An integrated mass spectrometry imaging and digital pathology workflow for objective detection of colorectal tumours by unique atomic signatures

Tumours are abnormal growths of cells that reproduce by redirecting essential nutrients and resources from surrounding tissue. Changes to cell metabolism that trigger the growth of tumours are reflected in subtle differences between the chemical composition of healthy and malignant cells. We used LA-ICP-MS imaging to investigate whether these chemical differences can be used to spatially identify tumours and support detection of primary colorectal tumours in anatomical pathology. First, we generated quantitative LA-ICP-MS images of three colorectal surgical resections with case-matched normal intestinal wall tissue and used this data in a Monte Carlo optimisation experiment to develop an algorithm that can classify pixels as tumour positive or negative. Blinded testing and interrogation of LA-ICP-MS images with micrographs of haematoxylin and eosin stained and Ki67 immunolabelled sections revealed Monte Carlo optimisation accurately identified primary tumour cells, as well as returning false positive pixels in areas of high cell proliferation. We analysed an additional 11 surgical resections of primary colorectal tumours and re-developed our image processing method to include a random forest regression machine learning model to correctly identify heterogenous tumours and exclude false positive pixels in images of non-malignant tissue. Our final model used over 1.6 billion calculations to correctly discern healthy cells from various types and stages of invasive colorectal tumours. The imaging mass spectrometry and data analysis methods described, developed in partnership with clinical cancer researchers, have the potential to further support cancer detection as part of a comprehensive digital pathology approach to cancer care through validation of a new chemical biomarker of tumour cells.

Digital pathology and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging reveals a unique elemental signature of colorectal cancer.     

Impact of neutral and acidic species on cycloalkenes nucleation

Non-covalent hydrogen bond interactions between the π cloud of cycloalkenes and three atmospheric common nucleation precursors (H₂S, H₂O, and MeOH) have been investigated using DFT and CCSD(T). The structures and the energies of the 1:1 and 1:2 adducts were computed with the B3LYP-D3 method. The analysis of the investigated electronic properties and geometric parameters shows that cyclohexene is a stronger hydrogen bond acceptor than cyclopentene, then followed by 1,4-cyclohexadiene and 1,3-cyclohexadiene. Comparable red shifts of the OH-/SH-stretching vibrational frequencies were noticed for the studied clusters. Increasing the ring size enhances the hydrogen bond interaction, and increasing the π delocalization decreases the hydrogen bond interactions. This is further confirmed by Bader’s quantum theory of atoms in molecules. The nonadditivity effects were observed in the trimolecular complexes. All the complexes were analyzed by energy decomposition analysis to divide the interaction energy into individual components. Furthermore, the dipole moments and atmospheric implications were also investigated.

     

Free radical polymerization of caffeine‐containing methacrylate monomers

The incorporation of acrylic functionality into caffeine enables the preparation of a vast array of novel thermoplastics and thermosets. A two‐step derivatization provided a novel caffeine‐containing methacrylate monomer capable of free radical polymerization. Copolymers of 2‐ethylhexyl methacrylate and caffeine methacrylate (CMA) allowed for a systematic study of the effect of covalently bound caffeine on polymer properties. ¹H NMR and UV‐vis spectroscopy confirmed caffeine incorporation at 5 and 13 mol %, and SEC revealed the formation of high molecular weight (co)polymers (>40,000 g/mol). CMA incorporation resulted in a multistep degradation profile with initial mass loss closely correlating to caffeine content. Differential scanning calorimetry, rheological, and thermomechanical analysis demonstrated that relatively low levels of CMA increased the glass transition temperature, resulting in higher moduli and elucidating the benefits of incorporating caffeine into polymers. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2829–2837     

Physical mechanisms responsible for the water-induced degradation of PC61BM P3HT photovoltaic thin films

