Immune checkpoint inhibitors, which unleash a patient’s own T cells to kill tumors, are revolutionizing cancer treatment. To unravel the genomic determinants of response to this therapy, we used whole-exome sequencing of non–small cell lung cancers treated with pembrolizumab, an antibody targeting programmed cell death-1 (PD-1). In two independent cohorts, higher nonsynonymous mutation burden in tumors was associated with improved objective response, durable clinical benefit, and progression-free survival. Efficacy also correlated with the molecular smoking signature, higher neoantigen burden, and DNA repair pathway mutations; each factor was also associated with mutation burden. In one responder, neoantigen-specific CD8+ T cell responses paralleled tumor regression, suggesting that anti–PD-1 therapy enhances neoantigen-specific T cell reactivity. Our results suggest that the genomic landscape of lung cancers shapes response to anti–PD-1 therapy.

https://science.sciencemag.org/content/sci/early/2015/03/11/science.aaa1348.full.pdf

Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer

Cancers develop in complex tissue environments, which they depend on for sustained growth, invasion and metastasis. Unlike tumor cells, stromal cell types within the tumor microenvironment (TME) are genetically stable and thus represent an attractive therapeutic target with reduced risk of resistance and tumor recurrence. However, specifically disrupting the pro-tumorigenic TME is a challenging undertaking, as the TME has diverse capacities to induce both beneficial and adverse consequences for tumorigenesis. Furthermore, many studies have shown that the microenvironment is capable of normalizing tumor cells, suggesting that re-education of stromal cells, rather than targeted ablation per se, may be an effective strategy for treating cancer. Here we discuss the paradoxical roles of the TME during specific stages of cancer progression and metastasis, as well as recent therapeutic attempts to re-educate stromal cells within the TME to have anti-tumorigenic effects.

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Microenvironmental regulation of tumor progression and metastasis.

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

/pdf/the-cancer-genome-atlas-pan-cancer-analysis-project-gw3srsikvs.pdf

The cancer genome atlas pan-cancer analysis project

BackgroundWe assessed the efficacy and safety of programmed cell death 1 (PD-1) inhibition with pembrolizumab in patients with advanced non–small-cell lung cancer enrolled in a phase 1 study. We also sought to define and validate an expression level of the PD-1 ligand 1 (PD-L1) that is associated with the likelihood of clinical benefit. MethodsWe assigned 495 patients receiving pembrolizumab (at a dose of either 2 mg or 10 mg per kilogram of body weight every 3 weeks or 10 mg per kilogram every 2 weeks) to either a training group (182 patients) or a validation group (313 patients). We assessed PD-L1 expression in tumor samples using immunohistochemical analysis, with results reported as the percentage of neoplastic cells with staining for membranous PD-L1 (proportion score). Response was assessed every 9 weeks by central review. ResultsCommon side effects that were attributed to pembrolizumab were fatigue, pruritus, and decreased appetite, with no clear difference according to dose or schedule. Among all ...

https://www.nejm.org/doi/pdf/10.1056/NEJMoa1501824

Pembrolizumab for the treatment of non-small cell lung cancer

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, with the landscape dominated by cisand trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

