Susan G. Komen Big Data for Breast Cancer Initiative: How Patient Advocacy Organizations Can Facilitate Using Big Data to Improve Patient Outcomes

Integrating different types of data, including electronic health records, imaging data, administrative and claims databases, large data repositories, the Internet of Things, genomics, and other omics data, is both a challenge and an opportunity that must be tackled head on. We explore some of the challenges and opportunities in optimizing data integration to accelerate breast cancer discovery and improve patient outcomes. Susan G. Komen convened three meetings (2015, 2017, and 2018) with various stakeholders to discuss challenges, opportunities, and next steps to enhance the use of big data in the field of breast cancer. Meeting participants agreed that big data approaches can enhance the identification of better therapies, improve outcomes, reduce disparities, and optimize precision medicine. One challenge is that databases must be shared, linked with each other, standardized, and interoperable. Patients want to be active participants in research and their own care, and to control how their data are used. Many patients have privacy concerns and do not understand how sharing their data can help to effectively drive discovery. Public education is essential, and breast cancer researchers who are skilled in using and analyzing big data are needed. Patient advocacy groups can play multiple roles to help maximize and leverage big data to better serve patients. Komen is committed to educating patients on big data issues, encouraging data sharing by all stakeholders, assisting in training the next generation of data science breast cancer researchers, and funding research projects that will use real-life data in real time to revolutionize the way breast cancer is understood and treated.

Follicle size and reproductive hormone profiles during a post-weaning altrenogest treatment in primiparous sows

This study investigated the endocrine background of follicle size changes during post-weaning altrenogest treatment. altrenogest-treated sows received a 20-mg dosage daily at 8.00 a.m. from Day -1 to Day 14 after weaning. On Day -1, only 3/13 altrenogest-treated sows showed LH pulses compared with 8/8 control sows (P=0.001). On Day 0, control sows showed a typical high frequency-low amplitude LH pattern, indicative for recruitment of oestrogenic follicles. In altrenogest-treated animals on Day 0, half of the sows showed high frequency-high amplitude pulses from 4-5h after weaning. In altrenogest-treated sows, average follicle size increased from 3.1±0.5 mm on Day 0 to 4.4±0.6mm on Day 5, then decreased to 3.7±0.5 mm on Day 7 and stabilised thereafter. FSH and oestradiol (E2) concentrations showed a distinct diurnal pattern; high at 7.00 a.m. and low at 3.00 p.m. E2 concentrations (7.00 a.m.) showed a 2.5-fold increase from Day -1 to Day 2, and subsequently a 2-fold decline to reach a plateau at Day 8. FSH concentrations reached maximum levels by Day 5 and slowly declined afterwards. In conclusion, once-daily administration of altrenogest starting one day before weaning delays the weaning-induced increase in LH pulses. Although FSH and follicle size increase until Day 5 after weaning, follicle E2 production already decreased from Day 2 after weaning. Post-weaning altrenogest treatment thus results in a follicular wave of follicles that lose oestrogenic competence at Day 2 after weaning, presumably related to the changed LH dynamics during altrenogest treatment.

Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCα invasive signaling axis

In cancer, deregulated signaling can produce an invasive cellular phenotype. We modeled the invasive transition as a theoretical switch between two cytoskeletal structures: focal adhesions and extracellular matrix-degrading invadopodia. We constructed molecular interaction networks of each structure and identified upstream regulatory hubs through computational analyses. We compared these regulatory hubs to the status of signaling components from head and neck carcinomas, which led us to analyze phosphatidylinositol 3-kinase (PI3K) and protein kinase C α (PKCα). Consistent with previous studies, PI3K activity promoted both the formation and the activity of invadopodia. We found that PI3K induction of invadopodia was increased by overexpression of SH2 (Src homology 2) domain-containing inositol 5'-phosphatase 2 (SHIP2), which converts the phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P(3)] that is produced by PI3K activity to phosphatidylinositol 3,4-bisphosphate [PI(3,4)P(2)], which is believed to promote invadopodia formation. Knockdown of PKCα had divergent effects on invadopodia formation, depending on the status of PI3K. Loss of PKCα inhibited invadopodia formation in cells with wild-type PI3K pathway status. Conversely, in cells with constitutively active PI3K (through activating PI3K mutants or lacking the endogenous opposing enzyme PTEN), PKCα knockdown increased invadopodia formation. Mechanistic studies revealed a negative feedback loop from PKCα that dampened PI3K activity and invasive behavior in cells with genetic hyperactivation of the PI3K pathway. These studies demonstrated the potential of network modeling as a discovery tool and identified PI3K and PKCα as interacting regulators of invasive behavior.