We show that [6,6]-phenyl-C61-butyric acid methyl ester (PC₆₁BM) at the surface of thin film blends of poly(3-hexylthiophene) (P3HT):PC₆₁BM can be patterned by water. Using a series of heating and cooling steps, water droplets condense onto the blend film surface. This is possible due to the liquid-like, water swollen layer of poly(3,4-ethylenedioxythiophene) polystyrene sulfonate. Breath pattern water deformation and subsequent drying on the film surface results in isolated PC₆₁BM structures, showing that migration of PC₆₁BM takes place. This was confirmed by selective wavelength illumination to spatially map the photoluminescence from the P3HT and PC₆₁BM. Within a device, redistribution of the surface PC₆₁BM into aggregates would be catastrophic, as it would markedly alter device performance. We also postulate that repeated volume change of the poly(3,4-ethylenedioxythiophene) polystyrene sulfonate layer by water swelling may be, in part, responsible for the delamination failure mechanism in thin film solar cells devices. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 141–146     

Silyl‐Phosphino‐Carbene Complexes of Uranium(IV)

Unprecedented silyl‐phosphino‐carbene complexes of uranium(IV) are presented, where before all covalent actinide–carbon double bonds were stabilised by phosphorus(V) substituents or restricted to matrix isolation experiments. Conversion of [U(BIPM^TMS)(Cl)(μ‐Cl)₂Li(THF)₂] ( 1 , BIPM^TMS=C(PPh₂NSiMe₃)₂) into [U(BIPM^TMS)(Cl){CH(Ph)(SiMe₃)}] ( 2 ), and addition of [Li{CH(SiMe₃)(PPh₂)}(THF)]/Me₂NCH₂CH₂NMe₂ (TMEDA) gave [U{C(SiMe₃)(PPh₂)}(BIPM^TMS)(μ‐Cl)Li(TMEDA)(μ‐TMEDA)_0.5]₂ ( 3 ) by α‐hydrogen abstraction. Addition of 2,2,2‐cryptand or two equivalents of 4‐N,N‐dimethylaminopyridine (DMAP) to 3 gave [U{C(SiMe₃)(PPh₂)}(BIPM^TMS)(Cl)][Li(2,2,2‐cryptand)] ( 4 ) or [U{C(SiMe₃)(PPh₂)}(BIPM^TMS)(DMAP)₂] ( 5 ). The characterisation data for 3 – 5 suggest that whilst there is evidence for 3‐centre P?C?U π‐bonding character, the U=C double bond component is dominant in each case. These U=C bonds are the closest to a true uranium alkylidene yet outside of matrix isolation experiments.     

Solid-phase synthesis of azidomethylene inhibitors targeting cysteine proteases

An efficient strategy for the solid-phase synthesis of azidomethylene inhibitors targeting cysteine proteases is described. The method is highlighted by its compatibility with readily available building blocks, as well as its ability to accommodate different functional groups. A 249-member library has thus far been successfully synthesized, characterized, and screened against Caspase-1, -3 and -7.     

Synthesis and characterization of mono- and micro6-sulfato hexanuclear zinc complexes of a new symmetric dinucleating ligand

Zinc complexes of a new symmetric dinucleating ligand, N,N'-Bis[2-carboxybenzomethyl]-N,N'-Bis[carboxymethyl]-1,3-diaminopropan-2-ol (H5ccdp) with mixed donating groups, have been studied in the solid state as well as in solution. In methanol, the reaction of stoichiometric and substoichiometric amounts of Zn(ClO4)2 x 6H2O and the ligand H5ccdp, in the presence of K2CO3 or Et3N, afforded a mononuclear zinc complex, [Zn(H2O)6][Zn(H2ccdp)(H2O)2]2 x 12H2O (1). The solid state structure of 1 contains two units of the zinc-ligand anion, [Zn(H2ccdp)(H2O)2]-, and one [Zn(H2O)6]2+ counter cation. The Zn(II) center of the anion is in a distorted octahedral geometry. However, in methanol, the reaction of ZnSO4 x 7H2O and the ligand Hsccdp in the presence of NaOH afforded a unique micro6-sulfato hexanuclear zinc complex, Na6[Zn6(ccdp)3(micro6-SO4)](OH) x 10.5H2O (2). The structure of 2 contains a [ZnII6(micro6-SO4)] core unit which is held together by three heptadentate bridging ligands, ccdp5-. Three of the Zn(II) centers are in highly distorted square pyramidal geometry, the other three Zn(II) centers are in a distorted octahedral geometry.     

