Evolution of Organic Solvent-Resistant DNA Polymerases

The introduction of thermostable polymerases revolutionized the polymerase chain reaction (PCR) and biotechnology. However, many GC-rich genes cannot be PCR-amplified with high efficiency in water, irrespective of temperature. Although polar organic cosolvents can enhance nucleic acid polymerization and amplification by destabilizing duplex DNA and secondary structures, nature has not selected for the evolution of solvent-tolerant polymerase enzymes. Here, we used ultrahigh-throughput droplet-based selection and deep sequencing along with computational free-energy and binding affinity calculations to evolve Taq polymerase to generate enzymes that are both stable and highly active in the presence of organic cosolvents, resulting in up to 10% solvent resistance and over 100-fold increase in stability at 97.5 °C in the presence of 1,4-butanediol, as well as tolerance to up to 10 times higher concentrations of the potent cosolvents sulfolane and 2-pyrrolidone. Using these polymerases, we successfully amplified a broad spectrum of GC-rich templates containing regions with over 90% GC content, including templates recalcitrant to amplification with existing polymerases, even in the presence of cosolvents. We also demonstrated dramatically reduced GC bias in the amplification of genes with widely varying GC content in quantitative polymerase chain reaction (qPCR). By expanding the scope of solvent systems compatible with nucleic acid polymerization, these organic solvent-resistant polymerases enable a dramatic reduction of sequence bias not achievable through thermal resistance alone, with significant implications for a wide range of applications including sequencing and synthetic biology in mixed aqueous-organic media.

Phase I dose escalation and expansion study of golidocitinib, a highly selective JAK1 inhibitor, in relapsed or refractory peripheral T-cell lymphomas

BACKGROUND

Relapsed or refractory peripheral T-cell lymphomas (r/r PTCLs) are a group of rare and aggressive diseases that lack effective therapies. Constitutive activation of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is reported to be associated with PTCLs. Golidocitinib is an oral, potent JAK1 selective inhibitor evaluated in a phase I/II multinational study in patients with r/r PTCLs.

PATIENTS AND METHODS

Patients with r/r PTCLs were eligible. The primary objectives were to assess safety and tolerability of golidocitinib and to define its recommended phase II dose (RP2D). The secondary objectives were to evaluate its antitumor activity and pharmacokinetics (PK).

RESULTS

A total of 51 patients were enrolled and received golidocitinib treatment at 150 or 250 mg once daily (QD). The median prior lines of therapies were 2 (range: 1-8). Golidocitinib was tolerated at both doses tested, while a higher incidence of serious adverse events and dose modifications at 250 mg were observed. The most common grade ≥3 drug-related treatment-emergent adverse events were neutropenia (27.5%) and thrombocytopenia (11.8%). An objective response rate of 39.2% and a complete response rate of 21.6% were observed. With median follow-up time of 14.7 and 15.9 months, the median duration of response (DoR) and progression-free survival were 8.0 and 3.3 months, respectively. Based on these data, 150 mg QD was defined as the RP2D. Golidocitinib demonstrated a favorable PK profile as an oral agent. Biomarker analysis suggested a potential correlation between JAK/STAT pathway aberrations and clinical activity of golidocitinib.

CONCLUSIONS

In this phase I study, golidocitinib demonstrated an acceptable safety profile and encouraging antitumor efficacy in heavily pretreated patients with r/r PTCLs. These results support the initiation of the multinational pivotal study in patients with r/r PTCLs.

Novel Functional Radiomics for Prediction of Cardiac PET Avidity in Lung Cancer Radiotherapy

PURPOSE/OBJECTIVE(S)

Traditional methods of evaluating cardiotoxicity focus solely on radiation doses to the heart and do not incorporate functional imaging information. Functional imaging has great potential to improve the ability to provide early prediction for cardiotoxicity for lung cancer patients undergoing radiotherapy. FDG-based PET/CT imaging is routinely obtained as part of standard staging work up for lung cancer patients. Although FDG PET/CT scans are typically used to evaluate the tumor, imaging guidelines note that FDG PET/CT scans are an FDA-approved method to image for cardiac inflammation, and studies have noted that the PET cardiac signal can be predictive of clinical outcomes. The purpose of this work was to develop a radiomics model to predict clinical cardiac assessment of standard of care FDG PET/CT scans.

MATERIALS/METHODS

The study included 100 consecutive lung cancer patients treated with radiotherapy who underwent standard pre-treatment FDG-PET/CT staging scans. A clinician reviewed the PET/CT scans per clinical cardiac assessment guidelines and classified the cardiac uptake as: 0 = uniform diffuse, 1 = absent, 2 = heterogeneous, with event rates of 20%, 44%, and 35%, respectively. The heart was delineated and 200 novel functional radiomics features were selected to classify cardiac FDG uptake patterns. We divided the data into an 80% training set and a 20% test set to train and evaluate the classification models. Feature reduction was carried out using the Wilcoxon test (with Bonferroni adjusted p<0.05), hierarchical clustering, and Recursive Feature Elimination. Two automatic machine learning (AutoML) frameworks were used to determine classification models: a Random Forest Classifier (Tree-based Pipeline Optimization Tool, TPOT) and Linear Discriminant Analysis (AutoSklearn). 10-fold cross validation was carried out for training and the accuracy of the ability of the models to predict for clinical cardiac assessment is reported.

RESULTS

Fifty-one independent radiomics features were reduced to 3 clinically pertinent features (PET 2D Skewness, PET Grey Level Co-occurrence Matrix Correlation, and PET Median) using feature reduction techniques. The model selected by TPOT showed 89.8% predictive accuracy in the cross validation of the training set and 85% predictive accuracy on the test set. The model selected by AutoSklearn showed 89.7% predictive accuracy in the cross validation of the training set and 80% predictive accuracy on the test set.