Progestagen supplementation during early pregnancy does not improve embryo survival in pigs

Progesterone supplementation during early pregnancy may increase embryo survival in pigs. The current study evaluated whether oral supplementation with an analogue of progesterone, altrenogest (ALT), affects embryo survival. A first experiment evaluated the effect of a daily 20-mg dosage of ALT during days 1-4 or 2-4 after onset of oestrus on embryo survival at day 42 of pregnancy. A control group (CTR1) was not treated. The time of ovulation was estimated by transrectal ultrasound at 12-h intervals. Altrenogest treatment significantly reduced pregnancy rate when start of treatment was before or at ovulation: 25% (5/20) compared to later start of treatment [85% (28/33)] and non-treated CTR1 [100% (23/23)]. Altrenogest treatment also reduced (p < 0.05) number of foetuses, from 14.6 ± 2.6 in CTR1 to 12.5 ± 2.5 when ALT started 1-1.5 days from ovulation and 10.7 ± 2.9 when ALT started 0-0.5 days from ovulation. In a second experiment, sows with a weaning-to-oestrous interval (WOI) of 6, 7 or 8-14 days were given ALT [either 20 mg (ALT20; n = 49) or 10 mg (ALT10; n = 48)] at day 4 and day 6 after onset of oestrus or were not treated (CTR2; n = 49), and farrowing rate and litter size were evaluated. Weaning-to-oestrous interval did not affect farrowing rate or litter size. ALT did not affect farrowing rate (86% vs 90% in CTR2), but ALT20 tended to have a lower litter size compared with CTR2 (11.7 ± 4.1 vs 13.3 ± 3.1; p = 0.07) and ALT10 was intermediate (12.3 ± 2.9). In conclusion, altrenogest supplementation too soon after ovulation reduces fertilization rate and embryo survival rate and altrenogest supplementation at 4-6 days of pregnancy reduces litter size. As a consequence, altrenogest supplementation during early pregnancy may reduce both farrowing rate and litter size and cannot be applied at this stage in practice as a remedy against low litter size.

Influence of cell cycle phase on apparent diffusion coefficient in synchronized cells detected using temporal diffusion spectroscopy

The relationship between the apparent diffusion coefficient of tissue water measured by MR methods and the physiological status of cells is of particular relevance for better understanding and interpretation of diffusion-weighted MRI. In addition, there is considerable interest in developing diffusion-dependent imaging methods capable of providing novel information on tissue microstructure, including intracellular changes. To this end, both the conventional pulsed gradient spin-echo methods and the oscillating gradient spin-echo method, which probes diffusion over very short distance (<<cell size) and time scales, were used to measure apparent diffusion coefficient of synchronized packed HL-60 cells at 7 T. The results show that the pulsed gradient spin-echo method with relatively long diffusion times does not detect changes in apparent diffusion coefficient when structural variations arise during cell division. On the contrary, the oscillating gradient spin-echo method can detect and quantify major changes in intracellular organization that occur during mitosis by appropriate choice of gradient frequency. Cell structural parameters, including cell size, intracellular diffusion coefficient, and surface-to-volume ratio were also obtained by fitting the oscillating gradient spin-echo data to simple analytical models. These oscillating gradient spin-echo features may be used in diffusion-weighted MRI to create parametric maps that may be useful for detecting cancer or changes caused by treatment.

