Grading gastrointestinal dysplasia and what to call it when you don't know what it is

Dysplasia in the gastrointestinal tract is defined as intraepithelial neoplasia (IEN) according to the WHO nomenclature. Neoplastic growth in the gastrointestinal tract evolves through stepwise tumour progression in which consecutive morphological stages are characterized by increasing genetic instability accompanied by specific genetic alterations. Invasive cancer is preceded by non-invasive precursor stages and the clonal epithelial cell proliferation in these pre-invasive stages is diagnosed as dysplasia or IEN. Dysplasia is therefore a marker for cancer risk and guides surveillance. Dysplasia is conventionally graded using a two-tier system and low- and high-grade dysplasia convey different connotations regarding cancer risk. This perspective argues that the critical differential diagnosis is the one between neoplastic and non-neoplastic epithelial cell proliferations and the relevance of grading dysplasia is questionable. It is furthermore expected that a molecular signature will predict the propensity to invasive carcinoma more accurately than routine histopathology in the near future. Research in this field needs to focus on a combination of biomarkers representing genetic instability, clonal mutations, and genetic clonal divergence.     

How to deal with the early GWAS data when imputing and combining different arrays is necessary

Genotype imputation has become an essential tool in the analysis of genome-wide association scans. This technique allows investigators to test association at ungenotyped genetic markers, and to combine results across studies that rely on different genotyping platforms. In addition, imputation is used within long-running studies to reuse genotypes produced across generations of platforms. Typically, genotypes of controls are reused and cases are genotyped on more novel platforms yielding a case-control study that is not matched for genotyping platforms. In this study, we scrutinize such a situation and validate GWAS results by actually retyping top-ranking SNPs with the Sequenom MassArray platform. We discuss the needed quality controls (QCs). In doing so, we report a considerable discrepancy between the results from imputed and retyped data when applying recommended QCs from the literature. These discrepancies appear to be caused by extrapolating differences between arrays by the process of imputation. To avoid false positive results, we recommend that more stringent QCs should be applied. We also advocate reporting the imputation quality measure (R(T)(2)) for the post-imputation QCs in publications.     

Further evidence that CENP-C is a necessary component of active centromeres: studies of a dic(X; 15) with simultaneous immunofluorescence and FISH

The stability of certain dicentric chromosomes in humans seemsto result from inactivation of one centromere, yielding a functionallymonocentric chromosome. Centromere protein C (CENP-C) was previouslyshown to be present at active centromeres but absent from theinactive centromere of one homologous dicentric rearrangement.We have combined indirect immunofluorescence detection of CENP-Cand fluorescence in situ hybridization with chromo-some-specific     

Stressful life‐events exposure is associated with 17‐year mortality,but it is health‐related events that prove predictive

Objectives Despite the widely‐held view that psychological stress is a major cause of poor health, few studies have examined the relationship between stressful life‐events exposure and death. The present analyses examined the association between overall life‐events stress load, health‐related and health‐unrelated stress, and subsequent all‐cause mortality. Design This study employed a prospective longitudinal design incorporating time‐varying covariates. Methods Participants were 968 Scottish men and women who were 56 years old. Stressful life‐events experience for the preceding 2 years was assessed at baseline, 8–9 years and 12–13 years later. Mortality was tracked for the subsequent 17 years during which time 266 participants had died. Cox's regression models with time‐varying covariates were applied. We adjusted for sex, occupational status, smoking, BMI, and systolic blood pressure. Results Overall life‐events numbers and their impact scores at the time of exposure and the time of assessment were associated with 17‐year mortality. Health‐related event numbers and impact scores were strongly predictive of mortality. This was not the case for health‐unrelated events. Conclusions The frequency of life‐events and the stress load they imposed were associated with all‐cause mortality. However, it was the experience and impact of health‐related, not health‐unrelated, events that proved predictive. This reinforces the need to disaggregate these two classes of exposures in studies of stress and health outcomes.     

Negative selection of the T‐cell repertoire: where and when does it occur?

