Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer types.

It has been well established that cancer cells can evade immune surveillance by mutating themselves. Understanding genetic alterations in cancer cells that contribute to immune regulation could lead to better immunotherapy patient stratification and identification of novel immune-oncology (IO) targets. In this report, we describe our effort of genome-wide association analyses across 22 TCGA cancer types to explore the associations between genetic alterations in cancer cells and 74 immune traits. Results showed that the tumor microenvironment (TME) is shaped by different gene mutations in different cancer types. Out of the key genes that drive multiple immune traits, top hit KEAP1 in lung adenocarcinoma (LUAD) was selected for validation. It was found that KEAP1 mutations can explain more than 10% of the variance for multiple immune traits in LUAD. Using public scRNA-seq data, further analysis confirmed that KEAP1 mutations activate the NRF2 pathway and promote a suppressive TME. The activation of the NRF2 pathway is negatively correlated with lower T cell infiltration and higher T cell exhaustion. Meanwhile, several immune check point genes, such as CD274 (PD-L1), are highly expressed in NRF2-activated cancer cells. By integrating multiple RNA-seq data, a NRF2 gene signature was curated, which predicts anti-PD1 therapy response better than CD274 gene alone in a mixed cohort of different subtypes of non-small cell lung cancer (NSCLC) including LUAD, highlighting the important role of KEAP1-NRF2 axis in shaping the TME in NSCLC. Finally, a list of overexpressed ligands in NRF2 pathway activated cancer cells were identified and could potentially be targeted for TME remodeling in LUAD.

Dual-polarization RF channelizer based on microcombs.

We report a dual-polarization radio frequency (RF) channelizer based on microcombs. Two high-Q micro-ring resonators (MRRs) with slightly different free spectral ranges (FSRs) are used: one MRR is pumped to yield soliton crystal microcombs ("active"), and the other MRR is used as a "passive" periodic optical filter supporting dual-polarization operation to slice the RF spectrum. With the tailored mismatch between the FSRs of the active and passive MRRs, wideband RF spectra can be channelized into multiple segments featuring digital-compatible bandwidths via the Vernier effect. Due to the use of dual-polarization states, the number of channelized spectral segments, and thus the RF instantaneous bandwidth (with a certain spectral resolution), can be doubled. In our experiments, we used 20 microcomb lines with ∼ 49 GHz FSR to achieve 20 channels for each polarization, with high RF spectra slicing resolutions at 144 MHz (TE) and 163 MHz (TM), respectively; achieving an instantaneous RF operation bandwidth of 3.1 GHz (TE) and 2.2 GHz (TM). Our approach paves the path towards monolithically integrated photonic RF receivers (the key components - active and passive MRRs are all fabricated on the same platform) with reduced complexity, size, and unprecedented performance, which is important for wide RF applications with digital-compatible signal detection.

Low-loss fiber-to-chip edge coupler for silicon nitride integrated circuits.

Silicon nitride (SiN) integrated optical waveguides have found a wide range of applications due to their low loss, broad wavelength transmission band and high nonlinearity. However, the large mode mismatch between the single-mode fiber and the SiN waveguide creates a challenge of fiber coupling to these waveguides. Here, we propose a coupling approach between fiber and SiN waveguides by utilizing the high-index doped silica glass (HDSG) waveguide as the intermediary to smooth out the mode transition. We achieved fiber-to-SiN waveguide coupling efficiency of lower than 0.8 dB/facet across the full C and L bands with high fabrication and alignment tolerances.

Investigating the thermal robustness of soliton crystal microcombs.

Soliton crystals are a novel form of microcomb, with relatively high conversion efficiency, good thermal robustness, and simple initiation among the methods to generate them. Soliton crystals can be easily generated in microring resonators with an appropriate mode-crossing. However, fabrication defects can significantly affect the mode-crossing placement and strength in devices. To enable soliton crystal states to be harnessed for a broader range of microcomb applications, we need a better understanding of the link between mode-crossing properties and the desired soliton crystal properties. Here, we investigate how to generate the same soliton crystal state in two different microrings, how changes in microring temperature change the mode-crossing properties, and how mode-crossing properties affect the generation of our desired soliton crystal state. We find that temperature affects the mode-crossing position in these rings but without major changes in the mode-crossing strength. We find that our wanted state can be generated over a device temperature range of 25 ∘C, with different mode-crossing properties, and is insensitive to the precise mode-crossing position between resonances.

