Germline genetic regulation of the colorectal tumor immune microenvironment.

OBJECTIVE: To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC). METHODS: Germline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication. RESULTS: We identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10- 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa. CONCLUSIONS: Our study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.

Ex vivo gene editing and cell therapy for hereditary tyrosinemia type 1.

BACKGROUND: We previously demonstrated the successful use of in vivo CRISPR gene editing to delete 4-hydroxyphenylpyruvate dioxygenase (HPD) to rescue mice deficient in fumarylacetoacetate hydrolase (FAH), a disorder known as hereditary tyrosinemia type 1 (HT1). The aim of this study was to develop an ex vivo gene-editing protocol and apply it as a cell therapy for HT1. METHODS: We isolated hepatocytes from wild-type (C57BL/6J) and Fah-/- mice and then used an optimized electroporation protocol to deliver Hpd-targeting CRISPR-Cas9 ribonucleoproteins into hepatocytes. Next, hepatocytes were transiently incubated in cytokine recovery media formulated to block apoptosis, followed by splenic injection into recipient Fah-/- mice. RESULTS: We observed robust engraftment and expansion of transplanted gene-edited hepatocytes from wild-type donors in the livers of recipient mice when transient incubation with our cytokine recovery media was used after electroporation and negligible engraftment without the media (mean: 46.8% and 0.83%, respectively; p=0.0025). Thus, the cytokine recovery medium was critical to our electroporation protocol. When hepatocytes from Fah-/- mice were used as donors for transplantation, we observed 35% and 28% engraftment for Hpd-Cas9 ribonucleoproteins and Cas9 mRNA, respectively. Tyrosine, phenylalanine, and biochemical markers of liver injury normalized in both Hpd-targeting Cas9 ribonucleoprotein and mRNA groups independent of induced inhibition of Hpd through nitisinone, indicating correction of disease indicators in Fah-/- mice. CONCLUSIONS: The successful liver cell therapy for HT1 validates our protocol and, despite the known growth advantage of HT1, showcases ex vivo gene editing using electroporation in combination with liver cell therapy to cure a disease model. These advancements underscore the potential impacts of electroporation combined with transplantation as a cell therapy.

Combined Pulmonary Fibrosis and Emphysema in a Patient With Chronic Occupational Exposure to Trichloroethylene.

Combined pulmonary fibrosis and emphysema (CPFE) is a clinical syndrome of upper-zone-predominant emphysema on high-resolution CT and a peripheral and basal-predominant diffuse pulmonary fibrosis. Multiple occupational and inhalational exposures have been associated with CPFE. We describe a U.S. veteran, who developed CPFE after a prolonged, intense exposure to trichloroethylene as an aircraft maintenance worker. We believe that this may be another example of occupational-associated CPFE.

Simultaneously Measured Kinetics of Two Amyloid Polymorphs Using Cross Peak Specific 2D IR Spectroscopy.

The origin of in vitro amyloid fibril polymorphs is debated, in part, because few techniques can simultaneously monitor the formation kinetics of multiple amyloid polymorphs. Using a cross-peak specific polarization scheme, ⟨0°,0°,60°,-60°⟩, we resolve 22 previously unseen cross peaks in the 2D IR spectra of amyloid fibrils formed by the human islet amyloid polypeptide (hIAPP). Those cross peaks include a subset assigned to a second fibril polymorph, which forms on a slower time scale. We simulated the data with three different kinetic models for polymorph formation. Only a model based on secondary nucleation reproduces the cross peak kinetics. These experiments are evidence that fibrils formed by secondary nucleation have a different polymorphic structure than the parent fibrils and illustrate the enhanced structural resolution of this new cross peak specific polarization scheme.

Heterozygote advantage at HLA class I and II loci and reduced risk of colorectal cancer.