Summary:  Because of the use of somewhat artificial models for the elucidation of negative selection [superantigen, T-cell receptor (TCR) transgenic mice], there is still considerable uncertainty at what stages of T-cell development negative selection can occur and whether it becomes manifest as developmental arrest, lineage diversion, or induction of apoptotic cell death. Here, experimental evidence is reviewed that excludes developmental arrest and lineage diversion as the sole mechanisms of negative selection. The data emphasize that both CD4⁺CD8⁺ double-positive cortical as well as semi-mature, single-positive, medullary thymocytes are targets of deletion in experimental models employing superantigen and TCR transgenic mice with premature as well as 'timely' onset of TCR expression.     

Hypermethylation of CpG islands is associated with increasing chromosomal damage in chinese lead‐exposed workers

Lead is a widely existing environmental pollutant with potential carcinogenicity. To investigate the association of blood lead level (B‐Pb) with potential chromosomal damage and cancer, we analyzed micronucleus (MN) frequency of peripheral blood lymphocytes (PBLs) and the methylation status of six human tumor suppressor genes (TSGs) post lead exposure. In the study, 147 lead‐exposed workers were divided into two groups according to their B‐Pb P₅₀ value, with other 50 lead‐unexposed workers as a control group. The cytokinesis‐blocked micronucleus (CBMN) assay was performed to detect chromosomal damage of PBLs of both lead‐exposed and ‐unexposed workers. The methylation‐specific polymerase chain reaction (MSP‐PCR) was further used to examine the methylation status of six TSGs (GSTP1, hMLH1, MGMT, p14, p15, and p16). Results showed that MN frequencies of high B‐Pb workers 8.1 ± 3.1‰ and low B‐Pb workers 5.7 ± 2.3‰ were significantly higher than that of control group 2.8 ± 1.9‰ (P < 0.01), while the MN frequency of high B‐Pb workers was also higher than that of the low B‐Pb workers (P < 0.01). The MN frequency in PBLs of lead‐exposed group with the methylated TSGs was significantly higher than that in PBLs with the unmethylated TSGs (P < 0.05). Notably, the CpG island methylator phenotype (CIMP) correlated with chromosome damage (P < 0.05). Additionally, workers with high B‐Pb had higher chromosome damage than those with low B‐Pb (P < 0.05). Taken altogether, the results suggest that lead‐exposed workers with CIMP positive and high B‐Pb have a higher risk of being vulnerable to tumorigenesis. Environ. Mol. Mutagen. 59:549–556, 2018. © 2018 Wiley Periodicals, Inc.     

Micronucleus incidence and their chromosomal origin related to therapy in acute lymphoblastic leukemia (ALL) patients: detection by micronucleus and FISH techniques.

Micronucleus assay and dual color-fluorescence in situ hybridization (DC-FISH), using centromere-specific and whole chromosome-specific painting probes, are considered a useful screening test to determine the incidence of micronucleus, their origin and contents. The patients with acute lymphoblastic leukemia (ALL), who had undergone chemotherapy, were analysed before and after treatment with vincristine, methotrexate, daunomycin, prednisone, and asparaginase. The incidence of micronuclei after the antileukemic agent treatment was significantly higher than before the treatment. Application of DC-FISH using a combination of whole chromosome-specific painting probes and the same chromosome-specific alpha-satellite centromeric probe showed that there were no significant differences in the micronucleus incidence for any specific chromosome (chromosomes 7, 8, 11, 17, X, and Y). There were no significant differences between the incidence of centromere-positive micronuclei and the incidence of centromere-negative micronucleus. We concluded that antileukemic agents induced the somatic genetic damage but this damage is not related to any specific chromosome studied.     

