Neratinib + fulvestrant + trastuzumab for HR-positive, HER2-negative, HER2-mutant metastatic breast cancer: outcomes and biomarker analysis from the SUMMIT trial.

BACKGROUND: HER2 mutations are targetable alterations in patients with hormone receptor-positive (HR+) metastatic breast cancer (MBC). In the SUMMIT basket study, patients with HER2-mutant MBC received neratinib monotherapy, neratinib + fulvestrant, or neratinib + fulvestrant + trastuzumab (N + F + T). We report results from 71 patients with HR+, HER2-mutant MBC, including 21 (seven in each arm) from a randomized substudy of fulvestrant versus fulvestrant + trastuzumab (F + T) versus N + F + T. PATIENTS AND METHODS: Patients with HR+ HER2-negative MBC with activating HER2 mutation(s) and prior cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) therapy received N + F + T (oral neratinib 240 mg/day with loperamide prophylaxis, intramuscular fulvestrant 500 mg on days 1, 15, and 29 of cycle 1 then q4w, intravenous trastuzumab 8 mg/kg then 6 mg/kg q3w) or F + T or fulvestrant alone. Those whose disease progressed on F + T or fulvestrant could cross-over to N + F + T. Efficacy endpoints included investigator-assessed objective response rate (ORR), clinical benefit rate (RECIST v1.1), duration of response, and progression-free survival (PFS). Plasma and/or formalin-fixed paraffin-embedded tissue samples were collected at baseline; plasma was collected during and at end of treatment. Extracted DNA was analyzed by next-generation sequencing. RESULTS: ORR for 57 N + F + T-treated patients was 39% [95% confidence interval (CI) 26% to 52%); median PFS was 8.3 months (95% CI 6.0-15.1 months). No responses occurred in fulvestrant- or F + T-treated patients; responses in patients crossing over to N + F + T supported the requirement for neratinib in the triplet. Responses were observed in patients with ductal and lobular histology, 1 or ≥1 HER2 mutations, and co-occurring HER3 mutations. Longitudinal circulating tumor DNA sequencing revealed acquisition of additional HER2 alterations, and mutations in genes including PIK3CA, enabling further precision targeting and possible re-response. CONCLUSIONS: The benefit of N + F + T for HR+ HER2-mutant MBC after progression on CDK4/6is is clinically meaningful and, based on this study, N + F + T has been included in the National Comprehensive Cancer Network treatment guidelines. SUMMIT has improved our understanding of the translational implications of targeting HER2 mutations with neratinib-based therapy.

Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.

BACKGROUND: The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS: We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS: In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS: To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 degrees C: 0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and -0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair.

NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.

Nucleotides in RNA that are not Watson-Crick-paired form unique structures for recognition or catalysis, but determinants of these structures and their stabilities are poorly understood. A single noncanonical pair of two guanosines (G) is more stable than other noncanonical pairs and can potentially form pairing structures with two hydrogen bonds in four different ways. Here, the energetics and structure of single GG pairs are investigated in several sequence contexts by optical melting and NMR. The data for r(5'GCAGGCGUGC3')(2), in which G4 and G7 are paired, are consistent with a model in which G4 and G7 alternate syn glycosidic conformations in a two-hydrogen-bond pair. The two distinct structures are derived from nuclear Overhauser effect spectroscopic distance restraints coupled with simulated annealing using the AMBER 95 force field. In each structure, the imino and amino protons of the anti G are hydrogen bonded to the O6 and N7 acceptors of the syn G, respectively. An additional hydrogen-bond connects the syn G amino group to the 5' nonbridging pro-R(p) phosphate oxygen. The GG pair fits well into a Watson-Crick helix. In r(5'GCAGGCGUGC3')(2), the G4(anti), G7(syn) structure is preferred over G4(syn), G7(anti). For single GG pairs in other contexts, exchange processes make interpretation of spectra more difficult but the pairs are also G(syn), G(anti). Thermodynamic data for a variety of duplexes containing pairs of G, inosine, and 7-deazaguanosine flanked by GC pairs are consistent with the structural and energetic interpretations for r(5'GCAGGCGUGC3')(2), suggesting similar GG conformations.

