Super-resolution imaging for in situ monitoring sub-cellular micro-dynamics of small molecule drug

Small molecule drugs play a pivotal role in the arsenal of anticancer pharmacological agents. Nonetheless, their small size poses a challenge when directly visualizing their localization, distribution, mechanism of action (MOA), and target engagement at the subcellular level in real time. We propose a strategy for developing triple-functioning drug beacons that seamlessly integrate therapeutically relevant bioactivity, precise subcellular localization, and direct visualization capabilities within a single molecular entity. As a proof of concept, we have meticulously designed and constructed a boronic acid fluorescence drug beacon using coumarin-hemicyanine (CHB). Our CHB design includes three pivotal features: a boronic acid moiety that binds both adenosine triphosphate (ATP) and adenosine diphosphate (ADP), thus depleting their levels and disrupting the energy supply within mitochondria; a positively charged component that targets the drug beacon to mitochondria; and a sizeable conjugated luminophore that emits fluorescence, facilitating the application of structured illumination microscopy (SIM). Our study indicates the exceptional responsiveness of our proof-of-concept drug beacon to ADP and ATP, its efficacy in inhibiting tumor growth, and its ability to facilitate the tracking of ADP and ATP distribution around the mitochondrial cristae. Furthermore, our investigation reveals that the micro-dynamics of CHB induce mitochondrial dysfunction by causing damage to the mitochondrial cristae and mitochondrial DNA. Altogether, our findings highlight the potential of SIM in conjunction with visual drug design as a potent tool for monitoring the in situ MOA of small molecule anticancer compounds. This approach represents a crucial advancement in addressing a current challenge within the field of small molecule drug discovery and validation.

Neoadjuvant nivolumab plus chemotherapy versus chemotherapy for resectable NSCLC: subpopulation analysis of Chinese patients in CheckMate 816

BACKGROUND

Neoadjuvant nivolumab plus chemotherapy significantly improved event-free survival (EFS) and pathologic complete response (pCR) versus chemotherapy alone in patients with resectable non-small-cell lung cancer (NSCLC) in the global phase III CheckMate 816 study. Here, we report post hoc exploratory efficacy, safety, and surgical outcomes in the Chinese subpopulation of this study.

METHODS

Adults with stage IB-IIIA resectable NSCLC were randomized to receive nivolumab 360 mg plus chemotherapy or chemotherapy alone every 3 weeks for three cycles followed by surgery. Primary endpoints included EFS and pCR (both per blinded independent review). EFS and pCR results were from 14 October 2022, and 16 September 2020, database locks, respectively.

RESULTS

The Chinese subpopulation comprised 97 patients (nivolumab plus chemotherapy, 44; chemotherapy, 53). At 38.2 months of minimum follow-up, median EFS was not reached [95% confidence interval (CI) 23.4 months-not reached] in the nivolumab plus chemotherapy arm and 13.9 months (95% CI 8.3-34.3 months) in the chemotherapy arm (hazard ratio 0.47, 95% CI 0.25-0.88). pCR rates were 25.0% (95% CI 13.2% to 40.3%) and 1.9% (95% CI 0.0% to 10.1%), respectively (odds ratio 11.05; 95% CI 1.41-86.49). Of 97 Chinese patients, 36 (82%) in the nivolumab plus chemotherapy arm and 41 (77%) in the chemotherapy arm underwent definitive surgery. Grade 3-4 treatment-related adverse events occurred in 18/43 patients (42%) treated with nivolumab plus chemotherapy and 22/53 patients (42%) treated with chemotherapy.

CONCLUSIONS

Consistent with findings in the global study population of CheckMate 816, neoadjuvant nivolumab plus chemotherapy improved EFS and pCR versus chemotherapy in the Chinese subpopulation without impacting treatment tolerability or the feasibility of surgery. These findings support the use of nivolumab plus chemotherapy as a standard neoadjuvant treatment option for Chinese patients with resectable NSCLC.

Fiber Bragg gratings inscribed in nanobore fibers

The nanobore fiber (NBF) is a promising nanoscale optofluidic platform due to its long nanochannel and unique optical properties. However, so far, the applications of NBF have been based only on its original fiber geometry without any extra functionalities, in contrast with various telecom fiber devices, which may limit its wide applications. Here, we provide the first, to the best of our knowledge, demonstration of NBF-based fiber Bragg gratings (FBGs) introduced by either the femtosecond (fs) laser direct writing technique or the ultraviolet (UV) laser phase mask technique. Moreover, the FBG fabricated via the UV laser was optimized, achieving a high reflectivity of 96.89% and simultaneously preserving the open nanochannel. The NBF-based FBGs were characterized in terms of temperature variation and the infiltration of different liquids, and they showed high potential for nanofluidic applications.

High-precision optical frequency transfer over a 96 km urban fiber link

We demonstrated the optical frequency transfer over a 96 km urban business network in Shanghai. The key factors affecting the optical frequency transmission system, such as fiber link quality, feedback compensation strength, and out-of-loop fiber temperature variation, are studied for the urban fiber link characteristics. The effective suppression technique of complex urban fiber link noise with different feedback compensation parameters is studied. With active phase noise suppression, the optical frequency stability can reach 1.9×10^-16 at 1 s and 2.2×10^-18 at 10,000 s over a 96 km urban fiber link. This work potentially plays an important role in optical clock frequency comparison, and it makes a good foundation for future research on long-distance optical frequency transfer over an urban business network.

An Investigation of All Fiber Free-Running Dual-Comb Spectroscopy

A dual-comb spectroscopy (DCS) system uses two phase-locked optical frequency combs with a slight difference in the repetition frequency. The spectrum can be sampled in the optical frequency (OF) domain and reproduces the characteristics in the radio frequency (RF) domain through asynchronous optical sampling. Therefore, the DCS system shows great advantages in achieving precision spectral measurement. During application, the question of how to reserve the mutual coherence between the two combs is the key issue affecting the application of the DCS system. This paper focuses on a software algorithm used to realize the mutual coherence of the two combs. Therefore, a pair of free-running large anomalous dispersion fiber combs, with a center wavelength of approximately 1064 nm, was used. After the signal process, the absorption spectra of multiple species were simultaneously obtained (simulated using the reflective spectra of narrow-bandwidth fiber Bragg gratings, abbreviated as FBG). The signal-to-noise ratio (SNR) could reach 13.97 dB (25) during the 100 ms sampling time. In this study, the feasibility of the system was first verified through the simulation system; then, a principal demonstration experiment was successfully executed. The whole system was connected by the optical fiber without additional phase-locking equipment, showing promise as a potential solution for the low-cost and practical application of DCS systems.