The CD4+ T‐cell epitope‐binding register is a critical parameter when generating functional HLA‐DR tetramers with promiscuous peptides

Detection of CD4⁺ T cells specific for tumor‐associated antigens is critical to investigate the spontaneous tumor immunosurveillance and to monitor immunotherapy protocols in patients. We investigated the ability of HLA‐DR^*1101 multimers to detect CD4⁺ T cells specific for three highly promiscuous MAGE‐A3 derived peptides: MAGE‐A3_191–205 (p39), MAGE‐A3_281–295 (p57) and MAGE‐A3_286–300 (p58). Tetramers stained specific CD4⁺ T cells only when loaded with p39, although all peptides activated the specific T cells when presented by plastic‐bound HLA‐DR^*1101 monomers. This suggested that tetramer staining ability was determined by the mode rather than the affinity of peptide binding to HLA‐DR^*1101. We hypothesized that peptides should bear a single P1 anchor residue to bind all arms of the multimer in a homogeneous register to generate peptide‐HLA‐DR conformers with maximal avidity. Bioinformatics analysis indicated that p39 contained one putative P1 anchor residue, whereas the other two peptides contained multiple ones. Designing p57 and p58 analogues containing a single anchor residue generated HLA‐DR^*1101 tetramers that stained specific CD4⁺ T cells. Producing HLA‐DR^*1101 monomers linked with the optimized MAGE‐A3 analogues, but not with the original epitopes, further improved tetramer efficiency. Optimization of CD4⁺ T‐cell epitope‐binding registers is thus critical to generate functional HLA‐DR tetramers.     

Clinical application of whole‐genome low‐coverage next‐generation sequencing to detect and characterize balanced chromosomal translocations

Individuals carrying balanced translocations have a high risk of birth defects, recurrent spontaneous abortions and infertility. Thus, the detection and characterization of balanced translocations is important to reveal the genetic background of the carriers and to provide proper genetic counseling. Next‐generation sequencing (NGS), which has great advantages over other methods such as karyotyping and fluorescence in situ hybridization (FISH), has been used to detect disease‐associated breakpoints. Herein, to evaluate the application of this technology to detect balanced translocations in the clinic, we performed a parental study for prenatal cases with unbalanced translocations. Eight candidate families with potential balanced translocations were investigated using two strategies in parallel, low‐coverage whole‐genome sequencing (WGS) followed‐up by Sanger sequencing and G‐banding karyotype coupled with FISH. G‐banding analysis revealed three balanced translocations, and FISH detected two cryptic submicroscopic balanced translocations. Consistently, WGS detected five balanced translocations and mapped all the breakpoints by Sanger sequencing. Analysis of the breakpoints revealed that six genes were disrupted in the four apparently healthy carriers. In summary, our result suggested low‐coverage WGS can detect balanced translocations reliably and can map breakpoints precisely compared with conventional procedures. WGS may replace cytogenetic methods in the diagnosis of balanced translocation carriers in the clinic.     

Lopinavir/ritonavir is associated with pneumonia resolution in COVID‐19 patients with influenza coinfection: A retrospective matched‐pair cohort study

During the early stages of the pandemic, some coronavirus disease (COVID‐19) patients were misdiagnosed as having influenza, which aroused the concern that some deaths attributed to influenza were actually COVID‐19‐related. However, little is known about whether coinfection with influenza contributes to severity of COVID‐19 pneumonia, and the optimal therapeutic strategy for these patients. We retrospectively studied 128 hospitalized patients with COVID‐19 pneumonia. All patients were positive severe acute respiratory syndrome coronavirus 2 positive by nucleic acid detection. Sixty‐four cases were coinfected with influenza A/B and the other 64 were influenza negative, matched by age, sex, and days from onset of symptoms. Among the 64 coinfected patients, 54 (84.4%) were coinfected with influenza A, and 10 (15.6%) with influenza B. The median duration of viral shedding time from admission was longer for patients with influenza coinfection (17.0 days) than for those without influenza coinfection (12.0 days) (P < .001). The multivariable Cox proportional hazards model showed that the hazards ratio of resolution in lung involvement was 1.878 (P = .020) for patients administered lopinavir/ritonavir, compared with those not administered lopinavir/ritonavir (95% confidence interval: 1.103‐3.196). Among influenza coinfected patients, those treated with lopinavir/ritonavir exhibited faster pneumonia resolution within 2 weeks after symptom onset (37% vs 1%; P = .001). There was no difference in lung involvement between influenza coinfected and noninfected groups. Lopinavir/ritonavir eliminated the difference of lung involvement between influenza coinfected and noninfected groups, indicating that lopinavir/ritonavir is associated with pneumonia resolution in COVID‐19.