Tetraspanin CD82 Correlates with and May Regulate S100A7 Expression in Oral Cancer.

Many metastatic cancers with poor prognoses correlate to downregulated CD82, but exceptions exist. Understanding the context of this correlation is essential to CD82 as a prognostic biomarker and therapeutic target. Oral squamous cell carcinoma (OSCC) constitutes over 90% of oral cancer. We aimed to uncover the function and mechanism of CD82 in OSCC. We investigated CD82 in human OSCC cell lines, tissues, and healthy controls using the CRISPR-Cas9 gene knockout, transcriptomics, proteomics, etc. CD82 expression is elevated in CAL 27 cells. Knockout CD82 altered over 300 genes and proteins and inhibited cell migration. Furthermore, CD82 expression correlates with S100 proteins in CAL 27, CD82KO, SCC-25, and S-G cells and some OSCC tissues. The 37-50 kDa CD82 protein in CAL 27 cells is upregulated, glycosylated, and truncated. CD82 correlates with S100 proteins and may regulate their expression and cell migration. The truncated CD82 explains the invasive metastasis and poor outcome of the CAL 27 donor. OSCC with upregulated truncated CD82 and S100A7 may represent a distinct subtype with a poor prognosis. Differing alternatives from wild-type CD82 may elucidate the contradictory functions and pave the way for CD82 as a prognostic biomarker and therapeutic target.

UBE2T promotes breast cancer tumor growth by suppressing DNA replication stress.

Breast cancer is a leading cause of cancer-related deaths among women, and current therapies benefit only a subset of these patients. Here, we show that ubiquitin-conjugating enzyme E2T (UBE2T) is overexpressed in patient-derived breast cancer samples, and UBE2T overexpression predicts poor prognosis. We demonstrate that the transcription factor AP-2 alpha (TFAP2A) is necessary for the overexpression of UBE2T in breast cancer cells, and UBE2T inhibition suppresses breast cancer tumor growth in cell culture and in mice. RNA sequencing analysis identified interferon alpha-inducible protein 6 (IFI6) as a key downstream mediator of UBE2T function in breast cancer cells. Consistently, UBE2T inhibition downregulated IFI6 expression, promoting DNA replication stress, cell cycle arrest, and apoptosis and suppressing breast cancer cell growth. Breast cancer cells with IFI6 inhibition displayed similar phenotypes as those with UBE2T inhibition, and ectopic IFI6 expression in UBE2T-knockdown breast cancer cells prevented DNA replication stress and apoptosis and partly restored breast cancer cell growth. Furthermore, UBE2T inhibition enhanced the growth-suppressive effects of DNA replication stress inducers. Taken together, our study identifies UBE2T as a facilitator of breast cancer tumor growth and provide a rationale for targeting UBE2T for breast cancer therapies.

Changes in the Transcriptome and Chromatin Landscape in BRAFi-Resistant Melanoma Cells.

Metastatic and drug-resistant melanoma are leading causes of skin cancer-associated death. Mitogen-associated protein kinase (MAPK) pathway inhibitors and immunotherapies have provided substantial benefits to patients with melanoma. However, long-term therapeutic efficacy has been limited due to emergence of treatment resistance. Despite the identification of several molecular mechanisms underlying the development of resistant phenotypes, significant progress has still not been made toward the effective treatment of drug-resistant melanoma. Therefore, the identification of new targets and mechanisms driving drug resistance in melanoma represents an unmet medical need. In this study, we performed unbiased RNA-sequencing (RNA-seq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify new targets and mechanisms that drive resistance to MAPK pathway inhibitors targeting BRAF and MAPK kinase (MEK) in BRAF-mutant melanoma cells. An integrative analysis of ATAC-seq combined with RNA-seq showed that global changes in chromatin accessibility affected the mRNA expression levels of several known and novel genes, which consequently modulated multiple oncogenic signaling pathways to promote resistance to MAPK pathway inhibitors in melanoma cells. Many of these genes were also associated with prognosis predictions in melanoma patients. This study resulted in the identification of new genes and signaling pathways that might be targeted to treat MEK or BRAF inhibitors resistant melanoma patients. The present study applied new and advanced approaches to identify unique changes in chromatin accessibility regions that modulate gene expression associated with pathways to promote the development of resistance to MAPK pathway inhibitors.