Discovery of mobocertinib, a potent, oral inhibitor of EGFR exon 20 insertion mutations in non-small cell lung cancer.

In the treatment of non-small cell lung cancer (NSCLC), patients harboring exon 20 insertion mutations in the epidermal growth factor receptor (EGFR) gene (EGFR) have few effective therapies because this subset of mutants is generally resistant to most currently approved EGFR inhibitors. This report describes the structure-guided design of a novel series of potent, irreversible inhibitors of EGFR exon 20 insertion mutations, including the V769_D770insASV and D770_N771insSVD mutants. Extensive structure-activity relationship (SAR) studies led to the discovery of mobocertinib (compound 21c), which inhibited growth of Ba/F3 cells expressing the ASV insertion with a half-maximal inhibitory concentration of 11 nM and with selectivity over wild-type EGFR. Daily oral administration of mobocertinib induced tumor regression in a Ba/F3 ASV xenograft mouse model at well-tolerated doses. Mobocertinib was approved in September 2021 for the treatment of adult patients with advanced NSCLC with EGFR exon 20 insertion mutations with progression on or after platinum-based chemotherapy.

Second-harmonic generation in a high-index doped silica micro-ring resonator.

We report the first, to the best of our knowledge, observation of second-harmonic generation (SHG) in a high-index doped silica micro-ring resonator, due to the symmetry-breaking-induced χ(2) at the core and cladding interface of the waveguide. The generated SH power is shown to have quadratic dependence on the in-cavity power of the fundamental pump at around 1550 nm. The pumping wavelength sweep method is adopted to fulfill the phase-matching condition for maximum conversion efficiency of SHG. This work offers a new approach to generate a visible source for the visible-light integrated optical platform from infrared-visible light conversion.

Wetting of surfaces decorated by gas-phase synthesized silver nanoparticles: Effects of Ag adatoms, nanoparticle aging, and surface mobility.

The wetting state of surfaces can be rendered to a highly hydrophobic state by the deposition of hydrophilic gas phase synthesized Ag nanoparticles (NPs). The aging of Ag NPs leads to an increase in their size, which is also associated with the presence of Ag adatoms on the surface between the NPs that have a strong effect on the wetting processes. Furthermore, surface airborne hydrocarbons were removed by UV-ozone treatment, providing deeper insight into the apparent mobility of the NPs on different surfaces and their subsequent ripening and aging. In addition, the UV-ozone treatment revealed the presence of adatoms during the magnetron sputtering process. This surface treatment lowers the initial contact angle of the substrates and facilitates the mobility of Ag NPs and adatoms on the surface of substrates. Adatoms co-deposited on clean high surface energy substrates will nucleate on Ag NPs that will remain closely spherical and preserve the pinning effect due to the water nanomeniscus. If the adatoms are co-deposited on a UV-ozone cleaned low surface energy substrate, their mobility is restricted, and they will nucleate in two-dimensional islands and/or nanoclusters on the surface instead of connecting to existing Ag NPs. This growth results in a rough surface without overhangs, where the wetting state is reversed from hydrophobic to hydrophilic. Finally, different material surfaces of transmission electron microscopy grids revealed strong differences in the sticking coefficient for the Ag NPs, suggesting another factor that can strongly affect their wetting properties.

Enhancing Performance of a GaAs/AlGaAs/GaAs Nanowire Photodetector Based on the Two-Dimensional Electron-Hole Tube Structure.

Here, we design and engineer an axially asymmetric GaAs/AlGaAs/GaAs (G/A/G) nanowire (NW) photodetector that operates efficiently at room temperature. Based on the I-type band structure, the device can realize a two-dimensional electron-hole tube (2DEHT) structure for the substantial performance enhancement. The 2DEHT is observed to form at the interface on both sides of GaAs/AlGaAs barriers, which constructs effective pathways for both electron and hole transport in reducing the photocarrier recombination and enhancing the device photocurrent. In particular, the G/A/G NW photodetector exhibits a responsivity of 0.57 A/W and a detectivity of 1.83 × 1010 Jones, which are about 7 times higher than those of the pure GaAs NW device. The recombination probability has also been significantly suppressed from 81.8% to 13.2% with the utilization of the 2DEHT structure. All of these can evidently demonstrate the importance of the appropriate band structure design to promote photocarrier generation, separation, and collection for high-performance optoelectronic devices.

