SUMMARY Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas. We present an expression-based variant impact phenotyping (eVIP) method that uses gene expression changes to distinguish impactful from neutral somatic mutations. eVIP identified 69% of mutations analyzed as impactful and 31% as functionally neutral. A subset of the impactful mutations induces xenograft tumor formation in mice and/or confers resistance to cellular EGFR inhibition. Among these impactful variants are rare somatic, clinically actionable variants including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and multiple BRAF variants, demonstrating that rare mutations can be functionally important in cancer.

of continental drift. A relative motion of the continents must involve the mantle to depths of several hundred kilometers; it is no longer possible to imagine thin continental blocks sailing over a fluid mantle.

Many enzymes have been reported to exist in more than one form within the same species. By several methods a number of molecular forms of lactic dehydrogenase (LDH) have been found in differing amounts in the various organs of one individual (1-4). This article describes studies which were undertaken in an attempt to elucidate the molecular nature of these multiple enzymatic forms and to follow their development. Most of the developmental studies were made on the chicken.Two "pure" lactic dehydrogenases occur in the chicken. One of them (CM) is found principally in the breast muscle, and the other (CH) in the heart, of adult chickens. These two enzymes are separate entities as judged by physical, enzymatic, and immunochemical criteria (1, 2, 5). During embryonic development the LDH enzymes of the chicken breast muscle shift from the enzymes related to CH, through several intermediate enzyme types, and appear in the adult as pure CM. The characterization of these intermediate enzyme types by several independent methods has led to the development of the hypothesis, which we present in this article, that the intermediate enzyme types which appear during embryonic development are "hybrid" enzymes, consisting of both CM and CH components. Furthermore, these "hybrids" also occur in the adult tissues of the chicken and in other animals. Immunological ApproachIn order to use immunological methods for the study of the development and structure of specific proteins, it is necessary that the immune systems be 962 fully characterized. Two immune systems were used in this study: (i) CH- (6), immunoelectrophoresis (7), and quantitative precipitation analyses (8, 9). Anti-CH was shown to be heterogeneous when measured by double diffusion in agar. After absorption with CM, two bands remained when tested with crude chicken heart extracts, only one of which showed LDH activity (10, 11). This absorption did not decrease the complement (C') fixation titer of CH-anti-CH (Fig. 1), nor did it remove antibody capable of neutralizing CH enzymatic activity. Thus, the heterogeneity in anti-CH reflected antibodies to impurities in the CH immunizing antigen (probably CM) and not anti-CH cross-reacting with CM. Figure 1 shows the C' fixation curves of CM and CH with anti-CM and anti-CH. After absorption with CM, anti-CH showed no reduction in titer against CH. Moreover, the C' fixation curves were identical when either crystalline CH or crude heart extracts were used as antigen. At the dilutions of antisera used (1/5000 for anti-CH and 1/2200 for anti-CM) no cross reactions between CM and CH are detectable. Figure 2 demonstrates the ability of C' fixation to resolve a mixture of pure CM and CH. The heights of the curves at peak fixation are the same in the mixture as in the two pure systems. By the shift in the abscissa at peak fixation it is possible to calculate the percentage of total enzyme activity which reacts with either anti-CM or anti-CH (9, 12). In an artificial mixture of pure CM and CH (Fig. 2), the percentages calculated by C' fi...

Lung adenocarcinoma is comprised of distinct mutational subtypes characterized by mutually exclusive oncogenic mutations in RTK/RAS pathway members KRAS, EGFR, BRAF and ERBB2, and translocations involving ALK, RET and ROS1. Identification of these oncogenic events has transformed the treatment of lung adenocarcinoma via application of therapies targeted toward specific genetic lesions in stratified patient populations. However, such mutations have been reported in only ∼55% of lung adenocarcinoma cases in the United States, suggesting other mechanisms of malignancy are involved in the remaining cases. Here we report somatic mutations in the small GTPase gene RIT1 in ∼2% of lung adenocarcinoma cases that cluster in a hotspot near the switch II domain of the protein. RIT1 switch II domain mutations are mutually exclusive with all other known lung adenocarcinoma driver mutations. Ectopic expression of mutated RIT1 induces cellular transformation in vitro and in vivo, which can be reversed by combined PI3K and MEK inhibition. These data identify RIT1 as a driver oncogene in a specific subset of lung adenocarcinomas and suggest PI3K and MEK inhibition as a potential therapeutic strategy in RIT1-mutated tumors.