The BRD9/7 Inhibitor TP-472 Blocks Melanoma Tumor Growth by Suppressing ECM-Mediated Oncogenic Signaling and Inducing Apoptosis.

Melanoma accounts for the majority of all skin cancer-related deaths and only 1/3rd of melanoma patients with distal metastasis survive beyond five years. However, current therapies including BRAF/MEK targeted therapies or immunotherapies only benefit a subset of melanoma patients due to the emergence of intrinsic or extrinsic resistance mechanisms. Effective treatment of melanoma will thus require new and more effective therapeutic agents. Towards the goal of identifying new therapeutic agents, we conducted an unbiased, druggable epigenetic drug screen using a library of 32 epigenetic inhibitors obtained from the Structural Genome Consortium that targets proteins encoding for epigenetic regulators. This chemical genetic screening identified TP-472, which targets bromodomain-7/9, as the strongest inhibitor of melanoma growth in both short- and long-term survival assays and in mouse models of melanoma tumor growth. Mechanistically, using a transcriptome-wide mRNA sequencing profile we identified TP-472 treatment downregulates genes encoding various extracellular matrix (ECM) proteins, including integrins, collagens, and fibronectins. Reactome-based functional pathway analyses revealed that many of the ECM proteins are involved in extracellular matrix interactions required for cancer cell growth and proliferation. TP-472 treatment also upregulated several pro-apoptotic genes that can inhibit melanoma growth. Collectively, our results identify BRD7/9 inhibitor TP-472 as a potentially useful therapeutic agent for melanoma therapy.

Berberine, A Phytoalkaloid, Inhibits Inflammatory Response Induced by LPS through NF-Kappaß Pathway: Possible Involvement of the IKKα.

Berberine (BBR), a plant alkaloid, is known for its therapeutic properties of anticancer, cardioprotective, antidiabetic, hypolipidemic, neuroprotective, and hepatoprotective activities. The present study was to determine the molecular mechanism of BBR's pharmacological activity in human monocytic (THP-1) cells induced by arachidonic acid (AA) or lipopolysaccharide (LPS). The effect of BBR on AA/LPS activated proinflammatory markers including TNF-α, MCP-1, IL-8 and COX-2 was measured by ELISA or quantitative real-time PCR. Furthermore, the effect of BBR on LPS-induced NF-κB translocation was determined by immunoblotting and confocal microscopy. AA/ LPS-induced TNF-α, MCP-1, IL-6, IL-8, and COX-2 markers were markedly attenuated by BBR treatment in THP-1 cells by inhibiting NF-κB translocation into the nucleus. Molecular modeling studies suggested the direct interaction of BBR to IKKα at its ligand binding site, which led to the inhibition of the LPS-induced NF-κB translocation to the nucleus. Thus, the present study demonstrated the anti-inflammatory potential of BBR via NF-κB in activated monocytes, whose interplay is key in health and in the pathophysiology of atherosclerotic development in blood vessel walls. The present study findings suggest that BBR has the potential for treating various chronic inflammatory disorders.

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus).

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14-20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

Dry leaf extracts of Tinospora cordifolia (Willd.) Miers attenuate oxidative stress and inflammatory condition in human monocytic (THP-1) cells.

