Patho-transcriptomic analysis of invasive mucinous adenocarcinoma of the lung (IMA): comparison with lung adenocarcinoma with signet ring cell features (SRCC).

Background: Invasive mucinous adenocarcinoma (IMA) comprises ∼5% of lung adenocarcinoma. There is no effective therapy for IMA when surgical resection is not possible. IMA is sometimes confused with adenocarcinoma with signet ring cell features (SRCC) pathologically since both adenocarcinomas feature tumor cells with abundant intracellular mucin. The molecular mechanisms by which such mucin-producing lung adenocarcinomas develop remain unknown. Methods: Using a Visium spatial transcriptomics approach, we analyzed IMA and compared it with SRCC patho-transcriptomically. Combining spatial transcriptomics data with in vitro studies using RNA-seq and ChIP-seq, we assessed downstream targets of transcription factors HNF4A and SPDEF that are highly expressed in IMA and/or SRCC. Results: Spatial transcriptomics analysis indicated that there are 6 distinct cell clusters in IMA and SRCC. Notably, two clusters (C1 and C3) of mucinous tumor cells exist in both adenocarcinomas albeit at a different ratio. Importantly, a portion of genes (e.g., NKX2-1 , GKN1 , HNF4A and FOXA3 ) are distinctly expressed while some mucous-related genes (e.g., SPDEF and FOXA2 ) are expressed in both adenocarcinomas. We determined that HNF4A induces MUC3A/B and TM4SF4 and that BI 6015, an HNF4A antagonist, suppressed the growth of IMA cells. Using mutant SPDEF that is associated with COVID-19, we also determined that an intact DNA-binding domain of SPDEF is required for SPDEF-mediated induction of mucin genes ( MUC5AC , MUC5B and AGR2 ). Additionally, we found that XMU-MP-1, a SPDEF inhibitor, suppressed the growth of IMA cells. Conclusion: These results revealed that IMA and SRCC contain heterogenous tumor cell types, some of which are targetable.

Two-fold addition reaction of silylene to C60: structural and electronic properties of a bis-adduct.

The addition reaction of C60 with silylene 1, a silicon analog of carbene, yielded the corresponding bis-adduct 3. The structure of 3 was determined by single-crystal X-ray structure analysis, representing the first example of a crystal structure of a silirane (silacyclopropane) derivative of fullerenes. Electrochemical measurements confirmed that the redox potentials of 3 are shifted cathodically compared to those of the parent mono-adduct 2. Density functional theory (DFT) calculations provided the basis for the electronic properties of compound 3.

Controlling the reactivity of La@C82 by reduction: reaction of the La@C82 anion with alkyl halide with high regioselectivity.

Endohedral metallofullerenes have excellent redox properties, which can be used to vary their reactivity to certain classes of molecules, such as alkyl halides. In this study, the thermal reaction of the La@C2v-C82 anion with benzyl bromide derivatives 1 at 110 °C afforded single-bonded adducts 2-5 with high regioselectivity. The products were characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and visible-near infrared spectroscopy. The reaction of La@C2v-C82 with alkyl halides using the same conditions showed no consumption of La@C2v-C82, indicating that the reactivity of La@C2v-C82 toward alkyl halides was effectively increased by one-electron reduction. Single-crystal X-ray diffraction analysis of the single-bonded adduct 3a revealed the addition site of the p-methoxybenzyl group on La@C2v-C82. Theoretical calculations indicated that the addition site carbons in neutral La@C2v-C82 have high spin density, whereas those in the La@C2v-C82 anion do not have high charge densities. Thus, the reaction is believed to occur via electron transfer, followed by the radical coupling of La@C2v-C82 and benzyl radicals, rather than by bimolecular nucleophilic substitution reaction of La@C2v-C82 anion with 1.

Recent progress in controlling the photoluminescence properties of single-walled carbon nanotubes by oxidation and alkylation.