Let S be a numerical monoid (i.e. an additive submonoid of ℕ0) with minimal generating set 〈n1,…,nt〉. For m ∈ S, if [Formula: see text], then [Formula: see text] is called a factorization length of m. We denote by [Formula: see text] (where mi < mi+1 for each 1 ≤ i < k) the set of all possible factorization lengths of m. The Delta set of m is defined by Δ(m) = {mi+1 - mi|1 ≤ i < k} and the Delta set of S by Δ(S) = ∪m∈SΔ(m). In this paper, we address some basic questions concerning the structure of the set Δ(S). In Sec. 2, we find upper and lower bounds on Δ(S) by finding such bounds on the Delta set of any monoid S where the associated reduced monoid S red is finitely generated. We prove in Sec. 3 that if S = 〈n, n + k, n + 2k,…,n + bk〉, then Δ(S) = {k}. In Sec. 4 we offer some specific constructions which yield for any k and v in ℕ a numerical monoid S with Δ(S) = {k, 2k,…,vk}. Moreover, we show that Delta sets of numerical monoids may contain natural "gaps" by arguing that Δ(〈n, n + 1, n2 - n - 1〉) = {1,2,…,n - 2, 2n - 5}.

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The binding of coenzyme and substrate are considered in relation to the known primary and tertiary structure of lactate dehydrogenase (EC 1,1.1.27). The adenine binds in a hydrophobic crevice, and the two coenzyme phosphates are oriented by interactions with the protein. The positively charged guanidinium group of arginine 101 then folds over the negatively charged phosphates, collapsing the loop region overtthe active center and positioning. the ulreactive B side of the nicoti namide in a hydrophobic protein environment. Collapse of the loop also introduces various charged groups into the vicinity of the substrate binding site. The substrate is situated between histidine 195 and the C4 position on the nicotiriamide ring, and is partially oriented by interactions between its carboxyl group and arginine 171. The spatial arrangements of these groups may provide the specificity for the L-isomer of lactate.In this paper coenzyme and substrate binding to dogfish (Squalus acanthius) M4 lactate dehydrogenase (LDH; EC 1.1.1.27) will be discussed in relation to the known amino-acid sequence, the crystal structure determinations, and the effect of various chemical modifications of the enzyme and coenzyme. A comparison of the preliminary 3.0-A resolution structure of the abortive LDH: NAD-pyruvate ternary complex (1) with the more complete 2.0-A resolution structure of the apoenzyme provides information on possible conformational changes during catalysis. Everse and Kaplan (4) have recently reviewed many of the properties of LDH. Evidence from kinetic data indicates that there is an obligatory binding order of coenzyme followed by substrate (Fig. 1), at least near neutral pH (6-8). McPherson (9) has presented evidence to show that the adenine moiety of the coenzyme is required for binding of the nicotinamide moiety.Coenzyme binding Studies on the conformations of adenosine, AMP, and ADP at 2.8-A resolution and of NAD+ at 5.0-resolution, when diffused into crystals of the apoenzyme, are discussed by Chandrasekhar et al. (10). Diffraction patterns of the NADH binary complex closely resemble those of the NAD+ binary complex. Although the structure of each of these binary complexes differs slightly from the other, as a class, their mode of binding of the coenzyme to the apoenzyme is distinct from that of the coenzyme in the ternary complex (Fig. 2). Fig. 3 demonstrates this by a comparison of the structure of NAD in the ternary complex (in black) with (a) NAD+ and (b) AMP in binary complexes. The protein conformation of the apoenzyme differs markedly from that of the ternary complex structure in that the loop (residues 98-114) has folded down over the active center pocket in the ternary complexes. Many smaller conformational changes within the protein are associated with the large movement of the loop and the different position and conformation of the coenzyme.The adenosine binds in a hydrophobic crevice lined by valine 27, glycine 28, an alanine, glycine and valine in the region 29-33, valine 52, valine 54, methionin...