Effects of intracellular organelles on the apparent diffusion coefficient of water molecules in cultured human embryonic kidney cells

The apparent diffusion coefficient (ADC) of water in tissues is dependent on the size and spacing of structures in the cellular environment and has been used to characterize pathological changes in stroke and cancer. However, the factors that affect ADC values remain incompletely understood. Measurements of ADC are usually made using relatively long diffusion times; so they reflect the integrated effects of cellular structures over a broad range of spatial scales. We used temporal diffusion spectroscopy to study diffusion in packed cultured human embryonic kidney cells over a range of effective diffusion times following microtubule and actin/cytoskeleton depolymerization and disassembly of the Golgi complex. While Golgi disruption did not change ADC, depolymerization of the microtubule and the actin filament networks caused small decreases in ADC at short diffusion times only. Temporal diffusion spectroscopy provided a novel way to assess intracellular influences on the diffusion properties of tissue water.

Incidence and prevention of early parturition in sows

A retrospective study, based on 60,990 farrowing records from 35 commercial herds, was performed to determine the incidence of early parturition (<114 d) and to investigate the relationship between early parturition and total number of piglets born, number of piglets born alive and percentage of stillborn piglets per litter. The mean gestation length was 115.4 ± 1.62 d, and early parturition occurred in 10% of all farrowing records. Sows with early parturition had significantly more stillborn piglets and a larger litter size compared to sows with a normal gestation length (114-117 d). Sows with a gestation length <114 d were 1.2 times (95% CI: 1.19-1.21; p<0.001) more likely to have an early parturition at the subsequent parity. A second study was performed in four herds (n=329) to investigate the efficacy of altrenogest administration on 110-112 d (T112) or 111-113 d (T113) of gestation for preventing early parturition and to investigate the effect of this treatment on the reproductive performance of sows. The interval between the last altrenogest treatment and the onset of parturition was 3.3 ± 1.32 (T112) or 2.0 ± 0.89 (T113) days. The gestation length of sows of the altrenogest group (T112 + T113) (115.3 ± 1.23 d) was significantly longer compared to gestation length of the non-treated sows (114.7 ± 1.69d) (p<0.01). Altrenogest treatment had no negative effect on the reproductive performances of the sows. In conclusion, the administration of altrenogest in late gestation is an effective and safe method to prevent early parturition and can counteract the reproductive losses because of premature farrowing, which may occur in a substantial part of the farrowing events.

Linking changes in epithelial morphogenesis to cancer mutations using computational modeling

Most tumors arise from epithelial tissues, such as mammary glands and lobules, and their initiation is associated with the disruption of a finely defined epithelial architecture. Progression from intraductal to invasive tumors is related to genetic mutations that occur at a subcellular level but manifest themselves as functional and morphological changes at the cellular and tissue scales, respectively. Elevated proliferation and loss of epithelial polarization are the two most noticeable changes in cell phenotypes during this process. As a result, many three-dimensional cultures of tumorigenic clones show highly aberrant morphologies when compared to regular epithelial monolayers enclosing the hollow lumen (acini). In order to shed light on phenotypic changes associated with tumor cells, we applied the bio-mechanical IBCell model of normal epithelial morphogenesis quantitatively matched to data acquired from the non-tumorigenic human mammary cell line, MCF10A. We then used a high-throughput simulation study to reveal how modifications in model parameters influence changes in the simulated architecture. Three parameters have been considered in our study, which define cell sensitivity to proliferative, apoptotic and cell-ECM adhesive cues. By mapping experimental morphologies of four MCF10A-derived cell lines carrying different oncogenic mutations onto the model parameter space, we identified changes in cellular processes potentially underlying structural modifications of these mutants. As a case study, we focused on MCF10A cells expressing an oncogenic mutant HER2-YVMA to quantitatively assess changes in cell doubling time, cell apoptotic rate, and cell sensitivity to ECM accumulation when compared to the parental non-tumorigenic cell line. By mapping in vitro mutant morphologies onto in silico ones we have generated a means of linking the morphological and molecular scales via computational modeling. Thus, IBCell in combination with 3D acini cultures can form a computational/experimental platform for suggesting the relationship between the histopathology of neoplastic lesions and their underlying molecular defects.

