Global insights into cellular organization and function require comprehensive understanding of interactome networks. Similar to how a reference genome sequence revolutionized human genetics, a reference map of the human interactome network is critical to fully understand genotype-phenotype relationships. Here we present the first human “all-by-all” binary reference interactome map, or “HuRI”. With ~53,000 high-quality protein-protein interactions (PPIs), HuRI is approximately four times larger than the information curated from small-scale studies available in the literature. Integrating HuRI with genome, transcriptome and proteome data enables the study of cellular function within essentially any physiological or pathological cellular context. We demonstrate the use of HuRI in identifying specific subcellular roles of PPIs and protein function modulation via splicing during brain development. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI thus represents an unprecedented, systematic reference linking genomic variation to phenotypic outcomes.

Abstract Introduction: Phase 1 clinical trials of novel therapeutics have historically focused on toxicity, but increasingly are doubling as efficacy studies in biomarker-enriched populations. Given the small sample sizes (∼3-6 patients per dose), response on imaging may be a coarse marker of therapeutic effect. Here we piloted serial ddPCR of plasma cfDNA as a PD marker in a phase I combination study of a MEK inhibitor and a CDK 4/6 inhibitor in patients with RAS mutated cancers. Methods / Results: Twenty-five pts with RAS-mutated cancer (incl. 17 patients with KRAS-mutant NSCLC) have been enrolled to date in a phase I dose escalation trial of the MEK inhibitor PD-0325901 with the CDK4/6 inhibitor palbociclib (NCT02022982). Plasma for cfDNA genotyping was collected at baseline prior to therapy and at the beginning of cycle 2. Plasma genotyping for KRAS G12X mutations was performed using a validated and highly quantitative droplet digital PCR assay. Pts were enrolled in 5 dose level cohorts ranging from 75 mg palbociclib daily (3 weeks on, 1 week off) with 2 mg PD-0325901 BID (3 weeks on 1week off) to 125 mg palbociclib daily with 8 mg PD-0325901 BID (Table). KRAS mutations were detected in 14/24 pts at baseline (59%, median 1402 copies/mL plasma, range: 11-93000), consistent with the previously reported sensitivity of 64%. A second blood draw at cycle 2 was obtained for all 14 pts. A positive plasma response, defined as decrease of KRAS G12X mutants from first to second dose, was observed in 6 pts (range -6% - -100%) with the most plasma responders (n = 4 pts) at the maximum administered dose. At lower administered doses, there was a median increase in plasma KRAS mutant levels. Conclusions: Increasing dose levels resulted in more consistent decreases in KRAS mutation in cfDNA, consistent with a dose-dependent pharmacodynamic effect.These results highlight the potential value of serial plasma ddPCR as a PD marker in early phase clinical trials. Dose LevelPalbociclib (QD, 3 wks on 1 wk off) mgPD-0325901 (BID, 3 wks on 1 wk off) mgN Enrolled (N analyzed)Median Plasma change KRAS mut(%)17523 (1)+2427543 (3)+60 (range +31 - +150)310048 (4)+150 (range -6 - +341)412544 (2)+9 (range -45 - +61)512587 (4)-27 (range -7 - -43) Citation Format: Cloud P. Paweletz, Geoffrey R. Oxnard, Nora Feeney, John F. Hilton, Leena Gandhi, Khanh T. Do, Adrienne Anderson, Andrew Wolanski, Alexander Tejeda, Jessie M. English, Paul T. Kirschmeier, Pasi A. Jänne, Geoffrey I. Shapiro. Serial droplet digital PCR (ddPCR) of plasma cell-free DNA (cfDNA) as pharmacodynamic (PD) biomarker in Phase 1 clinical trials for patients (pts) with KRAS mutant non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3157.

Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ∼14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ∼30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help “connect the dots” of the genomic revolution.