Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures.

Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.

Giant Enhancement of Second Harmonic Generation Accompanied by the Structural Transformation of 7-Fold to 8-Fold Interpenetrated Metal-Organic Frameworks (MOFs).

Interpenetration in metal-organic frameworks (MOFs) is an intriguing phenomenon with significant impacts on their properties, and functional applications. Herein, we show that a 7-fold interpenetrated MOF (1) is transformed into an 8-fold interpenetrated MOF by the loss of DMF in a single-crystal-to-single-crystal manner. This is accompanied by a giant enhancement of the second harmonic generation (SHG ca. 125 times) and two-photon photoluminescence (ca. 14 times). The strengthened π-π interaction between the individual diamondoid networks and intensified oscillator strength of the molecules aid the augment of dipole moments and boost the nonlinear optical conversion efficiency. Large positive and negative thermal expansions of 1 occur at 30-150 °C before the loss of DMF. These results offer an avenue to manipulate the NLO properties of MOFs using interpenetration and provide access to tunable single-crystal NLO devices.

Near-White Light Emission from Lead(II) Metal-Organic Frameworks.

Reaction of bpy (bpy = 4,4'-bipyridine) with Pb(OAc)2·3H2O in DMF (DMF = dimethylformamide) afforded a metal-organic framework (MOF), [Pb2(µ-bpy)(µ-O2CCH3)2(µ-O2CCH3)2]·H2O (1). Reaction of bpy with Pb(O2CCF3)2 in a methanol and chloroform mixture furnished another MOF, [Pb(µ-bpy)(µ-O2CCF3)2]·1/2CHCl3 (2). However, the reaction of bpy with Pb(OAc)2·3H2O in the presence of trifluoroacetic acid in a similar reaction condition yielded a hydrogen-bonded zwitter-ionic complex of Pb(II), [Pb(bpy-H)2(O2CCF3)4] (3). All compounds have been characterized by single crystal X-ray crystallography, FT-IR, and 1H NMR spectroscopies. Compound 1 forms four heptacoordinated Pb(II) joined by (OCCH3)-O- linkages, resulting in a 3D noninterpenetrated MOF net with a four-connected uninodal sra (SrAl2) topology. However, in 2, tetra-connected Pb4(O2CCF3)8 cluster units are linked further through eight bpy ligands to furnish a doubly interpenetrated MOF with a new topology but having the very similar connectivity of 1, whereas 3 forms a zigzag hydrogen-bonded chain structure. The variation of carboxylate anions, pH of the reaction medium, and the ratio of the reactants profoundly affected the final topological structure of the compounds synthesized. The solid-state photoluminescence of 1-3 was investigated at room temperature. Interestingly 1, 2, and 3 achieved close to white light emission when excited at 329, 376, and 330 nm, respectively. The systematic understanding of the photophysical properties of analogous Pb-based compounds may open new perspectives for developing single-phase white-light-emitting materials using Pb(II) based MOFs.

Mouse pancreatic beta cells express MHC class II and stimulate CD4(+) T cells to proliferate.

Type 1 diabetes results from destruction of pancreatic beta cells by autoreactive T cells. Both CD4(+) and CD8(+) T cells have been shown to mediate beta-cell killing. While CD8(+) T cells can directly recognize MHC class I on beta cells, the interaction between CD4(+) T cells and beta cells remains unclear. Genetic association studies have strongly implicated HLA-DQ alleles in human type 1 diabetes. Here we studied MHC class II expression on beta cells in nonobese diabetic mice that were induced to develop diabetes by diabetogenic CD4(+) T cells with T-cell receptors that recognize beta-cell antigens. Acute infiltration of CD4(+) T cells in islets occurred with rapid onset of diabetes. Beta cells from islets with immune infiltration expressed MHC class II mRNA and protein. Exposure of beta cells to IFN-γ increased MHC class II gene expression, and blocking IFN-γ signaling in beta cells inhibited MHC class II upregulation. IFN-γ also increased HLA-DR expression in human islets. MHC class II(+) beta cells stimulated the proliferation of beta-cell-specific CD4(+) T cells. Our study indicates that MHC class II molecules may play an important role in beta-cell interaction with CD4(+) T cells in the development of type 1 diabetes.