Epitope mapping of function-blocking monoclonal antibody CM6 suggests a "weak" integrin binding site on the laminin-332 LG2 domain

Laminin-332 (Ln-332) is an extracellular matrix molecule that regulates cell adhesion, spreading, and migration by interaction with cell surface receptors such as alpha3beta1 and alpha6beta4. Previously, we developed a function-blocking monoclonal antibody against rat Ln-332, CM6, which blocks hemidesmosome assembly induced by Ln-332-alpha6beta4 interactions. However, the location of its epitope on Ln-332 has remained unclear. In this study, we show that the CM6 epitope is located on the laminin G-like (LG)2 module of the Ln-332 alpha3 chain. To specify the residues involved in this epitope, we produced a series of GST-fused alpha3 LG2 mutant proteins in which rat-specific acids were replaced with human acids by a site-directed mutagenesis strategy. CM6 reactivity against these proteins showed that CM6 binds to the (1089)NERSVR(1094) sequence of rat Ln-332 LG2 module. In a structural model, this sequence maps to an LG2 loop sequence that is exposed to solvent according to predictions, consistent with its accessibility to antibody. CM6 inhibits integrin-dependent cell adhesion on Ln-332 and inhibits cell spreading on both Ln-332 and recombinant LG2 (rLG2; but not rLG3), suggesting the presence of an alpha3beta1 binding site on LG2. However, we were unable to show that rLG2 supports adhesion in standard assays, suggesting that LG2 may contain a "weak" integrin binding site, only detectable in spreading assays that do not require washes. These results, together with our previous findings, indicate that binding sites for alpha3beta1 and alpha6beta4 are closely spaced in the Ln-332 LG domains where they regulate alternative cell functions, namely adhesion/migration or hemidesmosome anchoring.

The proto-oncoprotein SYT (SS18) controls ATP release and regulates cyst formation by polarized MDCK cells

The SYT proto-oncoprotein (also known as SS18) is a gene expression regulator conserved across species. Although its biological function is still unknown, the importance of SYT as a housekeeping protein is illustrated by the lethal phenotype of SYT-null embryos. Notably, SYT is a component of the synovial sarcoma-associated translocation product, the SYT-SSX oncogene. SYT was previously reported as a mediator of cell adhesion. In the present study we show that SYT possesses distinct domains that control MDCK cyst formation in three-dimensional collagen cultures. While the carboxy-half of SYT, the QPGY domain, is required for cyst growth, the amino-terminal region appears to exert on this process a regulatory effect. Further analysis suggested that the purinergic G protein-coupled P2Y receptor signaling is involved in SYT-induced cystogenesis. Activation of this cascade is due to facilitation of ATP release in the extracellular space of polarized MDCK cells by SYT. These studies allow us to begin to understand the vital role of SYT in controlling epithelial morphogenesis and might explain the lethality of its loss in the developing embryo.

Model-controlled hydrodynamic focusing to generate multiple overlapping gradients of surface-immobilized proteins in microfluidic devices

Historically, it has been difficult to generate accurate and reproducible protein gradients for studies of interactions between cells and extracellular matrix. Here we demonstrate a method for rapid patterning of protein gradients using computer-driven hydrodynamic focusing in a simple microfluidic device. In contrast to published work, we are moving the complexity of gradient creation from the microfluidic hardware to dynamic computer control. Using our method, switching from one gradient profile to another requires only a few hours to devise a new control file, not days or weeks to design and build a new microfluidic device. Fitting existing protein deposition models to our data, we can extract key parameters needed for controlling protein deposition. Several protein deposition models were evaluated under microfluidic flow conditions. A mathematical model for our deposition method allows us to determine the parameters for a protein adsorption model and then predict the final shape of the surface density gradient. Simple and non-monotonic single and multi-protein gradient profiles were designed and deposited using the same device.

