Immune checkpoint gene VSIR predicts patient prognosis in acute myeloid leukemia and myelodysplastic syndromes.

BACKGROUND: Immune checkpoint proteins play critical functions during the immune response to cancer and have been targeted by immune checkpoint blockade therapy. V-domain Ig suppressor of T cell activation (VSIR) is one of these immune checkpoint genes and has been investigated extensively in recent years due to its conflicting roles in cancer immunity. Specifically, in acute myeloid leukemia (AML), the prognostic value of VSIR is debated. RESULTS: In both patient tumor samples and cancer cell lines we find that VSIR has the highest expression in AML out of all cancer types and, in AML, has the highest expression out of all other immune checkpoint genes. Survival analysis indicated that AML patients with higher VSIR expression have significantly shorter survival than those patients with lower expression, even within established AML subgroups (e.g., FAB subtypes). Importantly, VSIR expression is predictive of progression from myelodysplastic syndromes (MDS) patients into AML, suggesting its potential role during the very early stage of AML development and progression. In addition to AML, VSIR also demonstrates prognostic values in other cancer types, including multiple myeloma and mesothelioma. CONCLUSION: In summary, our analyses revealed the prognostic value of VSIR and its potential as a target for immunotherapy, especially in AML.

A B-Raf V600E gene signature for melanoma predicts prognosis and reveals sensitivity to targeted therapies.

BACKGROUND: B-Raf V600E mutations account for about half of all skin cutaneous melanoma cases, and patients with this mutation are sensitive to BRAF inhibitors. However, aberrations in other genes in the MAPK/ERK pathway may cascade a similar effect as B-Raf V600E mutations, rendering those patients sensitive to BRAF inhibitors. We rationalized that defining a signature based on B-Raf pathway activity may be more informative for prognosis and drug sensitivity prediction than a binary indicator such as mutation status. METHODS: In this study, we defined a B-Raf signature score using RNA-seq data from TCGA. A higher score is shown to not only predict B-Raf mutation status, but also predict other aberrations that could similarly activate the MAPK/ERK pathway, such as B-Raf amplification, RAS mutation, and EGFR amplification. RESULTS: We showed that patients dichotomized by the median B-Raf score is more significantly stratified than by other metrics of measuring B-Raf aberration, such as mutation status, gene expression, and protein expression. We also demonstrated that high B-Raf score predicts higher sensitivity to B-Raf inhibitors SB590885 and PLX4720, as expected, but also correlated with sensitivity to drugs targeting other relevant oncogenic pathways. CONCLUSION: The BRAF signature may better help guide targeted therapy for melanoma, and such a framework can be applied to other cancers and mutations to provide more information than mutation status alone.

Chr20q Amplification Defines a Distinct Molecular Subtype of Microsatellite Stable Colorectal Cancer.

Colorectal cancer is the third leading cause of cancer-related death in the United States. About 15% of colorectal cancers are associated with microsatellite instability (MSI) due to loss of function in the DNA mismatch repair pathway. This subgroup of patients has better survival rates and is more sensitive to immunotherapy. However, it remains unclear whether microsatellite stable (MSS) patients with colorectal cancer can be further stratified into subgroups with differential clinical characteristics. In this study, we analyzed The Cancer Genome Atlas data and found that Chr20q amplification is the most frequent copy number alteration that occurs specifically in colon (46%) and rectum (61%) cancer and is mutually exclusive with MSI. Importantly, MSS patients with Chr20q amplification (MSS-A) were associated with better recurrence-free survival compared with MSS patients without Chr20q amplification (MSS-N; P = 0.03). MSS-A tumors were associated with high level of chromosome instability and low immune infiltrations. In addition, MSS-A and MSS-N tumors were associated with somatic mutations in different driver genes, with high frequencies of mutated TP53 in MSS-A and mutated KRAS and BRAF in MSS-N. Our results suggest that MSS-A and MSS-N represent two subtypes of MSS colorectal cancer, and such stratification may be used to improve therapeutic treatment in an individualized manner. SIGNIFICANCE: This study shows that chromosome 20q amplification occurs predominately in microsatellite-stable colorectal cancer and defines a distinct subtype with good prognosis, high chromosomal instability, distinct mutation profiles, and low immune infiltrations.

Key Players and Biomarkers of the Adaptive Immune System in the Pathogenesis of Sarcoidosis.

