Abstract Background Randomized controlled trials with a survival endpoint are the gold standard for clinical research, but have failed to achieve cures for most advanced malignancies. The high costs of randomized clinical trials slow progress (thereby causing avoidable loss of life) and increase health care costs. Discussion A malignancy may be caused by several different mutations. Therapies effective vs one mutation may be discarded due to lack of statistical significance across the entire population. Conversely, expensive large randomized trials may have sufficient statistical power to demonstrate benefit despite the therapy only working in subgroups. Non-cost-effective therapy is then applied to all patients (including subgroups it cannot help). Randomized trials comparing therapies with different mechanisms of action are misleading since they may conclude the therapies are “equivalent” despite benefitting different subpopulations, or may erroneously conclude that one therapy is superior simply because it targets a larger subpopulation. Furthermore, minor variances in patient selection may determine study outcome, a therapy may be discarded as ineffective despite substantial benefit in one subpopulation if harmful in another, randomized trials may more effectively detect therapies with minor benefit in most patients vs marked benefit in subpopulations, and randomized trials in unselected patients may erroneously conclude that “shot-gun” combinations are superior to single agents when sequential administration of personalized single agents might work better and spare patients treatment with drugs that cannot help them. We must identify predictive biomarkers early by comparing responding to progressing patients in phase I-II trials. Enriching randomized trials for biomarker-positive patients can markedly reduce required patient numbers and costs despite expensive screening for biomarker-positive patients. Available data support approval of new drugs without randomized trials if they yield single-agent sustained responses in patients refractory to standard therapies. Conversely, new approaches are needed to guide development of drug combinations since both standard phase II approaches and phase II-III randomized trials have a high risk of misleading. Summary Traditional randomized clinical trials approaches are often inefficient, wasteful, and unreliable. New clinical research paradigms are needed. The primary outcome of clinical research should be “Who (if anyone) benefits?” rather than “Does the overall group benefit?”

Single cells recorded from primary auditory cortex (AI and AII) of unanesthetized paralyzed cats were tested for responses to visual stimulation. Fortysix cells recorded from normal animals responded to acoustic stimuli but showed no discrete response to light flashes or small spots and bars. Twenty-two cells recorded from a congenitally deaf cat were spontaneously active but showed no discrete response to either auditory or visual stimulation. © 1970.

Genomics is a disruptive technology, having revealed that cancers are tremendously complex and differ from patient to patient. Therefore, conventional treatment approaches fit poorly with genomic reality. Furthermore, it is likely that this type of complexity will also be observed in other illnesses. Precision medicine has been posited as a way to better target disease-related aberrations, but developing drugs and tailoring therapy to each patient's complicated problem is a major challenge. One solution would be to match patients to existing compounds based on in silico modeling. However, optimization of complex therapy will eventually require designing compounds for patients using computer modeling and just-in-time production, perhaps achievable in the future by three-dimensional (3D) printing. Indeed, 3D printing is potentially transformative by virtue of its ability to rapidly generate almost limitless numbers of objects that previously required manufacturing facilities. Companies are already endeavoring to develop affordable 3D printers for home use. An attractive, but as yet scantily explored, application is to place chemical design and production under digital control. This could be accomplished by utilizing a 3D printer to initiate chemical reactions, and print the reagents and/or the final compounds directly. Of interest, the Food and Drug Administration (FDA) has recently approved a 3D printed drug-levetiracetam-indicated for seizures. Further, it is now increasingly clear that biologic materials-tissues, and eventually organs-can also be "printed." In the near future, it is plausible that high-throughput computing may be deployed to design customized drugs, which will reshape medicine.