/pdf/the-genomic-and-transcriptomic-architecture-of-2-000-breast-c1simcg604.pdf

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

Introduction: In lymph node negative (LNN) colon cancer 20% of the patients develops disease recurrence. Identification of these patients is needed. MicroRNAs (MiRNAs), a group of short non-coding RNAs, can function as tumor suppressors or oncogenes. Hur et al recently found 6 differentially expressed MiRNAs when comparing primary colorectal cancer and matched liver metastasis (MiR-320, MiR-221, MiR-30b, MiR-10b, MiR-885-5p, Let-7i). The expression of 2 MiRNAs was significantly correlated with distant metastasis (low Let-7i expression and high MiR-10b) in primary colorectal cancers. When split at the median and combined into a signature (Let-7i high and MiR-10b low [n=22] vs. Let-7i low and/or MiR-10b high[n=122]), the first group showed 100% metastasis free survival (MFS). We assessed the prognostic value of these MiRNAs and the signature in a clinically well-defined cohort of primary colon cancers. Methods: Expression of the 6 MiRNAs were measured using RT-qPCR in a cohort of 232 colon cancer patients (n=155 untreated LNN and n=77 adjuvant treated lymph node positive [LNP] patients) selected from the MATCH-cohort. Expression levels were related to microsatellite instability (MSI), and MFS, hepatic metastasis free (HFS) and overall survival (OS). Results: MiR-221, Mir-30b, Mir-10b and MiR-885-5p levels were significantly associated with MSI. In univariate Cox regression analysis, MiR-30b was significantly associated with MFS (HR=1.23 p=0.004), and MiR-30b and Let-7i were associated with HFS (HR=2.52 p=0.005 and HR=0.40 p Conclusion: in our cohort and more specifically the LNN group, we confirmed Let-7i and identified MiR-30b as a prognostic factor for MFS and HFS. We did not confirm the prognostic value of Mir-10b. The combination of Let-7i and MiR-30b identified a group with a 100% HFS. Pathway analysis showed higher expression of the TGF-beta pathway in the MiR-30b high group, and higher expression of the EMT pathway in the Let-7i high group. Citation Format: Robert R. Coebergh van den Braak, Anieta M. Sieuwerts, Zarina S. Lalmahomed, Marcel Smid, Vanja de Weerd, Michelle van der Vlugt - Daane, Anne van Galen, Shanshan Xiang, Katharina Biermann, John A. Foekens, John W. Martens, Jan N. IJzermans. Validation and pathway analysis of a metastasis-specific microRNA signature in primary colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2530. doi:10.1158/1538-7445.AM2017-2530

Abstract 2530: Validation and pathway analysis of a metastasis-specific microRNA signature in primary colon cancer

Sulfonyl-substituted 3-amidino-phenylalanine derivatives (I) are used for the diagnosis, therapy or prevention of diseases associated with urokinase (UK) or UK receptors. Use of amidines of formula (I) (as the racemate or the D- or L-isomer) or their salts is claimed for the preparation of a composition for the diagnosis, therapy or prevention of diseases associated with UK or UK receptors. R1 = (i) OH, OR4 or NR5R6; (ii) 2- or 3-(COR7)-pyrrolidino, 2-, 3- or 4-(COR7)-piperidino (all optionally further substituted) or optionally 2-, 3- or 4-substituted piperidyl (all optionally having a fused aromatic or cycloaliphatic ring in the 2,3- or 3,4-position relative to the heteroatom); (iii) 4-(R8)-piperazino, COX, CONR'R'', CSNR'R'', SO2Y or (CH2)mX' (where the (CH2)m chain is optionally branched); or (iv) aralkyl, 5-8C cycloaliphatic ring, heteroaryl or heterocycloaliphatic group (all optionally ring substituted); R4 = optionally substituted 1-8C alkyl, 3-8C cycloalkyl or aralkyl; R5, R6 = arbitrary residues; R7 = OH, OR4, NR5R6 or 4-(R8)-piperazino; R8 = 1-6C alkyl, aryl, phenoxycarbonyl or benzyloxycarbonyl (all optionally substituted); or optionally unsaturated 1-6C alkoxy; X = H or (all optionally substituted) alkyl, aryl, heteroaryl or cycloalkyl; R', R'' = H or 1-4C alkyl; or R'' may also be aryl if R' = H; or NR'R'' = 5-7 membered heterocycloaliphatic ring, optionally containing a further heteroatom; Y = 1-8C alkyl, aryl, heteroaryl, aryloxy or heteroaryloxy (all optionally substituted); or NH2 or mono- or di-(1-3C alkyl)-amino; m = 1-8; X' = OH (optionally etherified by 1-4C alkyl, aralkyl, aryl or 1-4C hydroxyalkyl; or acylated by 2-7C alkanoyl), halo or tri-(1-3C alkyl)-amino (where the N may be part of a 5-7 membered ring optionally containing a further S heteroatom); R2 = optionally substituted phenyl; R3 = H or 1-4C alkyl; n = 0 or 1. Independent claims are included for: (1) N alpha -(2,4,6-triisopropyl-phenylsulfonyl)-3-amidino-D,L-phenylalanine-4-eth oxycarbonyl-piperazide (Ia), the corresponding L-enantiomer and their salts; (2) the use of compounds of formula R2-Z (II) or their salts for the preparation of a composition for targeting lymph cells; (3) a method for inhibiting UK in living organisms (especially humans) by adminstration of (I); and (4) a method for targeting lymph tissue in living organisms by administration of (II). Z = arbitrary group.

John A. Foekens

Papers

Abstract 2530: Validation and pathway analysis of a metastasis-specific microRNA signature in primary colon cancer

New inhibitor of urokinase