Objective: Reduced diversity at Human Leukocyte Antigen (HLA) loci may adversely affect the host's ability to recognize tumor neoantigens and subsequently increase disease burden. We hypothesized that increased heterozygosity at HLA loci is associated with a reduced risk of developing colorectal cancer (CRC). Methods: We imputed HLA class I and II four-digit alleles using genotype data from a population-based study of 5,406 cases and 4,635 controls from the Molecular Epidemiology of Colorectal Cancer Study (MECC). Heterozygosity at each HLA locus and the number of heterozygous genotypes at HLA class -I (A, B, and C) and HLA class -II loci (DQB1, DRB1, and DPB1) were quantified. Logistic regression analysis was used to estimate the risk of CRC associated with HLA heterozygosity. Individuals with homozygous genotypes for all loci served as the reference category, and the analyses were adjusted for sex, age, genotyping platform, and ancestry. Further, we investigated associations between HLA diversity and tumor-associated T cell repertoire features, as measured by tumor infiltrating lymphocytes (TILs; N=2,839) and immunosequencing (N=2,357). Results: Individuals with all heterozygous genotypes at all three class I genes had a reduced odds of CRC (OR: 0.74; 95% CI: 0.56-0.97, p= 0.031). A similar association was observed for class II loci, with an OR of 0.75 (95% CI: 0.60-0.95, p= 0.016). For class-I and class-II combined, individuals with all heterozygous genotypes had significantly lower odds of developing CRC (OR: 0.66, 95% CI: 0.49-0.87, p= 0.004) than those with 0 or one heterozygous genotype. HLA class I and/or II diversity was associated with higher T cell receptor (TCR) abundance and lower TCR clonality, but results were not statistically significant. Conclusion: Our findings support a heterozygote advantage for the HLA class-I and -II loci, indicating an important role for HLA genetic variability in the etiology of CRC.

Against the Norm: Non Irving-Williams Transmetalation in Transition Metal Dimers.

We report the synthesis and characterization of three dinuclear 3d3d' complexes, CuCu ([Cu2IIL(NO3)2]), MnMn ([Mn2IIL(MeOH)2(NO3)2]), and CuMn ([CuIIMnIIL(NO3)2]), that utilize the ligand, H2L (6,6'-dimethoxy-2,2'-[(1,3-propylene)dioxybis(nitrilomethylidyne)]diphenol). The relative stabilities of these complexes were investigated using experimental and computational techniques, revealing a non-Irving-Williams transmetalation, whereby a MnII ion can displace a CuII ion from its binding pocket in CuCu to yield the more stable CuMn complex. Magnetic characterization of the reported complexes revealed an unexpected ferromagnetic coupling between the two CuII ions of CuCu with J = +63.0 cm-1.

Metastable intermediate during hIAPP aggregation catalyzed by membranes as detected with 2D IR spectroscopy.

The aggregation of human islet amyloid polypeptide (hIAPP) into amyloid fibrils involves formation of oligomeric intermediates that are thought to be the cytotoxic species responsible for ß-cell dysfunction in type 2 diabetes. hIAPP oligomers permeating or disrupting the cellular membrane may be one mechanism of toxicity and so measuring the structural kinetics of aggregation in the presence of membranes is of much interest. In this study, we use 2D IR spectroscopy and 13C18O isotope labeling to study the secondary structure of the oligomeric intermediates formed in solution and in the presence of phospholipid vesicles at sites L12A13, L16V17, G24A25 and V32G33. Pairs of labels monitor the couplings between associated polypeptides and the dihedral angles between adjacent residues. In solution, the L12A13 residues form an oligomeric ß-sheet in addition to an α-helix whereas with the phospholipid vesicles they are α-helical throughout the aggregation process. In both solution and with DOPC vesicles, L16V17 and V32G33 have disordered structures until fibrils are formed. Similarly, under both conditions, G24A25 exhibits 3-state kinetics, created by an oligomeric intermediate with a well-defined ß-sheet structure. Amyloid fibril formation is often thought to involve intermediates with exceedingly low populations that are difficult to detect experimentally. These experiments establish that amyloid fibril formation of hIAPP when catalyzed by membranes includes a metastable intermediate and that this intermediate has a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution, thought to be the toxic species.

Structural trends in a series of bulky dialkylbiarylphosphane complexes of CuI.

CuI complexes containing the bulky dialkylbiarylphosphane 2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl (tBuXPhos, L) and an ancillary ligand (Cl-, Br-, I-, MeCN, ClO4- or SCN-) have been structurally characterized, namely, chlorido[2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP]copper(I), [CuCl(C29H45P)], 1, bromido[2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP]copper(I), [CuBr(C29H45P)], 2, [2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP]iodidocopper(I), [CuI(C29H45P)], 3, (acetonitrile-κN)[2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP]copper(I) hexafluoridophosphate, [Cu(CH3CN)(C29H45P)]PF6, 4, [2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP](perchlorato-κO)copper(I), [Cu(ClO4)(C29H45P)], 5, and di-µ-thiocyanato-κ2S:N;κ2N:S-bis{[2-(di-tert-butylphosphanyl)-2',4',6'-triisopropylbiphenyl-κP]copper(I)}, [Cu2(NCS)2(C29H45P)2], 6. Iodide complex 3 shows significant CuI-arene interactions, in contrast to its chloride 1 and bromide 2 counterparts, which is attributed to the weaker interaction between the iodide ion and the CuI centre. When replacing iodide with an acetonitrile (in 4) or perchlorate (in 5) ligand, the reduced interaction between the CuI atom and the ancillary ligand results in stronger CuI-arene interactions. No CuI-arene interactions are observed in dimer 6, due to the tricoordinated CuI centre having sufficient electron density from the coordinated ligands.