Single-cell responses are shaped by the geometry of signalling kinetic trajectories carved in a multidimensional space spanned by signalling protein abundances. It is, however, challenging to assay a large number (more than 3) of signalling species in live-cell imaging, which makes it difficult to probe single-cell signalling kinetic trajectories in large dimensions. Flow and mass cytometry techniques can measure a large number (4 to more than 40) of signalling species but are unable to track single cells. Thus, cytometry experiments provide detailed time-stamped snapshots of single-cell signalling kinetics. Is it possible to use the time-stamped cytometry data to reconstruct single-cell signalling trajectories? Borrowing concepts of conserved and slow variables from non-equilibrium statistical physics we develop an approach to reconstruct signalling trajectories using snapshot data by creating new variables that remain invariant or vary slowly during the signalling kinetics. We apply this approach to reconstruct trajectories using snapshot data obtained from in silico simulations, live-cell imaging measurements, and, synthetic flow cytometry datasets. The application of invariants and slow variables to reconstruct trajectories provides a radically different way to track objects using snapshot data. The approach is likely to have implications for solving matching problems in a wide range of disciplines.

We hypothesized that aberrations activating epidermal growth factor receptor (EGFR) via dimerization would be more sensitive to anti-dimerization agents (e.g., cetuximab). EGFR exon 19 abnormalities (L747_A750del; deletes amino acids LREA) respond to reversible EGFR kinase inhibitors (TKIs). Exon 20 in-frame insertions and/or duplications (codons 767 to 774) and T790M mutations are clinically resistant to reversible/some irreversible TKIs. Their impact on protein function/therapeutic actionability are not fully elucidated.In our study, the index patient with non-small cell lung cancer (NSCLC) harbored EGFR D770_P772del_insKG (exon 20). A twenty patient trial (NSCLC cohort) (cetuximab-based regimen) included two participants with EGFR TKI-resistant mutations ((i) exon 20 D770>GY; and (ii) exon 19 LREA plus exon 20 T790M mutations). Structural modeling predicted that EGFR exon 20 anomalies (D770_P772del_insKG and D770>GY), but not T790M mutations, stabilize the active dimer configuration by increasing the interaction between the kinase domains, hence sensitizing to an agent preventing dimerization. Consistent with predictions, the two patients harboring D770_P772del_insKG and D770>GY, respectively, responded to an EGFR antibody (cetuximab)-based regimen; the T790M-bearing patient showed no response to cetuximab combined with erlotinib. In silico modeling merits investigation of its ability to optimize therapeutic selection based on structural/functional implications of different aberrations within the same gene.

Background

In 31 solid tumor patients treated with the demethylating agent decitabine, we performed tumor biopsies before and after the first cycle of decitabine and used immunohistochemistry (IHC) to assess whether decitabine increased expression of various membrane transporters. Resistance to chemotherapy may arise due to promoter methylation/downregulation of expression of transporters required for drug uptake, and decitabine can reverse resistance in vitro. The endocytosis regulator RhoA, the folate carriers FOLR1 and RFC1, and the glucose transporter GLUT4 were assessed.

Results

Pre-decitabine RhoA was higher in patients who had received their last therapy >3 months previously than in patients with more recent prior therapy (P = 0.02), and varied inversely with global DNA methylation as assessed by LINE1 methylation (r = -0.58, P = 0.006). Tumor RhoA scores increased with decitabine (P = 0.03), and RFC1 also increased in patients with pre-decitabine scores ≤150 (P = 0.004). Change in LINE1 methylation with decitabine did not correlate significantly with change in IHC scores for any transporter assessed. We also assessed methylation of the RFC1 gene (alias SLC19A1). SLC19A1 methylation correlated with tumor LINE1 methylation (r = 0.45, P = 0.02). There was a small (statistically insignificant) decrease in SLC19A1 methylation with decitabine, and there was a trend towards change in SLC19A1 methylation with decitabine correlating with change in LINE1 methylation (r = 0.47, P <0.15). While SLC19A1 methylation did not correlate with RFC1 scores, there was a trend towards an inverse correlation between change in SLC19A1 methylation and change in RFC1 expression (r = -0.45, P = 0.19).

Conclusions

In conclusion, after decitabine administration, there was increased expression of some (but not other) transporters that may play a role in chemotherapy uptake. Larger patient numbers will be needed to define the extent to which this increased expression is associated with changes in DNA methylation.

Background

Although interest in sphincter-sparing treatments for anal fistulas is increasing, few large prospective studies of these approaches have been conducted.