Sarcoidosis is a systemic inflammatory disease characterized by development of granulomas in the affected organs. Sarcoidosis is often a diagnosis of exclusion, and traditionally used tests for sarcoidosis demonstrate low sensitivity and specificity. We propose that accuracy of diagnosis can be improved if biomarkers of altered lymphocyte populations and levels of signaling molecules involved in disease pathogenesis are measured for patterns suggestive of sarcoidosis. These distinctive biomarkers can also be used to determine disease progression, predict prognosis, and make treatment decisions. Many subsets of T lymphocytes, including CD8+ T-cells and regulatory T-cells, have been shown to be dysfunctional in sarcoidosis, and the predominant CD4+ T helper cell subset in granulomas appears to be a strong indicator of disease phenotype and outcome. Studies of altered B cell populations, B cell signaling molecules, and immune complexes in sarcoidosis patients reveal promising biomarkers as well as possible explanations of disease etiology. Furthermore, examined biomarkers raise questions about new treatment methods and sarcoidosis antigens.

Factors affecting lead release in sodium silicate-treated partial lead service line replacements.

Water quality parameters affecting sodium silicate performance in partial lead service line replacements were examined using a fractional factorial experimental design and static pipe systems. An external copper wire was used to create a galvanic connection between a former lead service line and a new copper pipe. The pipe systems were filled with lab prepared water made to mimic real water quality. Water was changed on a three times per week basis. A 2(4-1) fractional factorial design was used to evaluate the impact of alkalinity (15 mg L(-1) or 250 mg L(-1) as CaCO3), nitrate (1 mg L(-1) or 7 mg L(-1) as N), natural organic matter (1 mg L(-1) or 7 mg L(-1) as dissolved organic carbon), and disinfectant type (1 mg L(-1) chlorine or 3 mg L(-1) monochloramine), resulting in eight treatment conditions. Fractional factorial analysis revealed that alkalinity, natural organic matter and monochloramine had a significant positive effect on galvanic current. Natural organic matter and monochloramine also had a significant positive effect with respect to both total and dissolved lead release. For the treatment conditions examined, 67-98% of the lead released through galvanic currents was stored as corrosion scales and predominantly comprised of particulate lead (96.1-99.9%) for all eight treatments. The use of monochloramine and the presence of natural organic matter (7 mg L(-1)) were not favourable for corrosion control in sodium silicate-treated partial lead service line replacements, although further studies would be required to characterize optimal water quality parameters for specific water quality types. For utilities operating with sodium silicate as a corrosion inhibitor, this work offers further evidence regarding the consideration of chlorine as a secondary disinfectant instead of monochloramine, as well as the value of controlling natural organic matter in distributed water.

Differential subcellular localization renders HAI-2 a matriptase inhibitor in breast cancer cells but not in mammary epithelial cells.

The type 2 transmembrane serine protease matriptase is under tight control primarily by the actions of the integral membrane Kunitz-type serine protease inhibitor HAI-1. Growing evidence indicates that HAI-2 might also be involved in matriptase inhibition in some contexts. Here we showed that matriptase inhibition by HAI-2 depends on the subcellular localizations of HAI-2, and is observed in breast cancer cells but not in mammary epithelial cells. HAI-2 is co-expressed with matriptase in 21 out of 26 human epithelial and carcinoma cells examined. HAI-2 is also a potent matriptase inhibitor in solution, but in spite of this, HAI-2 inhibition of matriptase is not observed in all contexts where HAI-2 is expressed, unlike what is seen for HAI-1. Induction of matriptase zymogen activation in mammary epithelial cells results in the formation of matriptase-HAI-1 complexes, but matriptase-HAI-2 complexes are not observed. In breast cancer cells, however, in addition to the appearance of matriptase-HAI-1 complex, three different matriptase-HAI-2 complexes, are formed following the induction of matriptase activation. Immunofluorescent staining reveals that activated matriptase is focused at the cell-cell junctions upon the induction of matriptase zymogen activation in both mammary epithelial cells and breast cancer cells. HAI-2, in contrast, remains localized in vesicle/granule-like structures during matriptase zymogen activation in human mammary epithelial cells. In breast cancer cells, however, a proportion of the HAI-2 reaches the cell surface where it can gain access to and inhibit active matriptase. Collectively, these data suggest that matriptase inhibition by HAI-2 requires the translocation of HAI-2 to the cell surface, a process which is observed in some breast cancer cells but not in mammary epithelial cells.