Molecular Scissoring: Facile 3D to 2D Conversion of Lanthanide Metal Organic Frameworks Via Solvent Exfoliation.

Five lanthanide MOFs with pcu topology have been exfoliated into nanoplatelets of two-dimensional structures via sonication in the dimethylacetamide solvent. These nanosheets are fluorescent under two-photon excitation dominated by the ligand, indicating energy upconversion ability.

Formation of a Syndiotactic Organic Polymer Inside a MOF by a [2+2] Photo-Polymerization Reaction.

Getting suitable crystals for single-crystal X-ray crystallographic analysis still remains an art. Obtaining single crystals of metal-organic frameworks (MOFs) containing organic polymers poses even greater challenges. Here we demonstrate the formation of a syndiotactic organic polymer ligand inside a MOF by quantitative [2+2] photopolymerization reaction in a single-crystal-to-single-crystal manner. The spacer ligands with trans,trans,trans-conformation in the pillared-layer MOF with guest water molecules in the channels, undergo pedal motion to trans,cis,trans-conformation prior to [2+2] photo-cycloaddition reaction and yield single crystals of MOF containing two-dimensional coordination polymers fused with the organic polymer ligands. We also show that the organic polymer in the single crystals can be depolymerized reversibly by cleaving the cyclobutane rings upon heating. These MOFs also show interesting photoluminescent properties and sensing of small organic molecules.

Oxygen-initiated stereoselective thermal isomerisation of a cyclobutane derivative in the solid state.

Solid-state [2+2] photochemical cycloaddition reactions have been extensively studied after the classical work of Schmidt in the 1960s. Of these, trans-1,2-bis(4'-pyridyl)ethylene (bpe) is one of the well-studied alkenes to synthesize tetrakis(4-pyridyl)cyclobutane (tpcb). However, almost all the solid-state [2+2] cycloaddition reactions of bpe yielded, almost exclusively, one of the four possible isomers, namely, the rctt-tpcb (r=regio c=cis and t=trans). Here we describe a stereoselective synthesis of the tetrahedrally disposed rtct-tpcb by the solid-state thermal isomerization of the rctt-isomer in atmospheric air. We propose that this isomerization occurs through a topochemical unimolecular mechanism by a radical chain pathway, initiated by molecular oxygen. This is supported by the nature of products formed in air and nitrogen, detection of a radical in ESR spectral studies, ESI-MS crossover experiments, VT PXRD studies along with QM, MD and docking calculations. The formation of a unique isomer by thermal isomerization may be a general phenomenon to quantitatively synthesize other useful stereoisomers from the existing isomers of cyclobutane derivatives.

Bioengineered Hydrogels Recapitulate Fibroblast Heterogeneity in Cancer.

Recently mapped transcriptomic landscapes reveal the extent of heterogeneity in cancer-associated fibroblasts (CAFs) beyond previously established single-gene markers. Functional analyses of individual CAF subsets within the tumor microenvironment are critical to develop more accurate CAF-targeting therapeutic strategies. However, there is a lack of robust preclinical models that reflect this heterogeneity in vitro. In this study, single-cell RNA sequencing datasets acquired from head and neck squamous cell carcinoma tissues to predict microenvironmental and cellular features governing individual CAF subsets are leveraged. Some of these features are then incorporated into a tunable hyaluronan-based hydrogel system to culture patient-derived CAFs. Control over hydrogel degradability and integrin adhesiveness enabled derivation of the predominant myofibroblastic and inflammatory CAF subsets, as shown through changes in cell morphology and transcriptomic profiles. Last, using these hydrogel-cultured CAFs, microtubule dynamics are identified, but not actomyosin contractility, as a key mediator of CAF plasticity. The recapitulation of CAF heterogeneity in vitro using defined hydrogels presents unique opportunities for advancing the understanding of CAF biology and evaluation of CAF-targeting therapeutics.

