Human MAIT cells endowed with HBV specificity are cytotoxic and migrate towards HBV-HCC while retaining antimicrobial functions

Background & Aims: Virus-specific T cell dysfunction is a common feature of HBV-related hepatocellular carcinoma (HBV-HCC). Conventional T (ConT) cells can be redirected towards viral antigens in HBV-HCC when they express an HBV-specific receptor; however, their efficacy can be impaired by liver-specific physical and metabolic features. Mucosal-associated invariant T (MAIT) cells are the most abundant innate-like T cells in the liver and can elicit potent intrahepatic effector functions. Here, we engineered ConT and MAIT cells to kill HBV expressing hepatoma cells and compared their functional properties. Methods: Donor-matched ConT and MAIT cells were engineered to express an HBV-specific T cell receptor (TCR). Cytotoxicity and hepatocyte homing potential were investigated using flow cytometry, real-time killing assays, and confocal microscopy in 2D and 3D HBV-HCC cell models. Major histocompatibility complex (MHC) class I-related molecule (MR1)-dependent and MR1-independent activation was evaluated in an Escherichia coli THP-1 cell model and by IL-12/IL-18 stimulation, respectively. Results: HBV TCR-MAIT cells demonstrated polyfunctional properties (CD107a, interferon [IFN] γ, tumour necrosis factor [TNF], and IL-17A) with strong HBV target sensitivity and liver-homing chemokine receptor expression when compared with HBV TCR-ConT cells. TCR-mediated lysis of hepatoma cells was comparable between the cell types and augmented in the presence of inflammation. Coculturing with HBV+ target cells in a 3D microdevice mimicking aspects of the liver microenvironment demonstrated that TCR-MAIT cells migrate readily towards hepatoma targets. Expression of an ectopic TCR did not affect the ability of the MAIT cells to be activated via MR1-presented bacterial antigens or IL-12/IL-18 stimulation. Conclusions: HBV TCR-MAIT cells demonstrate anti-HBV functions without losing their endogenous antimicrobial mechanisms or hepatotropic features. Our results support future exploitations of MAIT cells for liver-directed immunotherapies. Lay summary: Chronic HBV infection is a leading cause of liver cancer. T cell receptor (TCR)-engineered T cells are patients’ immune cells that have been modified to recognise virus-infected and/or cancer cells. Herein, we evaluated whether mucosal-associated invariant T cells, a large population of unconventional T cells in the liver, could recognise and kill HBV infected hepatocytes when engineered with an HBV-specific TCR. We show that their effector functions may exceed those of conventional T cells currently used in the clinic, including antimicrobial properties and chemokine receptor profiles better suited for targeting liver tumours

Proteogenomics decodes the evolution of human ipsilateral breast cancer

Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy

PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures

Motivation: MicroRNAs (miRNAs) are short single-stranded non-coding molecules that usually function as negative regulators to silence or suppress gene expression. Due to interested in the dynamic nature of the miRNA and reduced microarray and sequencing costs, a growing number of researchers are now measuring high-dimensional miRNAs expression data using repeated or multiple measures in which each individual has more than one sample collected and measured over time. However, the commonly used site-by-site multiple testing may impair the value of repeated or multiple measures data by ignoring the inherent dependent structure, which lead to problems including underpowered results after multiple comparison correction using false discovery rate (FDR) estimation and less biologically meaningful results. Hence, new methods are needed to tackle these issues. Results: We propose a penalized regression model incorporating grid search method (PGS), for analyzing association study of high-dimensional microRNA expression data with repeated measures. The development of this analytical framework was motivated by a real-world miRNA dataset. Comparisons between PGS and the site-by-site testing revealed that PGS provided smaller phenotype prediction errors and higher enrichment of phenotype-related biological pathways than the site-by-site testing. Simulation study showed that PGS provided more accurate estimates and higher sensitivity than site-by-site testing with comparable specificities. Availability: R source code for PGS algorithm, implementation example, and simulation study are available for download at https://github.com/feizhe/PGS

Differential inflammatory microRNA and cytokine expression in pulmonary sarcoidosis

Sarcoidosis is a granulomatous disease of unknown etiology. The disease has an important inflammatory and immune component; however, its immunopathogenesis is not completely understood. Recently, the role of microRNAs (miRNAs), the small non-coding RNAs, has attracted attention as both being involved in pathogenesis and serving as disease markers. Accordingly, changes in the expression of some miRNAs have been also associated with different autoimmune pathologies. However, not much is known about the role of miRNAs in sarcoidosis. Therefore, the aim of this study was to compare the level of expression of selected miRNAs in healthy individuals and patients with sarcoidosis. We detected significantly increased level of miR-34a in peripheral blood mononuclear cells isolated from sarcoidosis patients. Moreover, significantly up-regulated levels of interferon (IFN)-γ, IFN-γ inducible protein (IP-10) and vascular endothelial growth factor were detected in sera of patients when compared to healthy subjects. Our results add to a known inflammatory component in sarcoidosis. Changes in the levels of miR-34a may suggest its involvement in the pathology of this disease

Utilizing intraoperative aberrometry and digital eye tracking to develop a novel nomogram for manual astigmatic keratotomy to effectively decrease mild astigmatism during cataract surgery