Distributed fiber mountain seismic monitoring and steady-state analysis under natural earthquakes

Mountain dynamic response monitoring plays important roles in geological disaster evolution monitoring and warning. A distributed mountain seismic monitoring and steady-state analysis method is demonstrated with distributed acoustic sensing (DAS) and a natural earthquake stimulus. In the field test, the seismic detection capability is first verified by comparing the recorded seismic waveforms from DAS and existing seismic stations. The vibration signal difference between steady-state and unsteady-state mountain parts is apparent; the operational modal analysis method is utilized to extract the response difference and to monitor the disaster evolution process. The proposed method has many advantages, including being easy to deploy, all-weather online monitoring, etc. It is believed that the proposed method will broaden the DAS application scope and promote the development of geological disaster early warning such as landslides and collapses.

Terahertz spectral identification and low-frequency vibrational analysis of dinitrotoluene isomers

Identifying dinitrotoluene (DNT) isomers has always been a challenging problem. In this study, five DNT isomers were investigated using terahertz time-domain spectroscopy (THz-TDS), which demonstrated significant spectral differences including variations in absorption positions and intensities. This suggests that THz-TDS is ideal for rapid identification of DNT isomers. We also employed density functional theory to further discuss the origin of these spectral differences. The results indicate that steric effects between substitute groups, rather than inter-molecular hydrogen bonding, lead to differences in low-frequency vibrations.

Stable optical and radio frequency joint transfer based on a passive phase compensation

We propose a novel scheme that uses only a single passive phase compensation device to achieve stable optical and radio frequency joint transfer. The phase noises of optical and radio frequency can be simultaneously compensated by passively embedding their phase information on the two optical carrier sidebands generated by an electro-optical modulator without using the phase discrimination and active servo controller. As a result, this scheme has many advantages, such as high spectral purity, short settling time and infinite compensation accuracy. We experimentally demonstrate the joint transfer of optical and 1 GHz RF over 120 km fiber spools. The optical frequency stability achieves 6.9 × 10^-17 at 1 s and 7.03 × 10^-19 at 10000 s, while the 1 GHz RF is 6.47 × 10^-13 at 1 s and 3.96 × 10^-16 at 10000 s.

Agile offset frequency locking for single-frequency fiber lasers

Single frequency fiber lasers (SFFLs) have seen increasing applications in state-of-the-art quantum technologies, which usually require precise and stable offset frequency locking (OFL). However, limited by the piezoelectric transducer bandwidth in SFFLs and the loop bandwidth of the OFL, the large-gap jumping between two locked offset frequencies will take an undesirable amount of time. In order to diminish that consuming time, we developed an agile offset frequency locking system based on a hybrid loop of a feed-forward path and a feedback path. In accordance with the experimental demonstration, we characterized the performances of the offset frequency locking system, as frequency-locking stability with an Allan deviation of 3.2 × 10^-14 at 1 s averaging time and jumping agility with a duration of 0.6 ms at 1.3 GHz frequency gap, which is a factor of 60 faster than that without the feed-forward path. This mechanism can find direct applications in existing quantum metrology experiments with SFFLs where high-speed frequency jumping or sweeping is needed.

Robust single-sideband-modulated Raman light generation for atom interferometry by FBG-based optical rectangular filtration

Low-phase-noise and pure-spectrum Raman light is vital for high-precision atom interferometry by two-photon Raman transition. A preferred and prevalent solution for Raman light generation is electro-optic phase modulation. However, phase modulation inherently brings in double sidebands, resulting in residual sideband effects of multiple laser pairs beside Raman light in atom interferometry. Based on a well-designed rectangular fiber Bragg grating and a plain electro-optic modulator, optical single-sideband modulation has been realized at 1560 nm with a stable suppression ratio better than -25 dB despite of intense temperature variations. After optical filtration and frequency doubling, a robust phase-coherent Raman light at 780 nm is generated with a stable SNR of better than -19 dB and facilitates measuring the local gravity successfully. This FBG-based all-fiber single-sideband-modulated Raman light source, proposed for the first time and characterized as robust, compact and low-priced, is practical and potential for field applications of portable atom interferometry.

High SNR Φ-OTDR with Multi-Transverse Modes Heterodyne Matched-Filtering Technology

Phase-sensitive optical time domain reflectometer (Φ-OTDR) has attracted attention in scientific research and industry because of its distributed dynamic linear response to external disturbances. However, the signal-to-noise ratio (SNR) of Φ-OTDR is still a limited factor by the weak Rayleigh Backscattering coefficient. Here, the multi-transverse modes heterodyne matched-filtering technology is proposed to improve the system SNR. The capture efficiency and nonlinear threshold are increased with multiple transverse modes in few-mode fibers; the incident light energy is permitted to be enlarged by a wider probe pulse by using heterodyne matched-filtering without spatial resolution being deteriorated. As far as we know, this is the first time that both multi-transverse modes integration method and digital heterodyne matched filtering method have been used to improve the SNR of Φ-OTDR simultaneously. Experimental results show that the noise floor is reduced by 11.4 dB, while the target signal is kept. We believe that this proposed method will help DAS find important applications in marine acoustic detection and seismic detection.

