differentiated to poorly differentiated; SBRT-stereotactic body radiotherapy.</p><p>Patient characteristics and tumor evaluation.</p

Patient characteristics.

<p>Patient characteristics.</p

High Throughput Kinomic Profiling of Human Clear Cell Renal Cell Carcinoma Identifies Kinase Activity Dependent Molecular Subtypes

<div><p>Despite the widespread use of kinase-targeted agents in clear cell renal cell carcinoma (CC-RCC), comprehensive kinase activity evaluation (kinomic profiling) of these tumors is lacking. Thus, kinomic profiling of CC-RCC may assist in devising a classification system associated with clinical outcomes, and help identify potential therapeutic targets. Fresh frozen CC-RCC tumor lysates from 41 clinically annotated patients who had localized disease at diagnosis were kinomically profiled using the PamStation®12 high-content phospho-peptide substrate microarray system (PamGene International). Twelve of these patients also had matched normal kidneys available that were also profiled. Unsupervised hierarchical clustering and supervised comparisons based on tumor vs. normal kidney and clinical outcome (tumor recurrence) were performed and coupled with advanced network modeling and upstream kinase prediction methods. Unsupervised clustering analysis of localized CC-RCC tumors identified 3 major kinomic groups associated with inflammation (A), translation initiation (B), and immune response and cell adhesions (C) processes. Potential driver kinases implicated include PFTAIRE (PFTK1), PKG1, and SRC, which were identified in groups A, B, and C, respectively. Of the 9 patients who had tumor recurrence, only one was found in Group B. Supervised analysis showed decreased kinase activity of CDK1 and RSK1-4 substrates in those which progressed compared to others. Twelve tumors with matching normal renal tissue implicated increased PIM’s and MAPKAPK’s in tumors compared to adjacent normal renal tissue. As such, comprehensive kinase profiling of CC-RCC tumors could provide a functional classification strategy for patients with localized disease and identify potential therapeutic targets.</p></div

Kinases altered in CC-RCC and relationship to clinical outcome.

<p>CC-RCC tumors that had matched normal fresh frozen material available (n = 12) were directly compared and statistically different phosphopeptides (p<0.001) were identified and are shown in (A). These significant peptides were used to query Kinexus Phosphonet as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139267#pone.0139267.g003" target="_blank">Fig 3</a> (and as described in Materials and Methods). Predicted upstream kinases that distinguish CC-RCC from matched normal kidney (indicated as increased or decreased in CC-RCC relative to normal kidney) are shown in (B). GeneGo MetaCore Network Modeling of the proteins that contain the significantly altered phosphopeptides (Listed as Uniprot ID’s in A) is shown in (C). Red circles indicate increased phosphorylation of the peptide while blue circles indicate decreased substrate phosphorylation. A supervised analysis of the CC-RCC tumors was performed to determine kinomic differences between patients who remained locally controlled after a minimum follow up of 18 months (NonProg) and those who progressed (Prog). Peptides significantly altered between these groups (D) were used to query Kinexus Phosphonet as above and are shown in (E) which were decreased. GeneGo MetaCore Network Modeling of the proteins containing the significantly altered phosphopeptides is shown in (F) where blue circles indicate decreased phosphorylation of the peptide.</p

Study Design.

<p>Study Design.</p