The functionalization of single-walled carbon nanotubes (SWCNTs) has received considerable attention in the last decade since highly efficient near-infrared photoluminescence (PL) has been observed to be red-shifted compared with the intrinsic PL peak of pristine SWCNTs. The PL wavelength has been manipulated using arylation reactions with aryldiazonium salts and aryl halides. Additionally, simple oxidation and alkylation reactions have proven effective in extensively adjusting the PL wavelength, with the resulting PL efficiency varying based on the chosen reaction techniques and molecular structures. This review discusses the latest developments in tailoring the PL attributes of SWCNTs by oxidation and alkylation processes. (6,5) SWCNTs exhibit intrinsic emission at 980 nm, and the PL wavelength can be controlled in the range of 1100-1320 nm by chemical modification. In addition, recent developments in chiral separation techniques have increased our understanding of the control of the PL wavelength, extending to the selection of excitation and emission wavelengths, by chemical modification of SWCNTs with different chiral indices.

Control of functionalized single-walled carbon nanotube photoluminescence via competition between thermal rearrangement and elimination.

We conducted the chiral separation of functionalized single-walled carbon nanotubes (SWNTs) with dibromopropane derivatives. Depending on their chirality and diameter, the thermal treatment of functionalized SWNTs leads to a shift in the emission radiation to longer wavelengths owing to rearrangement reaction in competition with elimination reaction.

Selective emergence of photoluminescence at telecommunication wavelengths from cyclic perfluoroalkylated carbon nanotubes.

Chemical functionalisation of semiconducting single-walled carbon nanotubes (SWNTs) can tune their local band gaps to induce near-infrared (NIR) photoluminescence (PL). However, tuning the PL to telecommunication wavelengths (>1300 nm) remains challenging. The selective emergence of NIR PL at the longest emission wavelength of 1320 nm was successfully achieved in (6,5) SWNTs via cyclic perfluoroalkylation. Chiral separation of the functionalised SWNTs showed that this functionalisation was also effective in SWNTs with five different chiral angles. The local band gap modulation mechanism was also studied using density functional theory calculations, which suggested the effects of the addenda and addition positions on the emergence of the longest-wavelength PL. These findings increase our understanding of the functionalised SWNT structure and methods for controlling the local band gap, which will contribute to the development and application of NIR light-emitting materials with widely extended emission and excitation wavelengths.

Stepwise Functionalization of Single-Walled Carbon Nanotubes with Subsequent Molecular Conversion to Control Photoluminescence Properties.

Functionalization of single-walled carbon nanotubes (SWCNTs) has attracted interest because it alters the near-infrared (NIR) photoluminescence (PL) wavelength and emission efficiency. These modifications depend on the binding configuration and degree of functionalization. Excessive functionalization reduces the emission efficiency as the integrity of the conjugated π system decreases; thus, controlling the degree of functionalization is essential. Because the binding configurations and degree of functionalization are affected by the reagent structure, a stepwise approach combining SWCNTs functionalization and subsequent reactions to introduce functional groups into the addenda could effectively control their PL properties and functionalities. We studied this approach by implementing the reductive alkylation of SWCNTs by using bromoalkanes with t-butyl carbamate (Boc)-protected amino groups and subsequent deprotection and amidation reactions. The reaction products were analyzed based on absorption, PL, and Raman spectroscopy and the Kaiser test. Depending on the structure of the reagent, deprotection and amidation reactions competed with the elimination reaction of addenda, altering the PL properties of the SWCNTs. Furthermore, the elimination reaction was inhibited in the adducts functionalized using dibromoalkane with Boc-protected amino groups, demonstrating that the use of appropriate reagents enables the molecular conversion of the functional groups of SWCNT adducts without affecting their PL properties.

Synthesis and Conformational Analysis of Fullerene Torsion Balances for Assessing the Contribution of Dispersion and Anionic Character in Non-Covalent Arene-Fullerene Interactions.

We employ a molecular torsion balance displaying bifurcated conformational isomerism to quantitatively evaluate the non-covalent interactions between the fullerene surface and substituted arene moieties containing elements with high atomic numbers, as well as the thermodynamic processes involved in the folding equilibrium using nuclear magnetic resonance spectroscopy. The interaction between fullerene and haloaryl groups was stronger in cases where the introduced halogen had a higher atomic number, indicating that dispersion forces play a significant role in the interaction between fullerenes and 4-haloaryl groups. The dispersion term also significantly contributed to the interaction between fullerene and the 4-mercaptophenyl group. Moreover, the addition of an appropriate base to the 4-mercaptophenyl-appended torsion balance formed the corresponding thiophenolate anion, resulting in a large negative change in the folding free energy in CDCl3 . Detailed analysis suggested that the observed attractive anionic arene-fullerene interactions predominantly originated from solvation effects.