BACKGROUND: Tinospora cordifolia (Willd.) Miers is known for its therapeutic value in Indian traditional medicine for treating diabetes, rheumatoid arthritis, jaundice and cardiac diseases. However, information regarding its protective role against inflammatory diseases at the molecular level is limited. PURPOSE: The objective of the present work is to study the antioxidant and anti-inflammatory effect of alcoholic and water extracts of T. cordifolia (Willd.) Miers leaves in activated human monocytic THP-1 cells. STUDY DESIGN/METHODS: Phytochemical analyses of the dry leaf extracts of T. cordifolia (Willd.) Miers prepared using the solvents alcohol (TCAE) or water (TCWE) are performed employing spectrophotometric methods for estimating total phenolic and flavonoid content, and the plant material was authenticated by detecting T. cordifolia (Willd.) Miers metabolite biomarkers using LC-MS/MS. Arachidonic acid (AA)- and lipopolysaccharide (LPS)-activated human monocytic (THP-1) cells were used as experimental models to investigate the antioxidant and anti-inflammatory activities of the plant extracts. Arachidonic acid (AA)-induced reactive oxygen species (ROS) in THP-1 cells were monitored by confocal microscopy/spectrofluorimetry and transcript of antioxidant enzyme catalase (CAT), by quantitative real time PCR. Lipopolysaccharide (LPS)-induced proinflammatory marker like TNF-α at transcription and protein levels in THP-1 cells were measured by quantitative real-time PCR or ELISA respectively. Further, the effect of T. cordifolia (Willd.) Miers extracts on LPS-induced NF-κB translocation, and IκB and P-IκB protein levels, were studied by immunoblotting and confocal microscopy. RESULTS: T. cordifolia (Willd.) Miers extracts exhibited significant amounts of total phenolic and flavonoid content, and LC-MS/MS analyses detected tinosponone, a TC-specific clerodane-derived diterpene. Both types of extracts attenuated AA-induced ROS generation via enhancing catalase enzyme activity in THP-1 cells. Real time PCR and ELISA experiments revealed that the elevated levels of LPS-induced TNF-α was remarkably attenuated in THP-1 cells pretreated with T. cordifolia (Willd.) Miers extracts. Western blot and confocal microscopy showed that the alcoholic extract's anti-inflammatory activity by attenuating NF-κB translocation into the nucleus in LPS-activated THP-1 cells via the inhibition of IκB degradation in the cytosol. CONCLUSION: Our findings suggest that T. cordifolia (Willd.) Miers dry leaf extracts possess antioxidant and anti-inflammatory properties via upregulation of antioxidant enzymes and attenuation of NF- κB nuclear translocation in activated human monocytic (THP-1) cells, therefore the present study supports our proposed molecular basis for the traditional use of T. cordifolia (Willd.) Miers for treating various inflammatory diseases.

Application of centrality measures in the identification of critical genes in diabetes mellitus.

The connectivity of a protein and its structure is related to its functional properties. Many experimental approaches have been employed for the identification of Diabetes Mellitus (DM) associated candidate genes. Therefore, it is of interest to use var ious graph centrality measures integrated with the genes associated with the human Diabetes Mellitus network for the identification of potential targets. We used 2728 genes known to cause Diabetes Mellitus from Jensenlab (Novo Nordisk Foundation Center for Protein Research, Denmark) for this analysis. A protein-protein interaction network was further constructed using a tool Centralities in Biological Networks (CentiBiN) with 1020 nodes after eliminating the duplicates, parallel edges, self -loop edges and unknown Human Protein Reference Database (HPRD) IDS. We used fourteen centralities measures which are useful in identifying the structural characteristic of individuals in the network. The results of the centrality measures are highly correlated. Thus, we identified genes that are critically associated with DM. We further report the top ten genes of all fourteen centrality measures for further consideration as targets for DM.

Alzheimer's disease care and management: role of information technology.

Alzheimer's disease (AD) an ailment that is supposed to affect people in old age. There are evidences that it might affect others also. The number of elders is increasing as the average life expectancy is increasing. AD afflicts its patients with the dementia and AD might increase in malignance over time. People with cognitive disabilities can be overwhelmed through cognitive prosthetics. With the help of information technology we can enhance the quality of life. Significant achievements are possible with an interdisciplinary approach that includes genomic, genetic, technological and therapeutic measures. The combination and coordination of Bioinformatics facilitates generation of various diagnostic tools for the people who are suffering from Alzheimer's disease. These tools help the care providers also. In this article, we emphasize the literature regarding the use of technology and its methodologies to improve the quality of care for the people with Alzheimer's disease.