Analysis of amyloid-like secondary structure in the Cryab-R120G knock-in mouse model of hereditary cataracts by two-dimensional infrared spectroscopy.

αB-crystallin is a small heat shock protein that forms a heterooligomeric complex with αA-crystallin in the ocular lens. It is also widely distributed in tissues throughout the body and has been linked with neurodegenerative diseases such as Alzheimer's, where it is associated with amyloid fibrils. Crystallins can form amorphous aggregates in cataracts as well as more structured amyloid-like fibrils. The arginine 120 to glycine (R120G) mutation in αB-crystallin (Cryab-R120G) results in high molecular weight crystallin protein aggregates and loss of the chaperone activity of the protein in vitro, and it is associated with human hereditary cataracts and myopathy. Characterizing the amorphous (unstructured) versus the highly ordered (amyloid fibril) nature of crystallin aggregates is important in understanding their role in disease and important to developing pharmacological treatments for cataracts. We investigated protein secondary structure in wild-type (WT) and Cryab-R120G knock-in mutant mouse lenses using two-dimensional infrared (2DIR) spectroscopy, which has been used to detect amyloid-like fibrils in human lenses and measure UV radiation-induced changes in porcine lenses. Our goal was to compare the aggregated proteins in this mouse lens model to human lenses and evaluate the protein structural relevance of the Cryab-R120G knock-in mouse model to general age-related cataract disease. In the 2DIR spectra, amide I diagonal peak frequencies were red-shifted to smaller wavenumbers in mutant mouse lenses as compared to WT mouse lenses, consistent with an increase in ordered secondary structure. The cross peak frequency and intensity indicated the presence of amyloid in the mutant mouse lenses. While the diagonal and cross peak changes in location and intensity from the 2DIR spectra indicated significant structural differences between the wild type and mutant mouse lenses, these differences were smaller than those found in human lenses; thus, the Cryab-R120G knock-in mouse lenses contain less amyloid-like secondary structure than human lenses. The results of the 2DIR spectroscopy study confirm the presence of amyloid-like secondary structure in Cryab-R120G knock-in mice with cataracts and support the use of this model to study age-related cataract.

Application of 2D IR Bioimaging: Hyperspectral Images of Formalin-Fixed Pancreatic Tissues and Observation of Slow Protein Degradation.

We used two-dimensional IR bioimaging to study the structural heterogeneity of formalin-fixed mouse pancreas. Images were generated from the hyperspectral data sets by plotting quantities associated with the amide I vibrational mode, which is created by the backbone carbonyl stretch. Images that measure the fundamental vibrational frequencies, cross peaks, and anharmonic shifts are presented. Histograms are generated for each quantity, providing averaged values and distributions around the mean that serve as metrics for protein structures. Images were generated from tissue that had been stored in a formalin fixation for 3, 8, and 48 weeks. Over this period, all three metrics show that that the ß-sheet content of the samples increased, consistent with protein aggregation. Our results indicate that formalin fixation does not entirely arrest the degradation of a protein structure in pancreas tissue.

Lung Cancer Risk among Patients with Asthma-Chronic Obstructive Pulmonary Disease Overlap.

Rationale: Chronic obstructive pulmonary disease (COPD) is a well-established independent risk factor for lung cancer; however, the literature on the association between asthma and lung cancer is mixed. Whether asthma-COPD overlap (ACO) is associated with lung cancer has not been studied. Objectives: We aimed to compare lung cancer risk among patients with ACO versus COPD and other conditions associated with airway obstruction. Methods: We studied 13,939 smokers from the National Lung Cancer Screening Trial who had baseline spirometry and used spirometric indices and history of childhood asthma to categorize participants into five specific airway disease subgroups. We used Poisson regression to compare unadjusted and adjusted lung cancer risk. Results: The incidence rate of lung cancer per 1,000 person-years was as follows: ACO, 13.2 (95% confidence interval [CI], 8.1-21.5); COPD, 11.7 (95% CI, 10.5-13.1); asthmatic smokers, 1.8 (95% CI, 0.6-5.4); Global Initiative for Chronic Obstructive Lung Disease-Unclassified, 7.7 (95% CI, 6.4-9.2); and normal spirometry smokers, 4.1 (95% CI, 3.5-4.8). Patients with ACO had increased adjusted risk of lung cancer compared with patients with asthma (incidence rate ratio [IRR], 4.5; 95% CI, 1.3-15.8) and normal spirometry smokers (IRR, 2.3; 95% CI, 1.3-4.2) in models adjusting for other risk factors. Adjusted lung cancer incidence in patients with ACO and COPD were not found to be different (IRR, 1.2; 95% CI, 0.7-2.1). Conclusions: The risk of lung cancer among patients with ACO is similar to those with COPD and higher than other groups of smokers. These results provide further evidence that COPD, with or without a history of childhood asthma, is an independent risk factor for lung cancer.