Influence of the depletion region in GaAs/AlGaAs quantum well nanowire photodetector.

In semiconductor nanowire (NW) photodetectors, the Schottky barrier formed by the contact between metal and semiconductor can act as a depletion layer. For NW structures with a smaller diameter, the depletion region is especially important to the carrier transport. We prepared a GaAs/AlGaAs quantum well NW photodetector with a two-dimensional electron-hole tube, in which the two-dimensional hole tube (2DHT) formed by the inner layer of GaAs and AlGaAs has the most important role in the regulation of carriers. By adjusting the bias voltage to vary the depth of the depletion region, we have confirmed the influence of the depletion region in a 2DHT. A significant inflection point was found in the responsivity-voltage curve at 1.5 V. By combining the depletion region and 2DHT, the responsivity of the fabricated device was increased by 18 times to 0.199 A W-1 and the detectivity is increased by 5 times to 5.8 × 1010 Jones, compared to the pure GaAs NW photodetector. Reasonable combination of depletion layer and 2DHT was proved to promote high-performance NW photodetector.

Computationally Efficient Direction Finding for a Mixture of Circular and Strictly Noncircular Sources with Uniform Rectangular Arrays.

In this paper, a novel two-dimensional (2D) direction-of-arrival (DOA) estimation algorithm for the mixed circular and strictly noncircular sources is proposed. A general array model with a mixture of signals is firstly built based on uniform rectangular arrays (URAs), and then, the approach, which uses the rank-reduction-based ROOT-MUSIC, can solve 2D DOA estimation problem. Besides, the theoretical error of the proposed algorithm, a criterion of the performance for evaluation, is analyzed by the first-order Taylor expression using second-order statistics. As verified by the simulation results, a better DOA estimation performance and a lower computational complexity are achieved by the proposed algorithm than the existing methods resorting to the noncircularity of the incoming signals.

Activity of ponatinib against clinically-relevant AC220-resistant kinase domain mutants of FLT3-ITD.

Secondary point mutations in the Fms-like tyrosine kinase 3 (FLT3) tyrosine kinase domain (KD) are common causes of acquired clinical resistance to the FLT3 inhibitors AC220 (quizartinib) and sorafenib. Ponatinib (AP24534) is a multikinase inhibitor with in vitro and clinical activity in tyrosine kinase inhibitor (TKI)-resistant chronic myeloid leukemia, irrespective of BCR-ABL KD mutation. Ponatinib has demonstrated early clinical efficacy in chemotherapy-resistant acute myeloid leukemia (AML) patients with internal tandem duplication (ITD) mutations in FLT3. We assessed the in vitro activity of ponatinib against clinically relevant FLT3-ITD mutant isoforms that confer resistance to AC220 or sorafenib. Substitution of the FLT3 "gatekeeper" phenylalanine with leucine (F691L) conferred mild resistance to ponatinib, but substitutions at the FLT3 activation loop (AL) residue D835 conferred a high degree of resistance. Saturation mutagenesis of FLT3-ITD exclusively identified FLT3 AL mutations at positions D835, D839, and Y842. The switch control inhibitor DCC-2036 was similarly inactive against FLT3 AL mutations. On the basis of its in vitro activity against FLT3 TKI-resistant F691 substitutions, further clinical evaluation of ponatinib in TKI-naïve and select TKI-resistant FLT3-ITD+ AML patients is warranted. Alternative strategies will be required for patients with TKI-resistant FLT3-ITD D835 mutations.

Low-loss and polarization insensitive 32 × 4 optical switch for ROADM applications.

Integrated switches play a crucial role in the development of reconfigurable optical add-drop multiplexers (ROADMs) that have greater flexibility and compactness, ultimately leading to robust single-chip solutions. Despite decades of research on switches with various structures and platforms, achieving a balance between dense integration, low insertion loss (IL), and polarization-dependent loss (PDL) remains a significant challenge. In this paper, we propose and demonstrate a 32 × 4 optical switch using high-index doped silica glass (HDSG) for ROADM applications. This switch is designed to route any of the 32 inputs to the express ports or drop any channels from 32 inputs to the target 4 drop ports or add any of the 4 ports to any of the 32 express channels. The switch comprises 188 Mach-Zehnder Interferometer (MZI) type switch elements, 88 optical vias for the 44 optical bridges, and 618 waveguide-waveguide crossings with three-dimensional (3D) structures. At 1550 nm, the fiber-to-fiber loss for each express channel is below 2 dB, and across the C and L bands, below 3 dB. For each input channel to all 4 drop/add channels at 1550 nm, the loss is less than 3.5 dB and less than 5 dB across the C and L bands. The PDLs for all express and input channels to the 4 drop/add channels are below 0.3 dB over the C band, and the crosstalk is under -50 dB for both the C and L bands.