Bioengineered hydrogels enhance ex vivo preservation of patient-derived tumor explants for drug evaluation.

Ex vivo patient-derived tumor slices (PDTS) are currently limited by short-term viability in culture. Here, we show how bioengineered hydrogels enable the identification of key matrix parameters that significantly enhance PDTS viability compared to conventional culture systems. As demonstrated using single-cell RNA sequencing and high-dimensional flow cytometry, hydrogel-embedded PDTS tightly preserved cancer, cancer-associated fibroblast, and various immune cell populations and subpopulations in the corresponding original tumor. Cell-cell communication networks within the tumor microenvironment, including immune checkpoint ligand-receptor interactions, were also maintained. Remarkably, our results from a co-clinical trial suggest hydrogel-embedded PDTS may predict sensitivity to immune checkpoint inhibitors (ICIs) in head and neck cancer patients. Further, we show how these longer term-cultured tumor explants uniquely enable the sampling and detection of temporal evolution in molecular readouts when treated with ICIs. By preserving the compositional heterogeneity and complexity of patient tumors, hydrogel-embedded PDTS provide a valuable tool to facilitate experiments targeting the tumor microenvironment.

Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis.

Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a subpopulation of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunts tumor invasion in patient-derived cultures. Furthermore, scRNAseq analyses of tumor-infiltrating CD8 + T-lymphocytes show two distinct trajectories to T-cell dysfunction, corroborated by their clonal architecture based on single-cell T-cell receptor sequencing. By determining key modulators of these trajectories, followed by validation using external datasets and functional experiments, we uncover a role for SOX4 in mediating T-cell exhaustion. Finally, interactome analyses between pre-metastatic tumor cells and CD8 + T-lymphocytes uncover a putative role for the Midkine pathway in immune-modulation and this is confirmed by scRNAseq of tumors from humanized mice. Aside from specific findings, this study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.

Clinical efficacy and biomarker analysis of dual PD-1/CTLA-4 blockade in recurrent/metastatic EBV-associated nasopharyngeal carcinoma.

Single-agent checkpoint inhibitor (CPI) activity in Epstein-Barr Virus (EBV) related nasopharyngeal carcinoma (NPC) is limited. Dual CPI shows increased activity in solid cancers. In this single-arm phase II trial (NCT03097939), 40 patients with recurrent/metastatic EBV-positive NPC who failed prior chemotherapy receive nivolumab 3 mg/kg every 2 weeks and ipilimumab 1 mg/kg every 6 weeks. Primary outcome of best overall response rate (BOR) and secondary outcomes (progression-free survival [PFS], clinical benefit rate, adverse events, duration of response, time to progression, overall survival [OS]) are reported. The BOR is 38% with median PFS and OS of 5.3 and 19.5 months, respectively. This regimen is well-tolerated and treatment-related adverse events requiring discontinuation are low. Biomarker analysis shows no correlation of outcomes to PD-L1 expression or tumor mutation burden. While the BOR does not meet pre-planned estimates, patients with low plasma EBV-DNA titre (<7800 IU/ml) trend to better response and PFS. Deep immunophenotyping of pre- and on-treatment tumor biopsies demonstrate early activation of the adaptive immune response, with T-cell cytotoxicity seen in responders prior to any clinically evident response. Immune-subpopulation profiling also identifies specific PD-1 and CTLA-4 expressing CD8 subpopulations that predict for response to combined immune checkpoint blockade in NPC.

Photochemical reactions of metal complexes in the solid state.