The structural manipulation of a series of Ni4 defective dicubanes: Synthesis, X-ray Structures, Magnetic and Computational analyses.

We report the synthesis and characterization of four new tetranuclear Ni(ii) complexes, C1-C4, all of which exhibit defective dicubane cores. C1-C4 are derived from the same salicylaldoxime derived ligand, H2L1. Complexes C1 and C4 have isostructural cores, differing in structure only by solvate molecules. Magnetic and computational analyses have revealed that complexes C1, C2, and C4 exhibit competing ferro- and antiferromagnetic interactions, however the different solvated species in C1 and C4 leads to notably different magnitudes in their magnetic coupling constants. Theoretical magneto-structural studies show that the pairwise magnetic exchange interaction is highly dependent on the Ni-X-Ni angle, as revealed by orbital overlap calculations.

Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics.

The majority of 2D IR spectrometers operate at 1-10 kHz using Ti:Sapphire laser technology. We report a 2D IR spectrometer designed around Yb:KGW laser technology that operates shot-to-shot at 100 kHz. It includes a home-built OPA, a mid-IR pulse shaper, and custom-designed electronics with optional on-chip processing. We report a direct comparison between Yb:KGW and Ti:Sapphire based 2D IR spectrometers. Even though the mid-IR pulse energy is much lower for the Yb:KGW driven system, there is an 8x improvement in signal-to-noise over the 1 kHz Ti:Sapphire driven spectrometer to which it is compared. Experimental data is shown for sub-millimolar concentrations of amides. Advantages and disadvantages of the design are discussed, including thermal background that arises at high repetition rates. This fundamental spectrometer design takes advantage of newly available Yb laser technology in a new way, providing a straightforward means of enhancing sensitivity.

A Different hIAPP Polymorph Is Observed in Human Serum Than in Aqueous Buffer: Demonstration of a New Method for Studying Amyloid Fibril Structure Using Infrared Spectroscopy.

There is enormous interest in measuring amyloid fibril structures, but most structural studies measure fibril formation in vitro using aqueous buffer. Ideally, one would like to measure fibril structure and mechanism under more physiological conditions. Toward this end, we have developed a method for studying amyloid fibril structure in human serum. Our approach uses isotope labeling, antibody depletion of the most abundant proteins (albumin and IgG), and infrared spectroscopy to measure aggregation in human serum with reduced protein content. Reducing the nonamyloid protein content enables the measurements by decreasing background signals but retains the full composition of salts, sugars, metal ions, etc. that are naturally present but usually missing from in vitro studies. We demonstrate the method by measuring the two-dimensional infrared (2D IR) spectra of isotopically labeled human islet amyloid polypeptide (hIAPP or amylin). We find that the fibril structure of hIAPP formed in serum differs from that formed via aggregation in aqueous buffer at residues Gly24 and Ala25, which reside in the putative "amyloidogenic core" or FGAIL region of the sequence. The spectra are consistent with extended parallel stacks of strands consistent with ß-sheet-like structure, rather than a partially disordered loop that forms in aqueous buffer. These experiments provide a new method for using infrared spectroscopy to monitor the structure of proteins under physiological conditions and reveal the formation of a significantly different polymorph structure in the most important region of hIAPP.

The Assessment of Forced Penetration: A Necessary and Further Step Toward Understanding Men's Sexual Victimization and Women's Perpetration.

A unique form of sexual victimization that often goes undiscussed and, therefore, underassessed is that of being forced to penetrate another person (i.e., forced penetration). Due to forced penetration being a relatively novel addition to the definition of rape, there is a lack of assessment tools that identify forced penetration cases. Thus, the goal of this study was to assess the utility and validity of new items designed to assess forced penetration. More than 1,000 participants were recruited across three different studies to assess forced penetration victimization and perpetration. The rate of forced penetration victimization ranged from 4.51% to 10.62%. Among men who reported victimization of any type, 33.8% to 58.7% of victimized men reported experiencing forced penetration across the samples, suggesting this experience is common. All new and unique cases of sexual victimization identified by the forced penetration items were those of heterosexual men. These findings suggest that assessing for forced penetration would increase the reported prevalence rates of sexual victimization, particularly in heterosexual men (and correspondingly, rates of perpetration in women).