Predicting oligonucleotide affinity to nucleic acid targets.

A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.

Thermodynamics of single mismatches in RNA duplexes.

The thermodynamic properties and structures of single mismatches in short RNA duplexes were studied in optical melting and imino proton NMR experiments. The free energy increments at 37 degrees C measured for non-GU single mismatches range from -2.6 to 1.7 kcal/mol. These increments depend on the identity of the mismatch, adjacent base pairs, and the position in the helix. UU and AA mismatches are more stable close to a helix end, but GG mismatch stability is essentially unaffected by the position in the helix. Approximations are suggested for predicting stabilities of single mismatches in short RNA duplexes.

Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.

Free energies for stacking of unpaired nucleotides (dangling ends) at the termini of oligoribonucleotide Watson-Crick helixes (DeltaG(0)37,stack) depend on sequence for 3' ends but are always small for 5' ends. Here, these free energies are correlated with stacking at helix termini in a database of 34 RNA structures determined by X-ray crystallography and NMR spectroscopy. Stacking involving GA pairs is considered separately. A base is categorized as stacked by its distance from (

The energetics of small internal loops in RNA.

The energetics of small internal loops are important for prediction of RNA secondary and tertiary structure, selection of drug target sites, and understanding RNA structure-function relationships. Hydrogen bonding, base stacking, electrostatic interactions, backbone distortion, and base-pair size compatibility all contribute to the energetics of small internal loops. Thus, the sequence dependence of these energetics are idiosyncratic. Current approximations for predicting the free energies of internal loops consider size, asymmetry, closing base pairs, and the potential to form GA, GG, or UU pairs. The database of known three-dimensional structures allows for comparison with the models used for predicting stability from sequence.

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.

Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of DeltaG degrees37 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within 3.2%, 6.0%, 6.8%, and 1.3 degreesC, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.

Testing of hypotheses about altitude decompression sickness by statistical analyses.

This communication extends a statistical analysis of forced-descent decompression sickness at altitude in exercising subjects (J Appl Physiol 1994; 76:2726-2734) with a data subset having an additional explanatory variable, rate of ascent. The original explanatory variables for risk-function analysis were environmental pressure of the altitude, duration of exposure, and duration of pure-O2 breathing before exposure; the best fit was consistent with the idea that instantaneous risk increases linearly as altitude exposure continues. Use of the new explanatory variable improved the fit of the smaller data subset, as indicated by log likelihood. Also, with ascent rate accounted for, replacement of the term for linear accrual of instantaneous risk by a term for rise and then decay made a highly significant improvement upon the original model (log likelihood increased by 37 log units). The authors conclude that a more representative data set and removal of the variability attributable to ascent rate allowed the rise-and-decay mechanism, which is expected from theory and observations, to become manifest.

Relationship of oxygen content to PO2 for stabilized bubbles in the circulation: theory.

Stabilized bubbles can pass through capillary beds, recirculate for a few minutes or hours, and carry O2 from the lungs to the tissues. Here, we develop the theory for the O2 content-PO2 relationship of bubbles and the alterations of the bubbles that are coupled to the O2 transport. We provide examples for bubbles stabilized by a slowly permeating gas; bubbles stabilized by mechanical structures may behave similarly. Because there are two mechanisms for O2 unloading (lowering of PO2 and shrinkage), the bubbles release a large fraction of their O2 content at high PO2; when pure O2 is breathed, one-half of the content of a 3-microns-radius bubble is released before PO2 falls to 500 Torr. The possibility that stabilized bubbles could become a clinical tool for therapeutic transport of O2 raises many issues to be investigated. The highunloading PO2 offers opportunities for delivering O2 by diffusion to poorly perfused regions of the tissue but also presents a hazard of O2 toxicity to perfused tissue.