CONCLUSION

The novelty of this work is that it is the first study to develop and evaluate functional cardiac radiomic features from standard of care FDG PET/CT scans with the data showing good predictive accuracy with clinical imaging evaluation. If validated, the current work provides automated methods to provide functional cardiac information using standard of care imaging that can be used as an imaging biomarker for early clinical toxicity prediction for lung cancer patients.

Dosimetric analysis of stereotactic rotational versus static intensity-modulated radiation therapy for pancreatic cancer

PURPOSE

Stereotactic body radiation therapy is a promising treatment modality for locally advanced pancreatic cancer. To determine the optimal radiation treatment, we compared the plan characteristics of volumetric-modulated arc therapy and intensity-modulated radiation therapy when administered with stereotactic body radiation therapy to treat pancreatic cancer.

PATIENTS AND METHODS

Fifteen patients with locally advanced pancreatic cancer were treated by stereotactic body radiation therapy at a dose of 24-32Gy in four fractions with marker-guided gated volumetric-modulated arc therapy. Four dimensional-computed tomography scans were used to assess the target and surrounding normal organs. The same images, contours, and dose constraints were used for dual-arc volumetric-modulated arc therapy and 9-field intensity-modulated radiation therapy planning. Plans were compared using dosimetric parameters and treatment performance.

RESULTS

Volumetric-modulated arc therapy required significantly lower monitor units (1726 vs. 4188; P<0.001) and shorter treatment delivery time in comparison with intensity-modulated radiation therapy (22.5min vs. 52.4min; P<0.001). Regarding target volume coverage, both modalities demonstrated comparable results (V_95%, 99.3% vs. 99.4%; P=0.796). Both modalities satisfied the dosimetric determinants for duodenal toxicity and the maximum and mean doses administered to normal organ were also statistically similar.

CONCLUSION

In comparison with 9-field intensity-modulated radiation therapy, volumetric-modulated arc therapy significantly reduces the number of monitoring units and treatment delivery times while administering similar dosimetric quality. Based on these results, volumetric-modulated arc therapy might be an appropriate treatment for locally advanced pancreatic cancer when combined with stereotactic body radiation therapy.

Positive Rates of Preliminary Crossmatches Among Transplantation Candidates Waitlisted for Different Organs in the Korean Network for Organ Sharing

OBJECTIVE

For deceased-donor organ transplantations, negative T cell crossmatches (XMs) are mandatory for kidney and pancreas allocation in the Korean Network for Organ Sharing (KONOS) organ allocation system. Submission and periodic renewal of serum to the KONOS is required for all transplantation candidates of kidney or pancreas and these sera are distributed to 23 laboratories for preliminary XMs. We have investigated how sensitization status varies among transplantation candidates waitlisted for different organs.

METHODS

Positive rates of T cell XMs performed during recent 1-year period (from March 2014 to February 2015) in the Korea Organ Donation Agency laboratory have been analyzed according to different organs. For 163 cases of deceased donors, 3605 recipients (22.1 recipients per one donor) were crossmatched using both of National Institutes of Health and antihuman globulin complement-dependent cytotoxicity (CDC) methods and flow cytometry method.

RESULTS

T cell XM positive rates varied among transplantation candidates for different organs. The positive rate was high for kidney (485/3,145, 15.4%), and low for pancreas or kidney/pancreas (7/200, 3.5%), lung (0/41, 0%), and heart (11/221, 5.0%). Among XM-positive individuals, nearly two-thirds of the kidney transplantation candidates showed strong sensitization status with CDC+/flow+ results (64.5%), whereas pancreas or kidney/pancreas transplantation candidates more commonly showed weaker sensitization status with CDC-/flow+ results (85.7%).

CONCLUSION

Kidney transplantation candidates show a much higher positive rate and stronger sensitization status than candidates for other organs. The results of this study would be useful for determining the number of candidates to be crossmatched for different organs.

SU-E-T-234: LET Measurement Using Nuclear Emulsion and Monte Carlo Simulation for Proton Beam

PURPOSE

The significant issue of particle therapy such as proton and carbon ion biological effect on tumors and normal tissue. This effect closely connected with linear-energy-transfer (LET). This work presents a Monte Carlo study using GEANT4 and the verification using Nuclear Emulsion to show LET for proton beam.

METHODS

National Cancer Center (NCC) has IBA Beam Nozzle and cyclotron for proton therapy. We use proton beam bragg peak range 14cm. Also, we already developed the simulation using GEANT4 and finished validation for scattering proton beam. In our simulation, we make same condition with experimental setup.Nuclear emulsion films interleaved with tissue equivalent absorbers can be fruitfully used to reconstruct proton tracks with very high precision. This Nuclear emulsion film has been supported from Nagoya University, analyzed in Pusan University, was irradiated with a therapeutic proton beam at NCC. The Emulsion packs was located at entrance and bragg peak region of proton. This position means low and high LET region. The scanning of the emulsions has been performed at Nagoya University, where a fully automated microscopic scanning technology has been developed for the OPERA experiment on neutrino oscillations.

RESULTS

We could see the reconstructed track of proton scanning emulsion. From film scanning, we got the LET distribution at low and high LET region for several proton tracks. Simulation results was similar distribution within standard deviation in acceptance level. Also we got the RBE distribution using LET measurement for proton beam.

CONCLUSIONS

We measured LET at entrance and bragg peak region using Monte Carlo study and Nuclear Emulsion film, for NCC proton beam. This results means the good observation of LET using the nuclear emulsion. And this method can be used successfully in medical field.