All-fiber narrow-bandwidth rectangular Optical filter with reconfigurable bandwidth and tunable center wavelength

In this manuscript, a novel narrow-bandwidth rectangular optical filter based on multi-phase-shifted fiber Bragg grating (MPSFBG) is proposed. Using the local temperature control technology, the precise controllable phase shifts are introduced at different positions of the fiber Bragg grating (FBG). Therefore, the bandwidth of the MPSFBG-based filter with good shape factor can be reconfigured from 70 MHz to 1050 MHz by flexibly controlling the numbers and the positions of the phase shifts introduced in the MPSFBG. In addition, the center wavelength of the MPSFBG-based filter can be tuned through controlling the MPSFBG's environment temperature, and the tuning range of 22 GHz is realized. This is one of the best results for the narrow-bandwidth rectangular optical tunable filter with reconfigurable bandwidth. It can be widely used in the processing of reconfigurable signals in the optical communication networks and microwave photonics.

Fiber-optic time-frequency transfer in gigabit ethernet networks over urban fiber links

We demonstrate a new optical pulse amplitude modulation (PAM) scheme where joint ultrastable time-frequency and gigabit ethernet data transfer with the same laser wavelength is realized. Time transmission is compatible with the White Rabbit (WR) based on gigabit ethernet networks, and frequency transmission is achieved by using 100MHz radio frequency (RF) modulation and the round-trip compensation methods. The laser is on-off keying (OOK) modulated by the WR signal, the RF and WR signal are modulated by optical PAM in a Mach-Zehnder interferometer modulator (MZM), and the local and remote site are connected by 96km urban fiber in Shanghai. The experimental results demonstrate that the frequency instabilities are 5.7E-14/1 s and 5.9E-17/10⁴s, and the time interval transfer of 1 pulse per second (PPS) signal with less than 300fs stability after 10⁴ s are obtained. This novel scheme can transmit frequency signals at hydrogen-maser-level stability in the gigabit ethernet network.

Narrow linewidth swept laser source based on cascaded multi-wavelength injection of DFB lasers

A linearly swept laser source over broadband with a fast sweep rate and narrow linewidth is realized using a novel optoelectronic scheme based on a multi-wavelengths (mutually coherent) injected distributed feedback (DFB) laser. Under the condition of multi-wavelengths injection, the injection-locking and four-wave mixing (FWM) process can occur simultaneously in the DFB laser, inducing a swept laser source with a sweep range of 100 GHz and sweep rate of 10 THz/s. Furthermore, with the phase noise character analyzation of the swept laser source, the phase noise deterioration due to the radio frequency (RF) signal is studied quantitatively. Besides the influence of the RF signal noise, the phase noise deterioration in the FWM process can be suppressed completely with the phase-locked pump beam and signal beam based on the injection-locking principle. This low phase noise swept laser source with sub-kilohertz linewidth could have wide applications in lidar.

Multi-source aliasing suppression for distributed fiber acoustic sensing with directionally coherent enhancement technology

Distributed fiber acoustic sensing (DAS) can detect almost all disturbances along the sensing fiber and is widely applied. However, the signals from multiple adjacent disturbance sources are superimposed, according to the sensing principle. A directionally coherent enhancement technology is demonstrated for DAS to suppress multi-source aliasing in air. In preliminary works, two situations are considered for feasibility verification. The submerged weak target signal is effectively extracted from strong broadband noise, and two different same-frequency signals from two sources are separately rebuilt with the same detected signal. As far as we know, this is the first time that the directionally coherent enhancement is proposed for DAS and the multi-source aliasing is suppressed. This technique will help DAS find new important foreground in acoustic detection of large-scale plants with many similar noisy devices, including discharge detection in high voltage substations and acoustic emission flaw detection in mechanical factories.

Ultralow noise DFB fiber laser with self-feedback mechanics utilizing the inherent photothermal effect

Single frequency laser sources with low frequency noise are now at the heart of precision high-end science, from the most precise optical atomic clocks to gravitational-wave detection, thanks to the rapid development of laser frequency stabilization techniques based on optical or electrical feedback from an external reference cavity. Despite the tremendous progress, these laser systems are relatively high in terms of complexity and cost, essentially suitable for the laboratory environment. Nevertheless, more and more commercial applications also demand laser sources with low noise to upgrade their performance, such as fiber optic sensing and LiDAR, which require reduced complexity and good robustness to environmental perturbations. Here, we describe an ultralow noise DFB fiber laser with self-feedback mechanics that utilizes the inherent photothermal effect through the regulation of the thermal expansion coefficient of laser cavity. Over 20 dB of frequency noise reduction below several tens of kilohertz Fourier frequency is achieved, limited by the fundamental thermal noise, which is, to date, one of the best results for a free-running DFB fiber laser. The outcome of this work offers promising prospects for versatile applications due to its ultralow frequency noise, simplicity, low cost, and environmental robustness.

Intensity noise in high-frequency range of an external cavity diode laser and its reduction by second harmonic generation

Characteristics of intensity noise of optically pumped vertical-cavity surface-emitting lasers and solid-state lasers, induced by the beating of the main lasing mode and non-lasing side modes and its reduction, have been reported in recent years. The mode beating noise of an external cavity diode laser composed of an electrically pumped edge-emitting laser diode chip is studied experimentally in this Letter. The noises due to the beating of the main mode with the first- to third-order side modes are observed, and multiple sub-peaks in the beating noise are measured. It is assumed that the new phenomena are coming from the enhanced four-wave mixing in the longer-active medium. Intensity noise reduction is also demonstrated by using the second harmonic generation of a beta barium borate crystal as a nonlinear absorber.

Abstract B071: Detecting ultra low-frequency variants and fusions using a novel amplicon-based Accu-CometTM method

We report the development of an ultra-accurate NGS technology, Accu-CometTM, which employs a concatemer-based error correction with amplicon workflow for the fast detection of low-frequency mutations including single-nucleotide variants (SNVs) and fusion events. We tested a non-small cell lung cancer (NSCLC) panel covering variants of EGFR, BRAF, and KRAS, as well as Alk fusion. Simulated cfDNA and cfDNA from healthy individuals were used to test the assay’s sensitivity and specificity. The analytic sensitivity of this panel was 100% detection at an allele frequency of 0.1% for 20ng of cf-DNA input. Similarly, the analytic sensitivity of the Alk fusion panel was 75% detection at an allele frequency of 0.1%, and 100% detection at an allele frequency of 0.25% for the same input. Clinical validation was performed via a comparative analysis of 171 NSCLC patients at different cancer stages and with different treatment plans. Among our patient cohort, 5 EGFR variants (19del, T790M, L858R, G719X, L861X) were detected. We also tested 47 noncancerous control samples and detected no false-positive variants at the reported cancer hot spots. Accu-CometTM demonstrated strong per-variant detection-rate concordance (> 96%) compared to ddPCR results, and >90% concordance when compared to tumor tissue ARMS result. The multiplex capacity, ultra sensitivity, and easy robust work flow of Accu-CometTM makes it well suited for supporting targeted therapy selection, drug resistance detection, and treatment monitoring.