FOXA2 Cooperates with Mutant KRAS to Drive Invasive Mucinous Adenocarcinoma of the Lung.

The endoderm-lineage transcription factor FOXA2 has been shown to inhibit lung tumorigenesis in in vitro and xenograft studies using lung cancer cell lines. However, FOXA2 expression in primary lung tumors does not correlate with an improved patient survival rate, and the functional role of FOXA2 in primary lung tumors remains elusive. To understand the role of FOXA2 in primary lung tumors in vivo, here, we conditionally induced the expression of FOXA2 along with either of the two major lung cancer oncogenes, EGFRL858R or KRASG12D, in the lung epithelium of transgenic mice. Notably, FOXA2 suppressed autochthonous lung tumor development driven by EGFRL858R, whereas FOXA2 promoted tumor growth driven by KRASG12D. Importantly, FOXA2 expression along with KRASG12D produced invasive mucinous adenocarcinoma (IMA) of the lung, a fatal mucus-producing lung cancer comprising approximately 5% of human lung cancer cases. In the mouse model in vivo and human lung cancer cells in vitro, FOXA2 activated a gene regulatory network involved in the key mucous transcription factor SPDEF and upregulated MUC5AC, whose expression is critical for inducing IMA. Coexpression of FOXA2 with mutant KRAS synergistically induced MUC5AC expression compared with that induced by FOXA2 alone. ChIP-seq combined with CRISPR interference indicated that FOXA2 bound directly to the enhancer region of MUC5AC and induced the H3K27ac enhancer mark. Furthermore, FOXA2 was found to be highly expressed in primary tumors of human IMA. Collectively, this study reveals that FOXA2 is not only a biomarker but also a driver for IMA in the presence of a KRAS mutation. SIGNIFICANCE: FOXA2 expression combined with mutant KRAS drives invasive mucinous adenocarcinoma of the lung by synergistically promoting a mucous transcriptional program, suggesting strategies for targeting this lung cancer type that lacks effective therapies.

Photoluminescence Properties of Single-Walled Carbon Nanotubes Influenced by the Tether Length of Reagents with Two Reactive Sites.

The functionalization of single-walled carbon nanotubes (SWNTs) is an effective method for controlling a local band gap, resulting in photoluminescence (PL) in the near-infrared region. Herein, SWNTs were functionalized using a series of bromoalkanes and dibromoalkanes to evaluate the effects of their length on the nanotube PL properties. When bromoalkanes (Cn H2n+1 Br) or dibromoalkanes (Cn H2n Br2 ) with tether lengths of six or more were utilized for six different semiconducting SWNTs, the obtained SWNT adducts exhibited two new PL peaks, whereas dibromoalkanes with tether lengths of 3-5 (Cn H2n Br2 : n=3-5) produced single peaks. Combined with theoretical calculations, the results suggested that the tether length of reagents changes the formation mechanism of functionalized adducts, that is, Cn H2n Br2 (n=3-5) tends to result in kinetic products.

Understanding the Nature and Strength of Noncovalent Face-to-Face Arene-Fullerene Interactions.

Face-to-face noncovalent arene-fullerene interactions are important in several research fields such as synthetic chemistry, materials chemistry, and medicinal chemistry; however, their nature and strength are still poorly understood. In this study, we prepare a fullerene-based torsion balance containing thioanisole, phenol, naphthalene, azulene, and pyrene moieties as a unimolecular model system. Moreover, we compare the folding free energies between the folded and the unfolded conformers of a series of the molecular torsion balances to quantify noncovalent interactions between arenes and the fullerene surface. This work demonstrates that the contributions of polarizabilities, anionic charges, electronic dipole moments, and the number of arene rings to the interactions can be experimentally measured by analyzing the folding equilibrium of the molecular torsion balances.

CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1.