A comparison of an optimised sequential extraction procedure and dilute acid leaching of elements in anoxic sediments, including the effects of oxidation on sediment metal partitioning

The effect of oxidation of anoxic sediment upon the extraction of 13 elements (Cd, Sn, Sb, Pb, Al, Cr, Mn, Fe, Co, Ni, Cu, Zn, As) using the optimised Community Bureau of Reference of the European Commission (BCR) sequential extraction procedure and a dilute acid partial extraction procedure (4 h, 1 mol L⁻¹ HCl) was investigated. Elements commonly associated with the sulfidic phase, Cd, Cu, Pb, Zn and Fe exhibited the most significant changes under the BCR sequential extraction procedure. Cd, Cu, Zn, and to a lesser extent Pb, were redistributed into the weak acid extractable fraction upon oxidation of the anoxic sediment and Fe was redistributed into the reducible fraction as expected, but an increase was also observed in the residual Fe. For the HCl partial extraction, sediments with moderate acid volatile sulfide (AVS) levels (1-100 μmol g⁻¹) showed no significant difference in element partitioning following oxidation, whilst sediments containing high AVS levels (>100 μmol g⁻¹) were significantly different with elevated concentrations of Cu and Sn noted in the partial extract following oxidation of the sediment. Comparison of the labile metals released using the BCR sequential extraction procedure (ΣSteps 1-3) to labile metals extracted using the dilute HCl partial extraction showed that no method was consistently more aggressive than the other, with the HCl partial extraction extracting more Sn and Sb from the anoxic sediment than the BCR procedure, whilst the BCR procedure extracted more Cr, Co, Cu and As than the HCl extraction.     

Improved methodology for the microwave digestion of carbonate-rich environmental samples

Microwave-assisted digestion permits a rapid and total dissolution of sediments and various other sample types, allowing easier and more accurate multi-element determinations. In this study, we present an optimised microwave digestion method for the complete digestion of 200 mg of carbonate-rich sediments. The optimised method prevents the formation of precipitates and assures a complete dissolution of the material. The optimised method involves treatment with concentrated hydrochloric acid (HCl) prior to microwave digestion, which prevents the formation of an insoluble calcium fluoride precipitate associated with the use of hydrofluoric acid (HF). Three different certified reference samples along with a pure calcium carbonate standard and a carbonate-rich in-house marine sediment sample were considered. Sediments were found to only be partially digested if insufficient HF was present, while a noticeable fluoride-based precipitate was found if excess HF was present. Twenty elements were analysed using sector field inductively coupled plasma mass spectrometry (ICP-MS) (Al, Ag, Ba, Ca, Cd, Co, Cr, Cu, Fe, Mg, Mn, Mo, Na, Ni, Sr, Th, Ti, U, V and Zn). A total sample digestion with average elemental recoveries above 90% was obtained by reacting carbonate-rich samples with HCl on a hotplate at 150°C for 2 h (time for the total release of generated CO₂), prior to any microwave digestion step. This extra step prevented the accumulation of gas in the sealed vessels during digestion, which would otherwise influence the carbonate chemical equilibria and make insoluble calcium available for precipitation. After this initial treatment, the improved digestion method consisted of microwave attack employing a mix of concentrated HCl, nitric acid (HNO₃) and HF (4 mL/10 mL/2 mL), followed by evaporation on a hotplate. The limits of detection (LOD) obtained using the optimised microwave protocol and ICP-MS measurements were below 0.1 µg/kg for the trace elements and below 0.2 mg/kg for major elements.