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Acquired mutations are pervasive across normal tissues. However, our understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMN). We find mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response (DDR) genes ( TP53, PPM1D, CHEK2 ). Sequential sampling provides definitive evidence that DDR clones outcompete other clones when exposed to certain therapies. Among cases where CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies.

We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyze germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2, and PALB2. Additionally, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B, and MLL3). Evidence for loss of heterozygosity was found in 100% and 76% of cases with germline BRCA1 and BRCA2 truncations respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 237 candidate functional germline truncation and missense variants, including 2 pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK, and MLL pathways.

The MDR1 P-glycoprotein (Pgp), a member of the ATP-binding cassette family of transporters, is a transmembrane ATPase efflux pump for various lipophilic compounds, including many anti-cancer drugs. mAb UIC2, reactive with the extracellular moiety of Pgp, inhibits Pgp-mediated efflux. UIC2 reactivity with Pgp was increased by the addition of several Pgp-transported compounds or ATP-depleting agents, and by mutational inactivation of both nucleotide-binding domains (NBDs) of Pgp. UIC2 binding to Pgp mutated in both NBDs was unaffected in the presence of Pgp transport substrates or in ATP-depleted cells, whereas the reactivities of the wild-type Pgp and Pgps mutated in a single NBD were increased by these treatments to the level of the double mutant. These results indicate the existence of different Pgp conformations associated with different stages of transport-associated ATP hydrolysis and suggest trapping in a transient conformation as a mechanism for antibody-mediated inhibition of Pgp.P-glycoprotein (Pgp), the product of the human MDR1 gene, acts as a broad specificity plasma membrane efflux pump for many hydrophobic compounds (1, 2) and recently was shown to function as a short chain lipid translocase (3). Pgp is a member of a superfamily of ATP-binding cassette (ABC) transporters, characterized by the presence of conserved ABC domains containing consensus nucleotide-binding domain (NBD) sequence motifs (4). ABC transporters of a subgroup that includes the MDR1 Pgp, a closely related MDR2 gene product that acts as a phospholipid translocase (5, 6), the yeast STE6 protein that transports the a pheromone (7), and the cystic fibrosis transmembrane conductance regulator (8), are characterized by a common architecture. These proteins are composed of two halves separated by a ''linker'' region; each half comprises a hydrophobic region with six predicted membrane-spanning segments and the ABC domain.Expression of the MDR1 Pgp in tumor cells is associated with a clinically important phenotype of crossresistance to many structurally diverse anti-cancer drugs, which are pumped out by Pgp. Pgp was shown to bind its transport substrates (9), an event that most probably occurs in the lipid bilayer of the plasma membrane (10), and to hydrolyze ATP (11). The ATPase activity of Pgp is strongly stimulated by the addition of Pgp transport substrates (12). The stoichiometry, temporal sequence, and structural transitions linking the binding and transport of a Pgp substrate with the binding and hydrolysis of ATP are as yet unknown.We previously have developed a mouse mAb UIC2, specific for the extracellular moiety of the human MDR1 Pgp (13). In contrast to several other mAbs that react with Pgp on the surface of intact cells, the addition of UIC2 to tissue culture media decreases the activity of Pgp toward all the tested Pgp transport substrates (13-16). The conformational epitope that is recognized by UIC2 is distinct from the epitopes of the other mAbs, because only UIC2 fails to react with a mutant Pgp that carries a d...