BACKGROUND: To identify host genetic variants (SNPs) associated with COVID-19 disease severity, a number of genome-wide association studies (GWAS) have been conducted. Since most of the identified variants are located at non-coding regions, such variants are presumed to affect the expression of neighbouring genes, thereby influencing COVID-19 disease severity. However, it remains largely unknown which genes are influenced by such COVID-19 GWAS loci. METHODS: CRISPRi (interference)-mediated gene expression analysis was performed to identify genes functionally regulated by COVID-19 GWAS loci by targeting regions near the loci (SNPs) in lung epithelial cell lines. The expression of CRISPRi-identified genes was investigated using COVID-19-contracted human and monkey lung single-nucleus/cell (sn/sc) RNA-seq datasets. FINDINGS: CRISPRi analysis indicated that a region near rs11385942 at chromosome 3p21.31 (locus of highest significance with COVID-19 disease severity at intron 5 of LZTFL1) significantly affected the expression of LZTFL1 (P<0.05), an airway cilia regulator. A region near rs74956615 at chromosome 19p13.2 (locus located at the 3' untranslated exonic region of RAVER1), which is associated with critical illness in COVID-19, affected the expression of RAVER1 (P<0.05), a coactivator of MDA5 (IFIH1), which induces antiviral response genes, including ICAM1. The sn/scRNA-seq datasets indicated that the MDA5/RAVER1-ICAM1 pathway was activated in lung epithelial cells of COVID-19-resistant monkeys but not those of COVID-19-succumbed humans. INTERPRETATION: Patients with risk alleles of rs11385942 and rs74956615 may be susceptible to critical illness in COVID-19 in part through weakened airway viral clearance via LZTFL1-mediated ciliogenesis and diminished antiviral immune response via the MDA5/RAVER1 pathway, respectively. FUNDING: NIH.

Primary mucinous adenocarcinoma of the thymus; a rare type of thymic carcinoma. Case Report.

Mucinous adenocarcinoma of the thymus is a particularly rare type among thymic carcinomas. Here, we report a patient who underwent complete surgical resection of the primary mucinous adenocarcinoma of the thymus. She was 74 years old and presented with a 60-mm multilocular cystic tumor in her right anterior mediastinum. We performed extended thymo-thymectomy with partial resection of the right upper lobe and pathologically diagnosed the patient with Masaoka stage II mucinous adenocarcinoma of the thymus. Immunohistochemistry showed the absence of PD-L1, suggesting that immune check point inhibitors targeting PD-1/PD-L1 might not be effective in this case. The increased preoperative serum levels of CA19-9 decreased after the operation. CA19-9 is a biomarker for disease status. Future reports should help elucidate the pathogenesis of this disease.

CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung.

The transcription factor NKX2-1/TTF-1 is involved in lung pathophysiology, including breathing, innate defense and tumorigenesis. To understand the mechanism by which NKX2-1 regulates genes involved in such pathophysiology, we have previously performed ChIP-seq and identified genome-wide NKX2-1-binding sites, which revealed that NKX2-1 binds to not only proximal promoter regions but also multiple intra- and inter-genic regions of the genes regulated by NKX2-1. However, the roles of such regions, especially non-proximal ones, bound by NKX2-1 have not yet been determined. Here, using CRISPRi (CRISPR/dCas9-KRAB), we scrutinize the functional roles of 19 regions/sites bound by NKX2-1, which are located in genes involved in breathing and innate defense (SFTPB, LAMP3, SFTPA1, SFTPA2) and lung tumorigenesis (MYBPH, LMO3, CD274/PD-L1). Notably, the CRISPRi approach reveals that a portion of NKX2-1-binding sites are functionally indispensable while the rest are dispensable for the expression of the genes, indicating that functional roles of NKX2-1-binding sites are unequally yoked.

Clinical application of a lung cancer organoid (tumoroid) culture system.

Despite high expectations for lung tumoroids, they have not been applied in the clinic due to the difficulty of their long-term culture. Here, however, using AO (airway organoid) media developed by the Clevers laboratory, we succeeded in generating 3 lung tumoroid lines for long-term culture (>13 months) from 41 lung cancer cases (primary or metastatic). Use of nutlin-3a was key to selecting lung tumoroids that harbor mutant p53 in order to eliminate normal lung epithelial organoids. Next-generation sequencing (NGS) analysis indicated that each lung tumoroid carried BRAFG469A, TPM3-ROS1 or EGFRL858R/RB1E737*, respectively. Targeted therapies using small molecule drugs (trametinib/erlotinib for BRAFG469A, crizotinib/entrectinib for TPM3-ROS1 and ABT-263/YM-155 for EGFRL858R/RB1E737*) significantly suppressed the growth of each lung tumoroid line. AO media was superior to 3 different media developed by other laboratories. Our experience indicates that long-term lung tumoroid culture is feasible, allowing us to identify NGS-based therapeutic targets and determine the responsiveness to corresponding small molecule drugs.

CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions.

Genome-wide association studies have identified lung disease-associated loci; however, the functions of such loci are not well understood in part because the majority of such loci are located at non-coding regions. Hi-C, ChIP-seq and eQTL data predict potential roles (e.g. enhancer) of such loci; however, they do not elucidate the molecular function. To determine whether these loci function as gene-regulatory regions, CRISPR interference (CRISPRi; CRISPR/dCas9-KRAB) has been recently used. Here, we applied CRISPRi along with Hi-C, ChIP-seq and eQTL to determine the functional roles of loci established as highly associated with asthma, cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Notably, Hi-C, ChIP-seq and eQTL predicted that non-coding regions located at chromosome 19q13 or chromosome 17q21 harboring single-nucleotide polymorphisms (SNPs) linked to asthma/CF/COPD and chromosome 11p15 harboring an SNP linked to IPF interact with nearby genes and function as enhancers; however, CRISPRi indicated that the regions with rs1800469, rs2241712, rs12603332 and rs35705950, but not others, regulate the expression of nearby genes (single or multiple genes). These data indicate that CRISPRi is useful to precisely determine the roles of non-coding regions harboring lung disease-associated loci as to whether they function as gene-regulatory regions at a genomic level.

A Fullerene-Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C60 Surface.

To investigate the nature and strength of noncovalent interactions at the fullerene surface, molecular torsion balances consisting of C60 and organic moieties connected through a biphenyl linkage were synthesized. NMR and computational studies show that the unimolecular system remains in equilibrium between well-defined folded and unfolded conformers owing to restricted rotation around the biphenyl C-C bond. The energy differences between the two conformers depend on the substituents and is ascribed to differences in the intramolecular noncovalent interactions between the organic moieties and the fullerene surface. Fullerenes favor interacting with the π-faces of benzenes bearing electron-donating substituents. The correlation between the folding free energies and corresponding Hammett constants of the substituents in the arene-containing torsion balances reflects the contributions of the electrostatic interactions and dispersion force to face-to-face arene-fullerene interactions.

Copper-Mediated Cascade Synthesis of Open-Cage Fullerenes.

An open-cage fullerene bearing an eight-membered ring orifice has been synthesized in one pot by the reaction of C60 with propargylic phosphate in the presence of CuCl. The reaction cascade involves the transformation of the phosphate to the 1,3-dienyl phosphate, which enables the reaction with C60 by [4 + 2] cycloaddition to form the cyclohexene-annulated intermediate, and subsequent intramolecular syn-elimination of the phosphodiester affords the cyclohexadiene-annulated fullerene derivative as the precursor for the open-cage fullerene.

Sonochemical reaction to control the near-infrared photoluminescence properties of single-walled carbon nanotubes.

The effect of ultrasonic irradiation on the optical properties of single-walled carbon nanotubes (SWNTs) was investigated. Upon sonication in D2O in the presence of sodium dodecylbenzene sulfonate (SDBS) under air, red-shifted photoluminescence (PL) peaks at ∼1043 and ∼1118 nm were observed from the aqueous suspensions of (6,4) and (6,5)SWNTs, accompanied by a decrease in the intensity of the intrinsic PL peaks. Upon sonication with SDBS under an Ar atmosphere, the rate of spectral change increased with the sonication time and new PL peaks emerged at 1043, 1118, and 1221 nm. Meanwhile, upon the addition of 1-butanol, the PL peaks emerged only at 1043 nm and 1118 nm, while the emergence of the peak at 1221 nm was inhibited. On the other hand, a suspension with highly dispersed SWNTs was obtained upon sonication in the presence of sodium cholate without any change in the intrinsic optical properties of SWNTs. These experimental results reveal that the PL characteristics of SWNTs can be controlled by controlling the sonication conditions such as the type of surfactant used, the concentration of SWNTs, reaction environment, and the presence of an inhibitor such as 1-butanol.

Thermodynamic control of quantum defects on single-walled carbon nanotubes.

Single-walled carbon nanotubes with designed quantum defects are prepared and characterized. The photoluminescence (PL) of the nanotubes can be modified by thermal treatment from 1215-1224 to 1249-1268 nm. Theoretical calculations suggest that the change in the PL spectra by thermal treatment can be explained by isomerization from kinetic to thermodynamic products.