Breathing a mixture of inert gases: disproportionate diffusion into decompression bubbles.

To study the consequences of diving with gas mixtures, we simulated growth of decompression bubbles using an equation system that accounts for major determinants of bubble behavior. When breathing a mixture, bubbles are smaller than expected from linear interpolation between bubbles with either of the unmixed component gases because of disproportionate diffusion effects: a) When few bubbles form, the inert gas that permeates fastest becomes over-represented, relative to the breathing gas, inside bubbles during growth; this slows further entrance of the fast gas and enhances entrance of the slower gas. b) With N2-He mixtures and few bubbles, the over-represented gas is He in aqueous tissue, but is N2 in lipid tissue. c) When many bubbles form, the over-represented gas is the one with higher tissue solubility. Our simulations indicate that the smallest bubbles always occur with breathing of one of the component gases, but which gas that is depends on whether the tissue is lipid or aqueous and whether few or many bubbles form.

Effects of physical properties of the breathing gas on decompression-sickness bubbles.

To explore the relative dangers of different inert gases, we developed mathematical relationships concerned with bubble growth, using equations that separate gas properties from other variables. Predictions for saturation exposures were as follows. 1) Peak volume of a bubble is proportional to solubility in tissue when bubble density is high and to the 3/2 power of the ratio of the permeation coefficient to the partition coefficient when density is low. 2) Bubble duration is inversely proportional to the partition coefficient for the inert gas. 3). Sizes and durations of bubbles for one inert gas relative to another depend on whether the tissue is aqueous or lipid but are independent of the magnitude of the decompression and tissue half time. 4). He should give smaller bubbles than N2, except in aqueous tissue with low bubble density; our prediction correlates qualitatively with relative dangers observed with animals but seems to overestimate the safety afforded by He. Numerical simulations illustrate how nonsaturation dives are less predictable because more variables are involved.

Bubbles in circulating blood: stabilization and simulations of cyclic changes of size and content.

Surface tension, blood pressure, and inherent unsaturation due to O2 metabolism promote diffusion of gases out of bubbles in the bloodstream. We review the mechanisms that can overcome the absorptive tendencies so small spherical bubbles can persist. One general type of stabilizer is a mechanical structure at the gas-liquid interface that can support a negative pressure so that gases inside can be in diffusion equilibrium with their counterparts outside; one possibility for mechanical stabilizers are surfactant films. We show that a slowly permeating gas is analogous to a mechanical stabilizer; it allows equilibration of other gases inside-to-outside by diluting the gases inside. By using numerically solved equations based on physics of diffusion, we demonstrate how nonrigid stabilized bubbles change size as they move through the circulatory system. In small pulmonary vessels, the bubbles enlarge because blood pressure is low, there is no inherent unsaturation, and O2 and N2 diffuse from lung gas into the bubble; these gases diffuse out again in the systemic circulation.

Behavior of bubbles of slowly permeating gas used for ultrasonic imaging contrast.

RATIONALE AND OBJECTIVES: The authors predict behavior of blood cell-sized bubbles containing a foreign gas that slowly crosses a gas-liquid interface. Such bubbles are being developed for ultrasonic contrast. METHODS: Using appropriate coefficients for N2, O2, CO2, and foreign gases, the authors simulate diffusion between bubbles and blood with a numerically solved equation system. RESULTS: Within 30 seconds after intravenous injection of bubbles, entrance of endogenous gases more than doubles the radius. In vivo size and duration of the bubbles are quantitatively related to the amount of the foreign gas inside. Size and ultrasonic imaging effectiveness of the circulating bubbles become larger in lungs than in the rest of the circulation. As the foreign gas is lost, imaging effectiveness diminishes more rapidly than bubble radius. CONCLUSIONS: Bubbles of slowly permeating gas change size and composition after injection and also during their passage through different parts of the circulation.

Simulation of gas bubbles in hypobaric decompressions: roles of O2, CO2, and H2O.