Citation Format: Ling Wang, Grace Q. Zhao, Li Weng, Xiao Chen, Min Li, Xue Yang, Jun Zhao, Hongyan Wang, Kang Ying, Malek Faham, Shengrong Lin, Jiatao Lou. Detecting ultra low-frequency variants and fusions using a novel amplicon-based Accu-CometTM method [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B071.

Abstract A035: CRC MRD detection using Accu-ActTM NGS technology

Circulating tumor DNA (ctDNA) is a promising biomarker for detecting minimal residual disease (MRD) and for monitoring treatment of patients with colorectal cancers (CRC). Any technology used for this purpose, however, will face extreme performance demands. In order to build a high-performance multiplex next-generation sequencing (NGS) platform suitable for cancer MRD using ctDNA, we developed Accu-ActTM, an NGS-based assay capable of detecting low-frequency variants in plasma ctDNA with high precision. In our protocol, rolling-circle amplification is used to circularize denatured double-stranded cell-free DNA (cfDNA) and convert it into long tandem repeats, thus enabling consensus-based concatemer error correction. We demonstrated Accu-ActTM’s sensitivity and specificity by testing it on cfDNA samples with known variant frequencies and cfDNA collected from healthy individuals (n = 100). Our results showed that the sensitivity of Accu-Act was 0.1% with an error rate of 1 in 1 million for 20ng of input cfDNA. Concordance analysis was performed using Accu-Act, a 61-gene assay, on 152 tumor/plasma pairings of preoperative samples derived from patients with CRC (stage I-IV). Depending on stage, we report 66-92% patient detection rate. Post-surgery ctDNA profiling was performed on 52 patients (stage I-IV) enrolled in our prospective MRD study. The results showed that 26% of patients had detectable postoperative ctDNA, among whom 72% had disease progression within two years. Only one out of the 41 patients without detectable postoperative ctDNA went on to relapse, and one patient died of a lung infection. Our study showed that ctDNA is a promising prognostic biomarker for CRC relapse after R0 resection (HR (95%CI) 33.00 (4.05 - 270), P<0.001). The Accu-ActTM NGS-based ctDNA assay has high accuracy and is suitable for MRD in CRC patients. Accu-ActTM should make a significant contribution in the development of personalized cancer treatment.

Citation Format: Xinxing Li, Grace Zhao, Xianwen Zhang, Yanping Sun, Yi Wang, Canping Ruan, Paul Tang, Malek Faham, Shengrong Lin, Kang Ying, Zhiqian Hu. CRC MRD detection using Accu-ActTM NGS technology [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A035.

Detecting ultra low-frequency variants and gene fusions in lung cancer patients using an amplicon-based Firefly NGS method

e23062

Background: The analysis of EGFR, KRAS, and BRAF mutations and Alk fusion is critical for guiding targeted therapy selection, detecting drug resistance, and monitoring residual disease in patients with NSCLC. Designing next-generation sequencing (NGS) assays for detecting low-frequency variants, however, is an ongoing challenge. The limited availability of cfDNA combined with the breadth of coverage necessary to create meaningful, clinically-actionable results requires a solution with multiplex capacity which, in turn, requires greater technological sensitivity and specificity. Here we aim to develop such a solution: an ultra-accurate NGS technology using concatmer-based error correction with amplicon workflow for fast detection of rare mutations including SNV and fusion. Methods: We developed an amplicon-based panel covering variants of EGFR, BRAF, and KRAS, as well as a panel to detect Alk fusion. CfDNA simulate and cfDNA from healthy individuals were used to test assay sensitivity and specificity. Further validation was performed via a comparative analysis of 64 late-stage lung cancer patients using both Firefly -Comet and ddPCR. Results: Analytical sensitivity of the EGFR-TKI 3-gene panel was 100% detection at an allele frequency of 0.1% for 20ng of cfDNA input. Similarly, analytical sensitivity of the Alk fusion panel was 75% detection at an allele frequency of 0.1% and 100% at an allele frequency of 0.25% for the same input. Among our patient cohort, 5 EGFR variants (19del, T790M, L858R, G719X, L861X) and 2 KRAS variant (G12X) were detected. Firefly-Comet demonstrated strong per-variant detection-rate concordance ( > 99%) compared to ddPCR results. The PPV is 100% and the NPV is 98.7%. Statistical analysis of reported allele frequency concordance between Firefly-Comet and ddPCR reveals R-Sq > 0.9. Conclusions: In summary, we have developed Firefly-Comet, an easy-to-use amplicon-based NGS assay capable of detecting single-digit copies of somatic mutants and gene fusions in cfDNA. The multiplex capacity of Firefly-Comet makes it well-suited for supporting targeted therapy selection, drug resistance detection, and treatment monitoring.

