Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA.

Drug resistance is the major cause of therapeutic failure in high-grade serous ovarian cancer (HGSOC). Yet, the mechanisms by which tumors evolve to drug resistant states remains largely unknown. To address this, we aimed to exploit clone-specific genomic structural variations by combining scaled single-cell whole genome sequencing with longitudinally collected cell-free DNA (cfDNA), enabling clonal tracking before, during and after treatment.

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer.

Whole-genome doubling (WGD) is a critical driver of tumor development and is linked to drug resistance and metastasis in solid malignancies. Here, we demonstrate that WGD is an ongoing mutational process in tumor evolution. Using single-cell whole-genome sequencing, we measured and modeled how WGD events are distributed across cellular populations within tumors and associated WGD dynamics with properties of genome diversification and phenotypic consequences of innate immunity.

Genomic and clinical characterization of a familial GIST kindred intolerant to imatinib.

Familial gastrointestinal stromal tumors (GIST) are rare. We present a kindred with multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene (c.

Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer.

Purpose: We report updated clinical outcomes from a phase II study of pembrolizumab, trastuzumab, and chemotherapy (PTC) in metastatic esophagogastric cancer in conjunction with outcomes from an independent Memorial Sloan Kettering (MSK) cohort.

Patients And Methods: The significance of pretreatment 89Zr-trastuzumab PET, plasma circulating tumor DNA (ctDNA) dynamics, and tumor HER2 expression and whole exome sequencing was evaluated to identify prognostic biomarkers and mechanisms of resistance in patients treated on-protocol with PTC. Additional prognostic features were evaluated using a multivariable Cox regression model of trastuzumab-treated MSK patients (n = 226).

Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis.

Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) analysis of tumors from 22 patients with TP53 germline pathogenic variants. We observe somatic mutations affecting Wnt, PI3K/AKT signaling, epigenetic modifiers and homologous recombination genes as well as mutational signatures associated with prior chemotherapy.

Widespread hypertranscription in aggressive human cancers.

Cancers are often defined by the dysregulation of specific transcriptional programs; however, the importance of global transcriptional changes is less understood. Hypertranscription is the genome-wide increase in RNA output. Hypertranscription's prevalence, underlying drivers, and prognostic significance are undefined in primary human cancer.

Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival.

Leiomyosarcomas (LMS) are genetically heterogeneous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site continues to dictate clinical management, the contribution of genetic factors to LMS subtype, origins, and timing are unknown.

Mutations in the RAS/MAPK Pathway Drive Replication Repair-Deficient Hypermutated Tumors and Confer Sensitivity to MEK Inhibition.

The RAS/MAPK pathway is an emerging targeted pathway across a spectrum of both adult and pediatric cancers. Typically, this is associated with a single, well-characterized point mutation in an oncogene. Hypermutant tumors that harbor many somatic mutations may obscure the interpretation of such targetable genomic events.

Comprehensive Analysis of Hypermutation in Human Cancer.

We present an extensive assessment of mutation burden through sequencing analysis of >81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations. Hypermutation was detected in tumor types not previously associated with high mutation burden. Replication repair deficiency was a major contributing factor.

Thickness of medial layers of arteries prior to and during hibernation.

The thickness of the media of the aorta and the carotid, iliac, and renal arteries was measured in hibernating and nonhibernating marmots. A positive correlation was found between body weight and the thickness of the media of carotid and iliac arteries. The relation noted apparently was not due to the mean arterial pressure prior to and during hibernation, since there was no difference in the thickness of the media between nonhibernating and hibernating females.

Plasma levels of atrial natriuretic factor in nonhibernating and hibernating marmots.

Plasma atrial natriuretic factor (ANF) was measured in 16 marmots at various times of the year. Nonhibernating males (n = 6) had an average plasma concentration of 56 +/- 8 pg/ml; nonhibernating females (n = 6) had an average plasma concentration of 61 +/- 4 pg/ml. During hibernation an additional group of females (n = 4) showed an average of 25 +/- 5 pg/ml.

Effects of anesthetics on cardiovascular responses of the marmot Marmota flaviventris.

The effects of pentobarbital (30 mg/kg), urethan (2 g/kg), chloralose/urethan (50 mg/kg, 500 mg/kg), and thiobutabarbital (Inactin, 100 mg/kg) on the mean arterial pressure (BP) and heart period (HP) of Marmota flaviventris were examined. Anesthesia significantly decreased BP by 22-27 mm Hg and HP by 123-151 msec. In a series of paired studies with eight marmots it was found that pentobarbital increased the BP response to phenylephrine and almost abolished the baroreflex HP responses to phenylephrine and nitroglycerin.

Seasonal variation of cardiovascular function in the marmot, Marmota flaviventris.

Monthly measurements of heart rate, mean arterial pressure, and cardiac output were made on active and hibernating marmots from the time of emergence from hibernation through the next hibernation period. From these measurements cardiac index, stroke index, and total peripheral resistance were calculated on the basis of estimated lean body mass. Heart rate was low after emergence (132 +/- 9.

Seasonal changes of food and water consumption and urine production of the marmot, Marmota flaviventris.

In early spring, food and water consumption and the excretion and clearances of urine and solutes reached maximal rates. Water consumption exceeded food intake and urine production and plasma osmolality was lowest. Toward early and late summer, water intake decreased faster than food consumption and urine production.

Factors that alter the plasma renin activity of the marmot.

The effects of low doses of norepinephrine (NE) and furosemide and a volume load (nonhibernators only) on plasma renin activity (PRA), mean arterial pressure (MAP), heart rate (HR), left renal (RBF) and right iliac (IBF) blood flow, cardiac index (CI), and total peripheral resistance (TPR) were determined in euthermic and hibernating marmots. In nonhibernating marmots NE produced an increase in CI and TPR and a decrease in RBF. In hibernators this dose of NE caused an increase in MAP, HR, and renal resistance, whereas it decreased PRA and did not alter iliac resistance.

Renal function of the pony and the horse.

Simultaneous renal clearances of inulin (CIN), p-aminohippurate (CPAH), and creatinine (CCR) were measured in hydrated mares (6 ponies and 2 horses). The CIN and CPAH were determined during steady-state infusion at 3 different infusion rates. A 6-fold change in plasma IN concentration did not produce alteration in CIN, nor was there a difference between the ponies and horses (P greater than 0.

Circannual renal function and plasma electrolytes of the marmot.

Studies with unanesthetized active (non-lethargic) marmots demonstrated circannual rhythms of renal function (clearances of p-aminohippurate, creatinine, and inulin), plasma osmolality, and plasma sodium and potassium concentrations. Effective renal plasma flow, glomerular filtration rate, the clearance of creatinine, and plasma potassium were highest in spring and lowest in the fall and winter. Plasma osmolality and plasma sodium concentrations tended to be highest during the winter months and lowest in the spring and summer.

Maintenance of ion concentration gradients in the cold in aorta from rat and ground squirrel.

Cell water and ionic content were measured in aortic smooth muscle from rats and ground squirrels during 48 h of incubation in oxygenated Krebs solution held at low temperatures. Cells from the ground squirrel, a hibernator, maintained sodium and potassium contents near normal levels during incubation at 7 degrees C. In sharp contrast, cells from the rat lost potassium and gained sodium with half times of 14 and 11 h, respectively.

Effect of intravenous infusion of ethanol on plasma glucose, lactic acid and pyruvic acid concentrations in miniature swine.

Fructose, infused intravenously with ethanol, alleviated ethanol-induced hypoglycemia in adult miniature swine at all concentrations tested. Increases in plasma lactic acid and pyruvic acid concentrations also were found.