Plasmodium vivax and Plasmodium falciparum infection in Neotropical primates in the western Amazon, Brazil.

The Brazilian Amazon is endemic for malaria and natural infections by Plasmodium spp. have been detected in Neotropical primates. Despite the diversity of primate species in the region, studies on infections by these agents are limited. The aim of the present study was to investigate the frequency of infection by Plasmodium vivax and P. falciparum in free-born primates that were kept in captivity, in the western Amazon, Brazil. Blood samples were collected from 98 Neotropical primates. Detection of P. vivax and P. falciparum DNA was performed using a semi-nested PCR, and the amplified products were sequenced. Plasmodium spp. DNA was detected in 6.12% (6/98) of the primates. P. vivax, and P. falciparum DNA was detected in 2.04% (2/98) and 4.08% (4/98) of these mammals, respectively. Sequencing and phylogenetic analysis confirmed the results obtained from the semi-nested PCR. The presence of infected non-human primates (NHP) can be auxiliary in the maintenance of P. falciparum and P. vivax and may have implications for the malaria surveillance and control in the Brazilian Amazon. It is necessary to structure an efficient surveillance system for the aetiological agents of malaria that infect NHP and humans to reduce the risk of Plasmodium spp. introduction into new areas, to protect all susceptible species.

New salicylaldoximato-borate ligands resulting from anion hydrolysis and their respective copper and iron complexes.

Anion hydrolysis reactions between salicylaldoximato ligands (L'-L''') and copper and iron BF4- metal salts, have resulted in the formation of new salicylaldoximato borate containing transition metal complexes: [Fe2(L' + 2H)2](BF4)2(MeOH)4 (C1), [Fe3(L'' + 4H)(OH)2(Py)2](BF4)2(H2O)2(Py)2 (C2), and [Cu2(L''' + H)2Cl2] (C3). Each of the complexes have been structurally characterised, revealing the indirect role boron plays in the formation of these complexes. For complexes C1 and C2, Mössbauer spectroscopy confirmed the existence of Fe(iii) oxidation states. SQUID magnetometry measurements were performed on complexes C2 and C3, revealing the presence of two competing exchange pathways between the three Fe(iii) centres in C2, with antiferromagnetic exchange dominating. For C3 weak antiferromagnetic exchange dominated between the two Cu(ii) centres.

Follow-up Soon After Discharge May Not Reduce COPD Readmissions.

We evaluated whether visiting a primary care provider (PCP) or medical subspecialist within 10 days of discharge reduces 30-day readmissions following hospitalization for acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Data were retrospectively collected from electronic health records for AECOPD-related hospitalizations at an urban, academic medical center for patients 40 years of age or older between June 2011 and June 2016. Primary outcome was probability of all-cause 30-day readmission. Follow-up was defined as visiting a PCP or any medical subspecialist within 10 days of discharge. Generalized linear mixed models were used to examine the association between hospital readmissions and a visit to a PCP or medical subspecialist. Of the 2653 hospital discharges, 17.6% (n=468) had a 30-day readmission. Follow-up did not affect 30-day readmission risk (adjusted odds ratio 1.14; 95% confidence interval 0.89, 1.47). Prompt follow-up is not associated with a reduced risk of 30-day readmission following AECOPD, highlighting the need for a comprehensive approach to chronic obstructive pulmonary disease (COPD).

The Spectrum of Non-asthmatic Airway Diseases Contributing to Cough in the Adult.

PURPOSE OF REVIEW: Cough becomes a pathologic reflex when the airways are inflamed and overwhelmed with excessive mucus. The goal of this review is to discuss acute and chronic cough syndromes caused by non-asthmatic airway diseases. RECENT FINDINGS: Acute cough syndrome is short-lived and self-limited. Acute bronchitis and diffuse acute infectious bronchiolitis (DAIB) are examples. The former is usually caused by a viral illness; the latter by Mycoplasma pneumoniae, influenza, and Haemophilus influenzae. Causes of chronic cough in the adult include chronic bronchitis, non-infectious bronchiolitis, and non-cystic fibrosis bronchiectasis. SUMMARY: Supportive measures are recommended for acute bronchitis and antibiotic use is discouraged. Antibiotics may be needed for DAIB. Smoking cessation and bronchodilators can control cough in chronic bronchitis. Therapeutic approaches for non-infectious bronchiolitis depend on the varied etiology. The hallmark of bronchiectasis is a chronic infection of the airways, and antibiotics, mucus clearance measures, and bronchodilators are all supportive.