Predictive value of circulating tumor DNA in locally advanced rectal cancer patients receiving neoadjuvant radiochemotherapy

e15125

Background: Neoadjuvant radiochemotherapy (RCT) is rapidly becoming the preferred treatment for patients diagnosed with late-stage locally advanced rectal cancer (LARC). Presently, tumor regression grades (TRG) is used to characterize treatment responsiveness; patients with low TRG scores have been shown to receive no benefit from surgery. To-date, however, there exists no reliable method for identifying low TRG-scoring patients without surgery. Here we propose the use of circulating tumor DNA (ctDNA) to identify low TRG-scoring patients to reduce overtreatment and improve quality of life. Methods: 30 LARC patients undergoing neoadjuvant RCT were prospectively enrolled in our study. Plasma was collected before treatment, immediately preceding cycle 3 chemotherapy, and 2 weeks following cycle 4 chemotherapy. Tumor tissue was also collected before treatment start. CtDNA and tumor DNA were sequenced using Accu-Act, a 61-gene NGS panel. Tumor response was classified as TRG1-5 according to Mandard classification system. Somatic mutation profiles were correlated with tumor response. The accuracy of ctDNA and tumor DNA in predicting TRG scores was calculated using the change of allele frequency. The predictive value of ctDNA was also compared to that of standard CEA and CA199 assays. Patients with CEA and CA199 scores below threshold were also considered for evaluation. Results: 18 of the 30 LARC patients enrolled had complete ctDNA profiling test among whom 13 had already undergone surgery. 17 somatic mutations were identified from the 10 patients with TRG scores of either 1, 2, or 3. Predictive accuracy of pretreatment ctDNA profiling was 70%, compared to that of CEA analysis (66%) and CA199 analysis (50%). TRG prediction using ctDNA successfully evaluated half of patients for whom CEA analysis failed to predict the change in tumor burden. Conclusions: Our findings suggest ctDNA mutation profiling may be a powerful tool for predicting TRG in LARC patients undergoing RCT. Further studies are needed to validate the utility of ctDNA in identifying patients who can be spared from unnecessary surgical treatment in LARC. Clinical trial information: NCT02031939.

Accuracy of profiling of circulating tumor DNA for CRC MRD and monitoring using NGS technology equipped with concatemer-based error correction

e23067

Background: Circulating tumor DNA (ctDNA) is a promising biomarker for the detection of minimal residual disease and monitoring treatment in patients with CRC. The performance demands of any technology used for this purpose, however, are tremendous. Here we aim to develop a high-performance multiplex NGS platform suitable for cancer MRD using ctDNA. Methods: We have developed Firefly, a NGS method capable of detecting low-frequency variants with high precision in plasma cfDNA. In our protocol, denatured double-stranded cfDNA is circularized and converted into long tandem repeats using rolling-circle amplification enabling consensus-based concatemer error correction. We demonstrated Firefly’s performance sensitivity and specificity by testing our technology on cfDNA samples with known variant frequencies and cfDNA collected from healthy individuals (n = 82). Further analysis of Firefly as a tool for MRD and treatment monitoring was performed by tracking ctDNA mutation profile concordance between 81 CRC tumor samples and their corresponding plasma samples collected from patients before and after treatment. Results: Performance sensitivity of Firefly NGS was 0.1% with an error-rate was 1 in 1 Million for 20ng of input ctDNA. Concordance analysis was performed on CRC tumor/plasma pairings derived from patients with CRC using, Accu-Act, a 61-gene assay. The number of tumor-matching mutations detected in plasma varied greatly on a per-patient basis (range, 0-28). Pre and post-treatment ctDNA profiling was performed on all 81 patients included in our study (surgery, n = 56; chemotherapy/radiotherapy, n = 30). Among patients who underwent surgery, 46% had detectable tumor-matching mutations in their plasma. Among patients who received neoadjuvant therapy, 70% ctDNA fluctuations consistent with tumor reduction based on surgical tumor regression grades evaluation(TRG1-3). Conclusions: We report a novel ultra-accurate NGS-based ctDNA assay suitable for MRD and monitoring in CRC patients. Firefly should ultimately make a significant contribution in the development of personalized cancer treatment.

Photothermal effects in phase shifted FBG with varied light wavelength and intensity

The intensity enhancement effect of a phase-shifted fiber Bragg grating (PSFBG) is investigated theoretically and experimentally in this paper. Due to the effect, both of the FBG reflection bands and the transmission peak show red-shift with the increase of pump light wavelength from the shorter side to the longer side of the Bragg wavelength. The transmission peak shifts in pace with the pump's wavelength, which is much faster than the reflection band. The maximum shift increases with the pump power. In contrast, the red-shift is very small when the pump light deceases from the longer side of the Bragg wavelength. Such asymmetric behavior is checked dynamically by using a frequency modulated laser in a serrated wave, showing push-pull behavior. The effect of the characteristics of thermal dissipation conditions is also measured. The fiber loss coefficient of FBG being tested is estimated from the measured data to be about 0.001 mm^-1, which may be attributed to the H₂-loading and UV exposure in FBG fabrication. The observed phenomena are believed of importance in application where PSFBG is utilized as a narrow linewidth filter.

All-optical noise reduction of fiber laser via intracavity SOA structure

We have designed a unique intracavity semiconductor optical amplifier (SOA) structure to suppress the relative intensity noise (RIN) for a fiber DFB laser. By exploiting the gain saturation effect of the SOA, a maximum noise suppression of 30 dB around the relaxation oscillation frequency is achieved, and the whole resonance relaxation oscillation peak completely disappears. Moreover, via a specially designed intracavity SOA structure, the optical intensity inside the SOA will be in a balanced state via the oscillation in the laser cavity, and the frequency noise of the laser will not be degraded with the SOA.

Abstract 1375: An ultra-sensitive cell free DNA liquid biopsy assay for cancer treatment monitoring

In order to take advantage of the narrow time window for optimal treatment efficacy, highly sensitive disease monitoring is critical in the successful management of cancer. Currently, treatment efficacy is assessed by using a combination of protein cancer biomarkers and imaging. However, both methods present limitations with regard to specificity or sensitivity due to their dependency on tumor size. Recently, a number of studies have suggested that monitoring cell free DNA (cfDNA) may provide a more specific alternative for tracking cancer treatment with greatly improved sensitivity. Here we introduce a novel next-generation sequencing based mutation detection system aimed at improving the sensitivity, reliability, and clinical utility of cancer treatment monitoring. Our system, comprised of Nebula, a whole genome amplification technology that is capable of amplifying nanogram quantities of cfDNA >1000-fold, and Firefly, a proprietary technology combining molecular biology and computational algorithm for error-suppression, has reduced the rate of random sequencing errors to 10-6. As a result, we are able to detect 1.5 variant copies from 10ng of input cfDNA with a detection rate of 46%. We have validated the Nebula-Firefly assay on a patient cohort with either colorectal (CRC) or lung cancer. Here we report the successful detection of drug resistant mutations and various genomic alterations associated with minimal residual detection (MRD) in sample cfDNA. These initial findings have led to the exploration of Nebula-Firefly as the technological backbone for a noninvasive, scalable approach for the early detection, treatment, and monitoring of cancer.