This perspective focusses on the solid-state reactivity and structural transformation driven by photochemical methods in discrete metal complexes, organometallic compounds, metallo-macrocycles and cages. Changes in the metal-metal bond distances, racemization of chiral centres, fusion of cages, formation of coordination polymers, expected [2 + 2] and [4 + 4] cycloaddition products, unusual phenyl-olefin dimerization, and linkage isomerization of -SO2, -NO & -NO2 ligands cause the structural transformations. Of these, [2 + 2] photo-cycloaddition reactions have been widely studied and the photoreactions are made possible by various supramolecular interactions including hydrogen bonds, metallophilic, ππ and C-Hπ interactions, ligand design and metallic clips to bring the reactive functional groups closely into correct orientation close to the transition state. These photoreactions are often accompanied by crystal bending, mechanical motion, and changes in the magnetic and photoluminescence properties. In several cases, the single crystals have been preserved at the end of the reactions, which are known as single-crystal-to-single-crystal (SCSC) reactions.

The role of structure and the metal ion in the fluorescence sensing of nitro compounds for a series of lanthanide(iii) 9,10-anthracene dicarboxylate coordination polymers.

Twenty-eight lanthanide coordination polymers (CPs) containing 9,10-anthracene dicarboxylate (ADC) linkers have been synthesized and characterized. For the earlier class of lanthanides La3+, Ce3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+ and Tb3+, the 3D pcu net was generated from dimethylformamide (DMF) while a 2D hcb net was formed using dimethylacetamide (DMA). Similarly for the later class of lanthanides, Dy3+, Ho3+, Er3+, Tm3+, Yb3+ and Lu3+, a 2D hcb net was formed when dimethylacetamide (DMA) was used. However, the formation of a crystalline product with DMF was possible only when DMSO was added together for these lanthanides, and they yielded 2D structures despite the usage of DMF. Only the single crystal structures of Er3+ and Ho3+ have been determined and the rest of the structures were confirmed by PXRD studies. These compounds have been used to sense various nitro compounds. In particular, they are the most sensitive to Brady's reagent, 2,4-dinitrohydrazobenzene. There was no difference in the quenching extent between the 3D and 2D early lanthanide CPs. For the later lanthanides which adopt 2D structures, the quenching efficiency is higher when DMA instead of DMSO is coordinated suggesting the solvent effect in emission quenching.

Curved crystal morphology, photoreactivity and photosalient behaviour of mononuclear Zn(II) complexes.

A dramatic effect of crystal morphology, photoreactivity and photosalient property is observed in a zinc(II) complex due to solvent effects and fluorine substitution at the backbone of the ligand. Of the two crystal forms with a 3-fluoro derivative, one yielded a curved morphology of single crystals and the second form shows photoreactivity in the solid state, whereas crystals of the 2-fluoro derivative pop during the [2 + 2] photocycloaddition reaction. This is the first report documenting curved single crystals of metal complexes obtained naturally during crystallization, although such bent crystals have been observed in extended solids naturally, or bent by mechanical force or by UV irradiation.

Granzyme A Deficiency Breaks Immune Tolerance and Promotes Autoimmune Diabetes Through a Type I Interferon-Dependent Pathway.

Granzyme A is a protease implicated in the degradation of intracellular DNA. Nucleotide complexes are known triggers of systemic autoimmunity, but a role in organ-specific autoimmune disease has not been demonstrated. To investigate whether such a mechanism could be an endogenous trigger for autoimmunity, we examined the impact of granzyme A deficiency in the NOD mouse model of autoimmune diabetes. Granzyme A deficiency resulted in an increased incidence in diabetes associated with accumulation of ssDNA in immune cells and induction of an interferon response in pancreatic islets. Central tolerance to proinsulin in transgenic NOD mice was broken on a granzyme A-deficient background. We have identified a novel endogenous trigger for autoimmune diabetes and an in vivo role for granzyme A in maintaining immune tolerance.

Multiphoton harvesting metal-organic frameworks.