Physical and oxidative stability of flaxseed oil-in-water emulsions prepared by natural lignin-carbohydrate complex.

Flaxseed oil, rich in α-linolenic acid, plays a crucial role in various physiological processes. However, its stability presents certain challenges. In this study, the natural lignin-carbohydrate complex (LCC) was used to prepare the physical and oxidative stability of flaxseed oil-in-water emulsions. The LCC was characterized by HPLC, GPC, and FT-IR. The stability of emulsions was evaluated by viscosity, modulus, and micro-morphology changes. Then, the oxidation products were monitored by UV-vis spectrophotometer and HPLC. The results revealed that the high internal phase emulsion (HIPE) was successfully prepared with 2.5 wt% LCC at an oil/water ratio of 75/25 (v/v). Small droplet size (13.361 µm) and high viscosity (36,500 mPa·s) were found even after 30-day storage. Steric interactions of the LCC play a crucial role in ensuring stability, intricately linked to the interfacial properties of the emulsion. Meanwhile, the oxidative stability of α-linolenic acid in the encapsulated flaxseed oil was significantly higher than that in the bulk flaxseed oil. The results revealed that the LCC as a suitable emulsifier opens a new window for the storage of functional lipids rich in polyunsaturated fatty acids.

Cryo-EM structures reveal two allosteric inhibition modes of PI3KαH1047R involving a re-shaping of the activation loop.

PI3Kα is a lipid kinase that phosphorylates PIP2 and generates PIP3. The hyperactive PI3Kα mutation, H1047R, accounts for about 14% of breast cancer, making it a highly attractive target for drug discovery. Here, we report the cryo-EM structures of PI3KαH1047R bound to two different allosteric inhibitors QR-7909 and QR-8557 at a global resolution of 2.7 Å and 3.0 Å, respectively. The structures reveal two distinct binding pockets on the opposite sides of the activation loop. Structural and MD simulation analyses show that the allosteric binding of QR-7909 and QR-8557 inhibit PI3KαH1047R hyper-activity by reducing the fluctuation and mobility of the activation loop. Our work provides a strong rational basis for a further optimization and development of highly selective drug candidates to treat PI3KαH1047R-driven cancers.

Potential regulatory mechanism of TNF-α/TNFR1/ANXA1 in glioma cells and its role in glioma cell proliferation.

The purpose of this study was to explore the regulatory mechanism of Annexin A1 (ANXA1) in glioma cells in the inflammatory microenvironment induced by tumour necrosis factor α (TNF-α) and its effects on glioma cell proliferation. CCK-8 analysis demonstrated that TNF-α stimulation promotes rapid growth in glioma cells. Changes in tumour necrosis factor receptor 1 (TNFR1) and ANXA1 expression in glioma cells stimulated with TNF-α were revealed through western blot analysis and immunofluorescence staining. Coimmunoprecipitation analysis revealed that ANXA1 interacts with TNFR1. Moreover, we found that ANXA1 promotes glioma cell growth by activating the p65 and Akt signalling pathways. Finally, immunohistochemistry analysis showed an obvious correlation between ANXA1 expression and Ki-67 in glioma tissues. In summary, our results indicate that the TNF-α/TNFR1/ANXA1 axis regulates the proliferation of glioma cells and that ANXA1 plays a regulatory role in the inflammatory microenvironment.

Urban Low-Rise Residential Areas Provide Preferred Song Post Sites for a Resident Songbird.

Urbanization is expanding rapidly worldwide, and brings additional selection pressure on animals. The song differences between urban and rural songbirds have been widely verified, but the effects of urban morphological variation on long-settled urban birds have been poorly explored. Here, we investigated the distribution and song differences of a common resident songbird-the oriental magpie-robin (Copsychus saularis) between three urban morphology types (i.e., urban park, low-rise residential area, and high-rise residential area). The results indicated that the population density in low-rise residential areas was significantly higher than in urban parks, while it was the lowest in high-rise residential areas. Males in low-rise residential areas had greater song length, syllable numbers, frequency bandwidth, and song diversity than those in urban parks. The song differences were mainly related to habitat types, independent of singing height and perch type. Our findings suggest that low-rise residential areas may provide preferred song post sites for the oriental magpie-robin, which is well-adapted to the low-rise building morphology, but rejects the emerging high-rise buildings. Future studies are needed to assess the effects of urban morphological variation on more resident animals to determine which urban morphologies are conducive to enhancing biodiversity and encouraging animals to settle in urban areas.