Citation Format: Grace Zhao, Li Weng, Paul Tang, Johnny Sun, Yi Huang, Lingchen Guo, Hongyan Wang, Xiaozheng Kang, Wei Shen, Kang Ying, Shengrong Lin. An ultra-sensitive cell free DNA liquid biopsy assay for cancer treatment monitoring. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1375.

Laser frequency offset locking via tripod-type electromagnetically induced transparency

We have demonstrated laser frequency offset locking via the Rb87 tripod-type double-dark resonances electromagnetically induced transparency (EIT) system. The influence of coupling fields' power and detuning on the tripod-type EIT profile is studied in detail. In a wide coupling field's detuning range, the narrower EIT dip has an ultranarrow linewidth of ∼590  kHz, which is about one order narrower than the natural linewidth of Rb87. Without the additional frequency stabilization of the coupling lasers, we achieve the relative frequency fluctuation of 60 kHz in a long time of ∼2000  s, which is narrower than the short-time linewidth of each individual laser.

Diversification and molecular evolution of ATOH8, a gene encoding a bHLH transcription factor

ATOH8 is a bHLH domain transcription factor implicated in the development of the nervous system, kidney, pancreas, retina and muscle. In the present study, we collected sequence of ATOH8 orthologues from 18 vertebrate species and 24 invertebrate species. The reconstruction of ATOH8 phylogeny and sequence analysis showed that this gene underwent notable divergences during evolution. For those vertebrate species investigated, we analyzed the gene structure and regulatory elements of ATOH8. We found that the bHLH domain of vertebrate ATOH8 was highly conserved. Mammals retained some specific amino acids in contrast to the non-mammalian orthologues. Mammals also developed another potential isoform, verified by a human expressed sequence tag (EST). Comparative genomic analyses of the regulatory elements revealed a replacement of the ancestral TATA box by CpG-islands in the eutherian mammals and an evolutionary tendency for TATA box reduction in vertebrates in general. We furthermore identified the region of the effective promoter of human ATOH8 which could drive the expression of EGFP reporter in the chicken embryo. In the opossum, both the coding region and regulatory elements of ATOH8 have some special features, such as the unique extended C-terminus encoded by the third exon and absence of both CpG islands and TATA elements in the regulatory region. Our gene mapping data showed that in human, ATOH8 was hosted in one chromosome which is a fusion product of two orthologous chromosomes in non-human primates. This unique chromosomal environment of human ATOH8 probably subjects its expression to the regulation at chromosomal level. We deduce that the great interspecific differences found in both ATOH8 gene sequence and its regulatory elements might be significant for the fine regulation of its spatiotemporal expression and roles of ATOH8, thus orchestrating its function in different tissues and organisms.

Antipsychotics and venous thromboembolism risk: a meta-analysis

BACKGROUND

Antipsychotics have been inconclusively implicated in susceptibility to venous thromboembolism (VTE).

OBJECTIVES AND METHODS

The aim of this study was to investigate the association between antipsychotic drugs and VTE risk by a meta-analysis. PubMed and EmBASE databases were searched for publications through to 10 October 2010. Statistical analysis was performed using Revman 4.2 and Stata 10.0 software.

RESULTS

7 case-control studies involving 31 095 cases and 143 472 controls were analyzed. The results indicate that antipsychotic exposure confers a 139 % increased risk of VTE (odds ratio [OR] = 2.39, 95 % confidence interval [CI]:1.71–3.35). Pooled estimates by drug type showed that use of low-potency antipsychotics (OR = 2.91, 95 % CI 1.80–4.71) is the most important risk factor for VTE, followed by atypical (OR = 2.20, 95 % CI 1.22–3.96), conventional (OR = 1.72, 95 % CI 1.31–2.24) and high-potency drugs (OR = 1.58, 95 % CI 1.50–1.67).

CONCLUSIONS

This meta-analysis suggests that antipsychotics are a risk factor for VTE. Additional studies in large cohorts are required to validate our findings. Future analyses should study potential eff ect modifications by different doses and durations of antipsychotic exposure in different populations.

Molecular Cloning and Characterization ofSGT1.2, a Novel Splice Variant ofHomo sapiens SGT1

SGT1.2, a novel splice variant of Homo sapiens SGT1 was isolated from a human fetal brain cDNA library. This cDNA is 1404 bp and contains an open reading frame from 68 to 1165 encoding a putative protein of 365 amino acids (SGT1.2) that share 90% identities to Homo sapiens SGT1, suppressor of G2 allele of SKP1 at protein level. RPS-BLAST searching revealed that SGT1.2 have a TPR domain, a p23 domain, a SGS domain and a CS domain. According to the search of the human genome database, SGT1.2 was mapped to human chromosome 13q14.13. Reversed transcription-polymerase chain reaction analysis indicated that it widely expressed in human adult tissues.

Cloning and Characterization of a novel splice variant of humanRab18gene (RAB18)

Rab GTPase proteins are a kind of small GTP-binding proteins, which functions mainly focus on regulating interacellular trafficking pathways during vesicular transport. To date, 60 distinct human RAB proteins have been identified. RAB18 gene is discovered from endothelial cells. Its function is considered as endosomes and plasma membrane recycling. Research indicates RAB18 may relate to inflammation and some kinds of tumor. Here we report a splice variant of RAB18, which is 2571 bp in length and has an open reading frame coding a predicted 235 amino-acids protein. RT-PCR shows that the cDNA has different expression pattern with RAB18 and is highly expressed in testis.