Multiphoton upconversion is a process where two or more photons are absorbed simultaneously to excite an electron to an excited state and, subsequently, the relaxation of electron gives rise to the emission of a photon with frequency greater than those of the absorbed photons. Materials possessing such property attracted attention due to applications in biological imaging, photodynamic therapy, three-dimensional optical data storage, frequency-upconverted lasing and optical power limiting. Here we report four-photon upconversion in metal-organic frameworks containing the ligand, trans, trans-9,10-bis(4-pyridylethenyl)anthracene. The ligand has a symmetrical acceptor-π-donor-π-acceptor structure and a singlet biradical electronic ground state, which boosted its multiphoton absorption cross-sections. We demonstrate that the upconversion efficiency can be enhanced by Förster resonance energy transfer within host-guest metal-organic frameworks consisting of encapsulated high quantum yielding guest molecules. Using these strategies, metal-organic framework materials, which can exhibit frequency-upconverted photoluminescence excited by simultaneous multiphoton absorption, can be rationally designed and synthesized.

Inactivation of Protein Tyrosine Phosphatases Enhances Interferon Signaling in Pancreatic Islets.

Type 1 diabetes (T1D) is the result of an autoimmune assault against the insulin-producing pancreatic ß-cells, where chronic local inflammation (insulitis) leads to ß-cell destruction. T cells and macrophages infiltrate into islets early in T1D pathogenesis. These immune cells secrete cytokines that lead to the production of reactive oxygen species (ROS) and T-cell invasion and activation. Cytokine-signaling pathways are very tightly regulated by protein tyrosine phosphatases (PTPs) to prevent excessive activation. Here, we demonstrate that pancreata from NOD mice with islet infiltration have enhanced oxidation/inactivation of PTPs and STAT1 signaling compared with NOD mice that do not have insulitis. Inactivation of PTPs with sodium orthovanadate in human and rodent islets and ß-cells leads to increased activation of interferon signaling and chemokine production mediated by STAT1 phosphorylation. Furthermore, this exacerbated STAT1 activation-induced cell death in islets was prevented by overexpression of the suppressor of cytokine signaling-1 or inactivation of the BH3-only protein Bim. Together our data provide a mechanism by which PTP inactivation induces signaling in pancreatic islets that results in increased expression of inflammatory genes and exacerbated insulitis.

Solid-state conversion of a MOF to a metal-organo polymeric framework (MOPF) via [2+2] cycloaddition reaction.

The bpeb ligands aligned in a slip-stacked manner in a two-fold interpenetrated non-porous metal-organic framework (MOF) [Zn2(bpeb)(bdc)(fa)2] undergo [2+2] cycloaddition reaction in a single-crystal to single-crystal manner to a non-interpenetrated 3D structure with a new topology comprising an organic polymer ligand and a 2D coordination polymer.

Deficiency in type I interferon signaling prevents the early interferon-induced gene signature in pancreatic islets but not type 1 diabetes in NOD mice.

Type I interferons (IFNs) have been implicated in the initiation of islet autoimmunity and development of type 1 diabetes. To directly test their involvement, we generated NOD mice deficient in type I IFN receptors (NOD.IFNAR1(-/-)). Expression of the type I IFN-induced genes Mx1, Isg15, Ifit1, Oas1a, and Cxcr4 was detectable in NOD islets as early as 1 week of age. Of these five genes, expression of Isg15, Ifit1, Oas1a, and Mx1 peaked at 3-4 weeks of age, corresponding with an increase in Ifnα mRNA, declined at 5-6 weeks of age, and increased again at 10-14 weeks of age. Increased IFN-induced gene expression was ablated in NOD.IFNAR1(-/-) islets. Loss of Toll-like receptor 2 (TLR2) resulted in reduced islet expression of Mx1 at 2 weeks of age, but TLR2 or TLR9 deficiency did not change the expression of other IFN-induced genes in islets compared with wild-type NOD islets. We observed increased ß-cell major histocompatibility complex class I expression with age in NOD and NOD.IFNAR1(-/-) mice. NOD.IFNAR1(-/-) mice developed insulitis and diabetes at a similar rate to NOD controls. These results indicate type I IFN is produced within islets in young mice but is not essential for the initiation and progression of diabetes in NOD mice.