UNLABELLED: To gain insight into the special features of bubbles that may form in aviators and astronauts, we simulated the growth and decay of bubbles in two hypobaric decompressions and a hyperbaric one, all with the same tissue ratio (TR), where TR is defined as tissue PN2 before decompression divided by barometric pressure after. We used an equation system which is solved by numerical methods and accounts for simultaneous diffusion of any number of gases as well as other major determinants of bubble growth and absorption. We also considered two extremes of the number of bubbles which form per unit of tissue. RESULTS: A) Because physiological mechanisms keep the partial pressures of the "metabolic" gases (O2, CO2, and H2O) nearly constant over a range of hypobaric pressures, their fractions in bubbles are inversely proportional to pressure and their large volumes at low pressure add to bubble size. B) In addition, the large fractions facilitate the entry of N2 into bubbles, and when bubble density is low, enhance an autocatalytic feedback on bubble growth due to increasing surface area. C) The TR is not closely related to bubble size; that is when two different decompressions have the same TR, metabolic gases cause bubbles to grow larger at lower hypobaric pressures. We conclude that the constancy of partial pressures of metabolic gases, unimportant in hyperbaric decompressions, affects bubble size in hypobaric decompressions in inverse relation to the exposure pressure.

Oxygen transport to tissue by persistent bubbles: theory and simulations.

Persistent gas bubbles able to traverse capillaries can be prepared from a slowly permeating gas or with a mechanical structure surrounding a gas phase. If they are permeable to gases, such bubbles will carry O2 from the lungs to the tissues via the blood stream. Using a mathematical model based on physical laws, we present simulations of the behavior of bubbles stabilized by a slowly permeating gas (gas X). We show that the bubble persists longer if the tissue and venous blood contain N2 to dilute gas X and slow its outward diffusion. A 6-microns -diam bubble carries 0.11 pl of O2 during the breathing of pure O2, so 4.6 x 10(8) bubbles/ml in the blood will supply a normal arteriovenous difference. In conditions used for hyperbaric O2 therapy, a bubble carries approximately 0.26 pl of O2. Stabilized bubbles have the potential to transport O2 efficiently; they release O2 to tissue at high PO2 and require injection of only small amounts of a foreign substance.

Probabilistic model of altitude decompression sickness based on mechanistic premises.

To develop a predictive equation and to test ideas about the mechanisms involved in hypobaric decompression sickness, we performed statistical analyses on published results of 7,023 exercising O2-breathing men subjected to one-step decompressions in altitude chambers. The dependent variable was signs or symptoms so severe that the person's trial was terminated (forced descent). The three independent variables were 1) duration of 100% O2 breathing at ground level (prebreathing), 2) atmospheric pressure after ascent, and 3) exposure duration. The best model, chosen from trial-and-error combinations of premises about bubble behavior, indicates that decompression sickness outcome depends on 1) prebreathing time, but with an unexpectedly long washout half time for N2; 2) time at altitude, as if bubbles grow; and 3) the estimated difference, raised to the fifth power, between the partial pressure of N2 in tissue before and that in bubbles after decompression, perhaps an index of the number of bubbles generated. We expect the model to provide accurate predictions for decompressions matching those of the bulk of the data; the mechanistic cues should be considered hypotheses for further investigation.

Simulation of exchanges of multiple gases in bubbles in the body.

This communication introduces a system of equations, for numerical solution, which simulates the generation, growth, and decay of bubbles. The system is an advance over previous works because it allows for simultaneous diffusion of any number of gases. Our purpose for developing the system is to gain insight into the bubbles that occur in the body in decompression sickness (DCS). We validate the calculation system by matching observed data of DCS bubbles and of large subcutaneous gas pockets in rats. We demonstrate how a temporary supersaturation and bubble formation can occur without change of ambient pressure when there is a change in the inert gas being breathed. With exposures to hypobaric environments, such as when astronauts work in space, simulations show that O2, CO2, and water vapor add appreciably to volume of bubbles and affect the diffusion of inert gas.