Cap1p plays regulation roles in redox, energy metabolism and substance transport: an investigation on Candida albicans under normal culture condition

Cap1p, a transcription factor in Candida albicans, is believed to be required for tolerance to oxidative stress. However, no information is available concerning its function on basal transcriptional profile. In this study, differentially expressed genes between the CAP1-deleted strain and its parental strain under normal culture condition were identified through microarray analysis. Notably, among the 48 down-regulated genes with the deletion of CAP1, there were three clusters, functionally related to intracellular redox, energy metabolism and substance transport. IPF7817, IPF11105 and FDH11, the three putative Cap1p target genes functionally related to redox, were shown to be activated by oxidative stress in a Cap1p-dependent manner. Furthermore, rhodamine 6G efflux analyses demonstrated that Cap1p contributed to the energy-driven efflux. Taken together, these results reveal that Cap1p plays a significant role in redox status regulation, energy metabolism and substance transport under normal culture condition.

Different gene expression profiles of AD293 and HEK293 cell lines that show contrasting susceptibility to apoptosis induced by overexpression of Bim L

Bim is a pro-apoptotic member of the Bcl-2 protein family. Overexpression of Bim proved to be highly cytotoxic for diverse cells. The AD293 cell line is derived directly from the HEK293 cell line but has been transfected with a gene that can improve cell adherence. We found that there was almost no apoptosis seen in Bim L-transfected AD293 cells, but more than half of Bim L-transfected HEK293 cells underwent apoptosis. Suppression subtractive hybridization was used to detect the different gene expression profile between these two cell lines. In 192 sequenced positive clones, there were 30 clones repeating twice or more. Ten genes were selected for identification by semi-quantitative RT-PCR. The transcripts of two adhesion-related genes (actin and parvin) and two apoptosis-related genes (cyclin 2 and protein phosphatase 1G) were up-regulated in AD293 cells. These results suggest that the high expression of cell adhesion-related proteins might be responsible for the different apoptosis status after the transfection of Bim L. Our data provide candidate genes responsible for the different apoptosis sensitivity of these two cell lines. Further investigation on the differential expression profile between AD293 and HEK293 might improve our understanding of cell apoptosis mechanism.

cDNA microarray analysis of differential gene expression and regulation in clinically drug-resistant isolates of Candida albicans from bone marrow transplanted patients

Fungi have emerged as the fourth most common pathogens isolated in nosocomial bloodstream infections, and Candida albicans is the most common human fungal pathogen. Only a few antibiotics are effective in the treatment of fungal infections. In addition, the repetition and lengthy duration of fluconazole therapy has led to an increased incidence of azole resistance and treatment failure associated with C. albicans. To investigate the mechanism of drug resistance and explore new targets to treat clinically resistant fungal pathogens, we examined the large-scale gene expression profile of two sets of matched fluconazole-susceptible and -resistant bloodstream C. albicans isolates from bone marrow transplanted (BMT) patients for the first time by microarray analysis. More than 198 differentially expressed genes were identified and they were confirmed and validated by RT-PCR independently. Not surprisingly, the resistant phenotype is associated with increased expression of CDR mRNA, as well as some common genes involved in drug resistance such as CaIFU5, CaRTA2 and CaIFD6. Meanwhile, some special functional groups of genes, including ATP binding cassette (ABC) transporter genes (IPF7530, CaYOR1, CaPXA1), oxidative stress response genes (CaALD5, CaGRP1, CaSOD2, IPF10565), copper transport and iron mobilization-related genes (CaCRD1/2, CaCTR1/2, CaCCC2, CaFET3) were found to be differentially expressed in the resistant isolates. Furthermore, among these differentially expressed genes, some co-regulated with CaCDR1, CaCDR2 and CaIFU5, such as CaPDR16 and CaIFD6, have a DRE-like element and may interact with TAC1 in the promoter region. These findings may shed light on mechanisms of azole resistance in C. albicans and clinical antifungal therapy.

Cap1p is involved in multiple pathways of oxidative stress response in Candida albicans

Cap1p, a transcription factor in Candida albicans, is thought to participate in oxidative stress tolerance, but the pathways involved are still unclear. The study was designed to reveal the possible pathways by examining changes in the transcription profile after H2O2 treatment with both the cap1-deleted strain CJD21 and its parental strain CAI4 using microarray analysis. Of the identified 89 genes differentially expressed in CAI4 after exposure to H2O2, 76 genes were in a Cap1p-dependent expression pattern. We have shown that Cap1p is involved in the oxidative stress response in C. albicans via multiple pathways, including the cellular antioxidant defense system (e.g., thioredoxin reductase, glutathione reductase, glutathione S-transferase), carbohydrate metabolism and energy metabolism (e.g., glucose-6-phosphate dehydrogenase, transaldolase, glyoxalase I, NADH-dependent flavin oxidoreductase), protein degradation (e.g., 26S proteasome regulatory subunit, ubiquitin-specific protease), ATP-dependent RNA helicase (e.g., DEAD box protein ATP-dependent RNA helicase), and resistance pathways (e.g., multidrug resistance protein, ABC transporter essential for cadmium resistance). Real-time reverse transcription-PCR analysis further confirmed the results of microarray. Collectively, this study provides new insight into the biological functions of Cap1p in oxidative stress response.

Enzymatic and physico-chemical characteristics of recombinant cMDH and mMDH of Clonorchis sinensis

The cytosol and mitochondrial malate dehydrogenases (MDHs, EC 1.1.1.37) of Clonorchis sinensis were expressed in Escherichia coli as a fusion protein with a 6xHis and GST tag, respectively. The cytosol MDH of Clonorchis sinensis (Cs-cMDH) has higher resistibility to acid than mitochondrial MDH (Cs-mMDH). The Cs-cMDH also has higher heat resistibility and thermal stability than Cs-mMDH. Although there is only 22.8% identity between the amino acid sequences of Cs-cMDH and Cs-mMDH, they share several conserved residues. There are some differences between the circular dichroism spectra of Cs-cMDH and Cs-mMDH, but they have approximate percentages of helix. 4,4'-Bisdimethylamino diphenylcarbinol can decrease the Cs-mMDH activity but not the Cs-cMDH activity. Paraziquantel, metronidazole and albendazole did not inhibit the enzymes' activity, but adenosine 5'-monophosphate showed competitive inhibition to enzyme, with the Ki for Cs-cMDH and Cs-mMDH being 2.81 and 0.49 mM, respectively.