PURPOSE: The purpose of the study is to develop a novel nomogram and validate with a retrospective comparative study for manual astigmatic keratotomy (MAK) with the assistance of intraoperative aberrometry (Optiwave Refractive Analysis [ORA]) and digital eye tracking (VERION) in mild astigmatic correction enhancement. SETTING: The study was conducted in Honolulu, Hawaii. DESIGN: This was a single-surgeon comparative study with retrospective data collection. METHODS: Sixty consecutive adult cataract surgery cases with regular astigmatism of 1.25 D or less were included for study from April 2016 to April 2017. VERION was used preoperatively in all cases. MAK was performed before phacoemulsification according to the surgeon's own nomogram. ORA then was utilized to obtain the axis and remaining cylinder power after phacoemulsification and intraocular lens implant implantation. MAK extension was performed for eyes with 1 D or more of remaining cylinder. Extensions were carried out slowly and slightly until the amount of cylinder was 1½ D or less under ORA. The mean degrees of extension plus the original MAK plan were calculated to develop the new nomogram. Sixty consecutive similar cases by the same surgeon using the surgeon's nomogram without using ORA/VERION for enhancement were reviewed from April 2015 to April 2016 for comparison. All patients included in this study signed the consent form. RESULTS: Using Alpins vector analysis for comparison, the proportion of patients with cylinder <0.5 D 3 months postoperatively was 87% in the ORA/VERION group compared to 70% in the non-ORA/VERION group (P < 0.05). Better than 20/25 best-corrected visual acuity was achieved more in the ORA/VERION group compared to non-ORA/VERION group. CONCLUSIONS: This novel nomogram developed by the surgeon may have better outcomes than the old surgeon's own nomogram. Further prospective control study is needed to validate the efficacy. If validated, those surgeons who do not have ORA/VERION can hopefully use this nomogram with greater success

New Target Genes of MITF-Induced microRNA-211 Contribute to Melanoma Cell Invasion

The non-coding microRNAs (miRNA) have tissue- and disease-specific expression patterns. They down-regulate target mRNAs, which likely impacts on most fundamental cellular processes. Differential expression patterns of miRNAs are currently being exploited for identification of biomarkers for early disease diagnosis, prediction of progression for melanoma and other cancers and as promising drug targets, since they can easily be inhibited or replaced in a given cellular context. Before successfully manipulating miRNAs in clinical settings, their precise expression levels, endogenous functions and thus their target genes have to be determined. MiR-211, a melanocyte lineage-specific small non-coding miRNA, is located in an intron of TRPM1, a target gene of the microphtalmia-associated transcription factor (MITF). By transcriptionally up-regulating TRPM1, MITF, which is critical for both melanocyte differentiation and survival and for melanoma progression, indirectly drives the expression of miR-211. Expression of this miRNA is often reduced in melanoma samples. Here, we investigated functional roles of miR-211 by identifying and studying new target genes. We show that MITF-correlated miR-211 expression levels are mostly but not always reduced in a panel of 11 melanoma cell lines and in primary and metastatic melanoma compared to normal melanocytes and nevi, respectively. MiR-211 itself only marginally impacted on cell invasion and migration, while perturbation of some new miR-211 target genes, such as AP1S2, SOX11, IGFBP5, and SERINC3 significantly increased invasion. These results and the variable expression levels of miR-211 raise serious doubts on the value of miR-211 as a melanoma tumor-suppressing miRNA and/or as a biomarker for melanoma

Comparison of a healthy miRNome with melanoma patient miRNomes: are microRNAs suitable serum biomarkers for cancer?

MiRNAs are increasingly recognized as biomarkers for the diagnosis of cancers where they are profiled from tumor tissue (intracellular miRNAs) or serum/plasma samples (extracellular miRNAs). To improve detection of reliable biomarkers from blood samples, we first compiled a healthy reference miRNome and established a well-controlled analysis pipeline allowing for standardized quantification of circulating miRNAs. Using whole miRNome and custom qPCR arrays, miRNA expression profiles were analyzed in 126 serum, whole blood and tissue samples of healthy volunteers and melanoma patients and in primary melanocyte and keratinocyte cell lines. We found characteristic signatures with excellent prognostic scores only in late stage but not in early stage melanoma patients. Upon comparison of melanoma tissue miRNomes with matching serum samples, several miRNAs were identified to be exclusively tissue-derived (miR-30b-5p, miR-374a-5p and others) while others had higher expression levels in serum (miR-3201 and miR-122-5p). Here we have compiled a healthy and widely applicable miRNome from serum samples and we provide strong evidence that levels of cell-free miRNAs only change significantly at later stages of melanoma progression, which has serious implications for miRNA biomarker studies in cancer

Representation of Race and Gender in News-Gazette Crime Coverage (Initial Report - December 15, 2015)

This study set out to analyze demographic characteristics of criminal suspects included in crime reporting published by the Champaign (Illinois) News-Gazette newspaper, and to compare the demographics of suspects in the news to the demographics of suspects arrested or jailed in Champaign County. To our knowledge, no such study has previously been performed for any news outlet in Champaign County. Examining newspaper coverage over a three-month period from June 1, 2015 to September 1, 2015, we found differences between the demographic characteristics of Champaign County crime suspects in the news and those of suspects in county arrest and jail booking records from the same time period. Black suspects were overrepresented in news coverage relative to arrest and jail booking records, while White suspects were underrepresented. Our analysis of suspect imagery in the news found that White suspects were underrepresented while Black suspects were overrepresented in news photographs of crime suspects, relative to their proportions in arrest and jail booking records. In addition, males were overrepresented as suspects in crime stories and females were underrepresented, relative to arrest and jail booking records.Ope