Involvement of tissue inhibition of metalloproteinases-1 in learning and memory in mice

Tissue inhibitor of metalloproteinases (TIMP-1) is one of the four-member family (TIMPs-1-4) of multifunctional proteins that inhibit matrix metalloproteinases (MMPs). Its expression in the hippocampus is neuronal-activity-dependent and dramatically induced by stimuli leading to long-term potentiation (LTP), suggesting that TIMP-1 is a candidate plasticity protein potentially involved in learning and memory processes. We tested this hypothesis in a hippocampus-dependent task using the new olfactory tubing maze, with mice carrying a null mutation for TIMP-1 (TIMP-1 KO) and mice overexpressing TIMP-1 (TIMP-1 (tg)). The TIMP-1 KO mice were significantly impaired in making correct odor-reward associations when compared with their respective wild type (WT) littermates, while TIMP-1 overexpressing mice performed better than their WT controls. Both genetically modified mice learned the paradigm and the timing of the task, like their respective WTs, and no olfactory dysfunctioning was observed. These data suggest that TIMP-1 is involved in learning and memory processes related to the hippocampus, and support the hypothesis that the MMP/TIMP ratio, and hence MMP activity, modulates neuronal plasticity in normal learning and memory processes, while altered proteolytic activity could impair cognitive functions.

Variability of energy metabolism and nuclear T3-receptors within the skeletal muscle tissue of pigs different with respect to the halothane gene

Energy metabolism of skeletal muscle tissue of pigs growing from approximately 12 to 18 kg (12 homozygous halothane negative, HH; 16 heterozygotes, Hh; 17 homozygous halothane susceptible, hh) was measured in vivo using 31P nuclear magnetic resonance (NMR) spectroscopy. Data for intracellular pH, phosphocreatine (PCr), phosphomonoesters (PME), and ATP were analyzed by canonical discriminant analysis, an artificial neural network approach, and analysis of variance. Within the hh pigs, two subpopulations could be distinguished before the application of halothane treatment. Some of the hh pigs had a high PME concentration in the biceps femoris muscle (hh(pme+)), whereas others had a low concentration (hh(pme-)) (2.18 +/- .12 for hh(pme+) vs 1.68 +/- .12 mM for hh(pme-), P < .004). The hh(pme+) pigs were statistically different from HH pigs for pH (P < .03), PME (P < .004), and PCr (P < .008) before halothane treatment. The hh(pme-) pigs were not different from the Hh and HH pigs with respect to PME when measured before halothane treatment (P > .05). However, intracellular pH (P < .03) and PCr (P < .008) of the hh(pme-) pigs were different from those of HH pigs (7.15 vs 7.19 for pH and 38.7 vs 35.1 for PCr, respectively). When combining intracellular pH, PME, and PCr within a canonical discriminant analysis, all were measured before halothane treatment, Hh pigs were found to be different from HH pigs (Mahalanobis distance different from zero, P < .02). In a second experiment, growth rate, depth of longissimus muscle, and maximal binding capacity of nuclear T3-receptors of skeletal muscle tissue were different (P < .05, P < .002, and P < .02, respectively) among pigs selected from the same genetic lines. Of the variability in depth of the longissimus muscle, 22% was explained by variability in maximal binding capacity of nuclear T3-receptors. These results, if confirmed with a large number of pigs, might open new possibilities for selection procedures for leanness because, with respect to halothane susceptibility, a shift between genotypic and phenotypic variability was observed.

Transport of pigs different with respect to the halothane gene: stress assessment

Two transport experiments were carried out with 18 pigs each. These pigs originated from three genetic lines (homozygous halothane-positive and -negative and heterozygotes). Half the pigs were unfed for 12 h before transport. All pigs were transported twice for 2 h. Before and after transport pigs were anesthetized to take blood samples from the jugular vein and biopsies from the biceps femoris. At the same time equipment to measure body temperature and heart rate were attached or detached. Plasma cortisol and beta-endorphin concentrations were measured as well as the glycogen concentration in the muscle sample. Line differences were detected with respect to body temperature (P < .04), heart rate (P < .05), and cortisol (P < .01). The withholding of feed influenced (P < .04) plasma beta-endorphin concentration. Body temperature (P < .02), heart rate (P < .001), cortisol (P < .01), and beta-endorphin (P < .001) were different before and after transport, whereas a training effect of the transport number was observed for heart rate (P < .07) and plasma beta-endorphin (P < .02). No interactions between treatments were observed. The relationship between cortisol and beta-endorphin suggests a nonconcomitant release of ACTH and beta-endorphin.