Discovery of 2,4-bis-arylamino-1,3-pyrimidines as insulin-like growth factor-1 receptor (IGF-1R) inhibitors.

The insulin-like growth factor-1 receptor (IGF-1R) plays an important role in the regulation of cell growth and differentiation, and in protection from apoptosis. IGF-1R has been shown to be an appealing target for the treatment of human cancer. Herein, we report the synthesis, structure-activity relationships (SAR), X-ray cocrystal structure and in vivo tumor study results for a series of 2,4-bis-arylamino-1,3-pyrimidines.

Discovery of 5-(arenethynyl) hetero-monocyclic derivatives as potent inhibitors of BCR-ABL including the T315I gatekeeper mutant.

Ponatinib (AP24534) was previously identified as a pan-BCR-ABL inhibitor that potently inhibits the T315I gatekeeper mutant, and has advanced into clinical development for the treatment of refractory or resistant CML. In this study, we explored a novel series of five and six membered monocycles as alternate hinge-binding templates to replace the 6,5-fused imidazopyridazine core of ponatinib. Like ponatinib, these monocycles are tethered to pendant toluanilides via an ethynyl linker. Several compounds in this series displayed excellent in vitro potency against both native BCR-ABL and the T315I mutant. Notably, a subset of inhibitors exhibited desirable PK and were orally active in a mouse model of T315I-driven CML.

Mobocertinib (TAK-788): A Targeted Inhibitor of EGFR Exon 20 Insertion Mutants in Non-Small Cell Lung Cancer.

Most EGFR exon 20 insertion (EGFRex20ins) driver mutations in non-small cell lung cancer (NSCLC) are insensitive to approved EGFR tyrosine kinase inhibitors (TKI). To address the limitations of existing therapies targeting EGFR-mutated NSCLC, mobocertinib (TAK-788), a novel irreversible EGFR TKI, was specifically designed to potently inhibit oncogenic variants containing activating EGFRex20ins mutations with selectivity over wild-type EGFR. The in vitro and in vivo activity of mobocertinib was evaluated in engineered and patient-derived models harboring diverse EGFRex20ins mutations. Mobocertinib inhibited viability of various EGFRex20ins-driven cell lines more potently than approved EGFR TKIs and demonstrated in vivo antitumor efficacy in patient-derived xenografts and murine orthotopic models. These findings support the ongoing clinical development of mobocertinib for the treatment of EGFRex20ins-mutated NSCLC. SIGNIFICANCE: No oral EGFR-targeted therapies are approved for EGFR exon 20 insertion (EGFRex20ins) mutation-driven NSCLC. Mobocertinib is a novel small-molecule EGFR inhibitor specifically designed to target EGFRex20ins mutants. Preclinical data reported here support the clinical development of mobocertinib in patients with NSCLC with EGFR exon 20 insertion mutations.See related commentary by Pacheco, p. 1617.This article is highlighted in the In This Issue feature, p. 1601.

Colorimetric Detection of Sulfide Anions via Redox-Modulated Surface Chemistry and Morphology of Au-Hg Nanorods.

A new colorimetric assay for the detection of sulfide anions with high sensitivity and selectivity is reported, utilizing Au-Hg alloy nanorods (Au-HgNRs) as probe. Au-HgNRs were prepared by modifying gold nanorods (AuNRs) with reducing agent and mercury ions. In an aqueous solution with sulfide anions, the formation of mercuric sulfide due to redox reaction between the amalgams and sulfide anions greatly changed the surface chemistry and morphology of the Au-HgNRs, leading to a red shift of the localized surface plasmon resonance (LSPR) absorption peak, accompanied by a change in colorimetric response. A good linear relationship was obtained between the LSPR peak wavelength shift and concentration of sulfide anion in the range of 1 × 10-5-1 × 10-4 mol/L. The selectivity of this method has been investigated by other anions. The colorimetric sensing system successfully detected sulfide in wastewater from leather industry.