Objective

The study assessed outcomes after implantation of a synthetic bioabsorbable anal fistula plug.

Design

A prospective, multicenter investigation was performed.

Setting

The study was conducted at 11 colon and rectal centers.

Patients

Ninety-three patients (71 men; mean age, 47 years) with complex cryptoglandular transsphincteric anal fistulas were enrolled. Exclusion criteria included Crohn's disease, an active infection, a multitract fistula, and an immunocompromised status.

Intervention

Draining setons were used at the surgeon's discretion. Patients had follow-up evaluations at 1, 3, 6, and 12 months postoperatively.

Main outcome measures

The primary end point was healing of the fistula, defined as drainage cessation plus closure of the external opening, at 6 and 12 months. Secondary end points were fecal continence, duration of drainage from the fistula, pain, and adverse events during follow-up.

Results

Thirteen patients were lost to follow-up and 21 were withdrawn, primarily to undergo an alternative treatment. The fistula healing rates at 6 and 12 months were 41% (95% CI, 30%-52%; total n = 74) and 49% (95% CI, 38%-61%; total n = 73). Half the patients in whom a previous treatment failed had healing. By 6 months, the mean Wexner score had improved significantly (p = 0.0003). By 12 months, 93% of patients had no or minimal pain. Adverse events included 11 infections/abscesses, 2 new fistulas, and 8 total and 5 partial plug extrusions. The fistula healed in 3 patients with a partial extrusion.

Limitations

The study was nonrandomized and had relatively high rates of loss to follow-up.

Conclusion

Implantation of a synthetic bioabsorbable fistula plug is a reasonably efficacious treatment for complex transsphincteric anal fistulas, especially given the simplicity and low morbidity of the procedure.

Natural killer (NK) cells perform immunosurveillance of virally infected and transformed cells, and their activation depends on the balance between signaling by inhibitory and activating receptors. Cytokine receptor signaling can synergize with activating receptor signaling to induce NK cell activation. We investigated the interplay between the signaling pathways stimulated by the cytokine interleukin-2 (IL-2) and the activating receptor NKG2D in immature (CD56^bright) and mature (CD56^dim) subsets of human primary NK cells using mass cytometry experiments and in silico modeling. Our analysis revealed that IL-2 changed the abundances of several key proteins, including NKG2D and the phosphatase CD45. Furthermore, we found differences in correlations between protein abundances, which were associated with the maturation state of the NK cells. The mass cytometry measurements also revealed that the signaling kinetics of key protein abundances induced by NKG2D stimulation depended on the maturation state and the pretreatment condition of the NK cells. Our in silico model, which described the multidimensional data with coupled first-order reactions, predicted that the increase in CD45 abundance was a major enhancer of NKG2D-mediated activation in IL-2-treated CD56^bright NK cells but not in IL-2-treated CD56^dim NK cells. This dependence on CD45 was verified by measurement of CD107a mobilization to the NK cell surface (a marker of activation). Our mathematical framework can be used to glean mechanisms underlying synergistic signaling pathways in other activated immune cells.

It takes on average 6-12 years to develop new anticancer drugs from discovery to approval. Effective new agents prolong survival. To demonstrate the importance of rapid drug approval, we calculated life-years potentially saved if selected agents were approved more rapidly. As illustrative examples, we used 27 trials documenting improvements in survival. We multiplied improvement in median survival by numbers of patients dying annually and multiplied this by number of years from drug discovery until approval. For every year by which time to drug approval could have been shortened, there would have been a median number of life-years potentially saved of 79,920 worldwide per drug. Median number of life-years lost between time of drug discovery and approval was 1,020,900 per example. If we were able to use available opportunities to decrease the time required to take a drug from discovery to approval to 5 years, the median number of life-years saved per example would have been 523,890 worldwide. Various publications have identified opportunities to speed drug development without sacrificing patient safety. While many investigational drugs prove to be ineffective, some significantly prolong survival and/or reduce suffering. These illustrative examples suggest that a substantial number of life-years could potentially be saved by increasing the efficiency of development of new drugs for advanced malignancies.