Co-evolutionary analysis of insulin/insulin like growth factor 1 signal pathway in vertebrate species

Insulin/insulin like growth factor 1 signaling pathway plays an essential role on the regulation of variant, interrelated and fundamental processes, such as metabolism, growth, reproduction and aging. This pathway is highly conserved during evolution. We analyzed eight vertebrate species' insulin/insulin like growth factor 1 pathway and examined the co-evolutionary relationship between different protein components by quantifying similarity of phylogenetic trees. The collected species include Takifugu rubripes, Danio rerio, Xenopus laevis, Gallus gallus, Mus musculus, Rattous norvegicus, Pan troglodytes and Homo sapiens. Results show that interacting proteins in this pathway share highly co-evolutionary relationship while contrarily the proteins without interaction have low co-evolutionary relationship. We also predict some receptor and ligand partners enjoy highly binding potential in corresponding species' pathway.

Analysis of common gene expression patterns in four human tumor cell lines exposed to camptothecin using cDNA microarray: identification of topoisomerase-mediated DNA damage response pathways

Camptothecin (CPT) is a potent inhibitor of DNA topoisomerase I with a wide spectrum of anti-tumor activity. Relatively little information is available regarding the relation of known topoisomerase-mediated DNA damage with other intracellular pathways. To gain an insight into the intracellular molecular mechanisms of Topoisomerase I inhibitor camptothecin-mediated DNA damage leading to cell death, we used a high-density cDNA microarray to assess sensitive early gene expression profiles in SGC7901 (gastric cancer), Hela (cervical adenocarcinoma), K562 (chronic myelogenous leukemia) and HL60 (promyelocytic leukemia) tumor cells stimulated with camptothecin for 1 h at the concentrations of GI50 (50 % growth inhibition after 24 h of treatment). Analysis of the differentially expressed genes obtained 29 response genes common to all four cell lines. Moreover, these cell lines also shared the direction of regulation. Most of these common response genes were functionally related to cell proliferation or apoptosis, and some of them were involved in ATM (ataxia-telangiectasia mutated) and ATR (ATM-and Rad3 related) checkpoint pathways, JNK (c-Jun N-terminal kinase) pathway, the survival phosphatidylinositol (PI) 3 kinase-Akt-dependent pathway, mitochondrial cell death pathway, endoplasmic reticulum (ER)-related cell death pathway, and to ubiquitin/proteasome dependent protein degradation pathway. The data provides evidence for a linkage between topoisomerase-mediated DNA damage and intracellular signaling events, which may facilitate our understanding of the camptothecin mediated molecular mechanisms of action.

Genes differentially expressed in responsive and refractory acute leukemia

DNA microarray in 22 patients with acute leukemia revealed genes which were differentially expressed. Ribosomal protein SA (RPSA), minichromosome maintenance deficient 2 (MCM2) and heterogeneous nuclear ribonucleoprotein A1 (HNRPA1) were significantly upregulated (p<0.05, t test) in refractory patients, suggesting that they may play a role in refractoriness in acute leukemia and could be biomarkers of prognosis.

Different gene expression profiles of AD293 and HEK293 cell lines that show contrasting susceptibility to apoptosis induced by overexpression of Bim L

Bim is a pro-apoptotic member of the Bcl-2 protein family. Overexpression of Bim proved to be highly cytotoxic for diverse cells. The AD293 cell line is derived directly from the HEK293 cell line but has been transfected with a gene that can improve cell adherence. We found that there was almost no apoptosis seen in Bim L-transfected AD293 cells, but more than half of Bim L-transfected HEK293 cells underwent apoptosis. Suppression subtractive hybridization was used to detect the different gene expression profile between these two cell lines. In 192 sequenced positive clones, there were 30 clones repeating twice or more. Ten genes were selected for identification by semi-quantitative RT-PCR. The transcripts of two adhesion-related genes (actin and parvin) and two apoptosis-related genes (cyclin 2 and protein phosphatase 1G) were up-regulated in AD293 cells. These results suggest that the high expression of cell adhesion-related proteins might be responsible for the different apoptosis status after the transfection of Bim L. Our data provide candidate genes responsible for the different apoptosis sensitivity of these two cell lines. Further investigation on the differential expression profile between AD293 and HEK293 might improve our understanding of cell apoptosis mechanism.

[Impacts of donor and recipient's SNP of cytokine and cytokine receptor on early acute renal allograft rejection]

OBJECTIVE

To investigate the impact of donor and recipient's SNP of cytokine and cytokine receptor on early acute rejection after renal transplantation.

METHODS

(1) 129 cases of cadaveric renal allograft recipients were divided into two groups according to the presence or absence of acute graft rejection. The distribution of 21 single nucleotide polymorphisms in cytokines and cytokine receptors gene were compared between two groups as well as latent factors affecting the development of acute rejection. (2) Based on the result of HLA-DR matching between donor and recipient, the recipients with AR were stratified into two conditions, 0-1 locus mismatched (0-1MM) and completely mismatched (2MM). By aids of SPSS 11.5 software, association analysis was assessed using Kruskal Wallis test, 2 x 2 or 2 x n contingency table, the Chi-square test.

RESULTS

(1) Of 129 recipients of renal transplantation, 39 developed acute graft rejection (30.2%). (2) Compared with recipients without acute rejection, the number of HLA-DR mismatching was significantly higher in rejection group. (3) In rejection group and non-rejection group, the gene polymorphism distribution was significantly different. (4) 0-1MM group and 2MM group were various in the gene polymorphism distribution.

CONCLUSIONS

In the whole, the susceptibility of acute rejection after renal transplantation may be predicted by the donor and recipient's SNP of cytokine and cytokine receptor.