An investigation for phylogenetic characterization of human Pancreatic cancer microbiome by 16SrDNA Sequencing and Bioinformatics techniques.

Pancreatic cancer is a significant public health concern, with increasing incidence rates and limited treatment options. Recent studies have highlighted the role of the human microbiome, particularly the gut microbiota, in the development and progression of this disease. Microbial dysbiosis, characterized by alterations in the composition and function of the gut microbiota, has been implicated in pancreatic carcinogenesis through mechanisms involving chronic inflammation, immune dysregulation, and metabolic disturbances. Researchers have identified specific microbial signatures associated with pancreatic cancer, offering potential biomarkers for early detection and prognostication. By leveraging advanced sequencing and bioinformatics tools, scientists have delineated differences in the gut microbiota between pancreatic cancer patients and healthy individuals, providing insights into disease pathogenesis and potential diagnostic strategies. Moreover, the microbiome holds promise as a therapeutic target in pancreatic cancer treatment. Interventions aimed at modulating the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, have demonstrated potential in enhancing the efficacy of existing cancer therapies, including chemotherapy and immunotherapy. These approaches can influence immune responses, alter tumor microenvironments, and sensitize tumors to treatment, offering new avenues for improving patient outcomes and overcoming therapeutic resistance. Overall, understanding the complex interplay between the microbiome and pancreatic cancer is crucial for advancing our knowledge of disease mechanisms and identifying innovative therapeutic strategies. Here we report phylogenetic analysis of the 16S microbial sequences of the pancreatic cancer mice microbiome and corresponding age matched healthy mice microbiome. We successfully identified differentially abundance of microbiota in the pancreatic cancer.

A Study to Investigate the Role of Noncoding RNA miR146 Alpha as a Potential Biomarker in Prostate Cancer.

There is a need for additional biomarkers for the diagnosis and prognosis of prostate cancer. MicroRNAs are a class of non-protein coding RNA molecules that are frequently dysregulated in different cancers including prostate cancer and show promise as diagnostic biomarkers and targets for therapy. Here we describe the role of micro RNA 146 a (miR-146a) which may serve as a diagnostic marker for prostate cancer, as indicated from the data presented in this report. Also, a pilot study indicated differential expression of miR-146a in prostate cancer cell lines and tissues from different racial groups. This report provides a novel insight into understanding the prostate carcinogenesis.

Efferocytosis and the Story of "Find Me," "Eat Me," and "Don't Eat Me" Signaling in the Tumor Microenvironment.

The process of efferocytosis involves removal of dying or dead cells by phagocytosis. Another term "efferosome" is used which means a fluid-filled membrane vesicle which engulfs dead cells. The process of efferocytosis works in coordination with apoptosis because before the contents of apoptotic cells are bleached out, they are engulfed by efferosomes. Thus, the microenvironment is not polluted with toxic enzymes and oxidants. A defect in the apoptotic cell clearance may participate in autoimmunity and chronic inflammation for homeostasis and proper tissue development, for which removal of dead cells is essential. This also protects from chronic inflammation and autoimmunity. In different tumor types and other diseases, efferocytosis has been studied extensively and potential pathways identified. A few of the intermediates in different pathways, which create aggressive and tolerogenic tumor microenvironment, might be considered for therapeutic or interventional purposes. Since the key players in efferocytosis are macrophages and dendritic cells, development of antigen-dependent antitumor immunity is affected by efferocytosis. The literature analysis suggests that efferocytosis is an underappreciated immune checkpoint, perhaps one that might be therapeutically targeted in the setting of cancer. The current status of efferocytosis and its role in tumor microenvironment is discussed in this article.

An Investigation to Study the Role of Novel Rhenium Compounds on Endometrial Uterine Cancer Cell Lines.

Endometrial cancer of the uterus is highly maslignant with an increase rate of morbidity and mortality in both childbearing age and postmenopausal women. Rhenium compounds have been shown to have therapeutic properties against various cancers both in vitro cell lines and in vivo animal models. In this in vitro study, we investigated the effects of a novel group of Rhenium ligands on a uterine cancer cell line. Our initial results showed that these compounds are cytotoxic, induces apoptosis and prevents tubulin polymerization in these uterine cancer cell lines, we also found these novel Rhenium compounds to be noncytocidal to healthy human blood lymphocyte cells, thus proving their safety and efficacy in future translational studies.

Cervical Cancer Prevention in Racially Disparate Rural Populations.

Background: Undergoing a timely Pap smear, high-risk human papilloma virus (HPV)- and colposcopy-based testing can reduce HPV-associated cervical cancer (CC) development in women. However, in rural areas, women and minorities without insurance do not undergo periodic assessment and remain at greater risk of HPV infection and CC. Methods: In this study, 173 women from rural East Texas with various ethnic backgrounds were examined thorough HPV/Pap-based testing and colposcopic assessment. Results: Of the 113 informative cases, 77% (87/113) were positive for high-risk HPV infection and 23% of subjects (26/113) were negative. Associations between HPV positivity with young age (p = 0.002), and a low number of pregnancy (p = 0.004) and births (p = 0.005) were evident. Women with long-term use of contraceptives (OR 1.93, 95% CI, 0.80-4.69) were associated with increased risk of HPV infection. African-American women had a higher risk of abnormal Pap outcome compared to Caucasians (OR 5.31, 95% CI, 0.67-42.0). HPV seemed to be a predictor of abnormal Pap outcome (OR 1.77, 95% CI, 0.48-6.44) in these subjects. Unmarried/widowed/divorced women had an increased abnormal Pap test outcome compared to married women or women living with a partner (p = 0.01), with over 278% increased odds (OR 3.78 at 95% CI, 1.29-11.10). Insured women undergoing periodic checkups were detected early with high-risk HPV infection and abnormal Pap test/colposcopic outcome. Conclusions: Comprehensive and timely screening of uninsured women and minorities in rural East Texas are warranted, which could potentially prevent the onset of HPV-associated CC.

Human Papilloma Virus-Associated Cervical Cancer and Health Disparities.

Cervical cancer develops through persistent infection with high-risk human papilloma virus (hrHPV) and is a leading cause of death among women worldwide and in the United States. Periodic surveillance through hrHPV and Pap smear-based testing has remarkably reduced cervical cancer incidence worldwide and in the USA. However, considerable discordance in the occurrence and outcome of cervical cancer in various populations exists. Lack of adequate health insurance appears to act as a major socioeconomic burden for obtaining cervical cancer preventive screening in a timely manner, which results in disparate cervical cancer incidence. On the other hand, cervical cancer is aggressive and often detected in advanced stages, including African American and Hispanic/Latina women. In this context, our knowledge of the underlying molecular mechanism and genetic basis behind the disparate cervical cancer outcome is limited. In this review, we shed light on our current understanding and knowledge of racially disparate outcomes in cervical cancer.

Role of Microbiome in Carcinogenesis Process and Epigenetic Regulation of Colorectal Cancer.

Epigenetic changes during the development of colorectal cancer (CRC) play a significant role. Along with factors such as diet, lifestyle, and genetics, oncogenic infection, bacteria alone or whole microbiome, has been associated with this tumor type. How gut microbiome contributes to CRC pathogenesis in the host is not fully understood. Most of the epigenetic studies in CRC have been conducted in populations infected with Helicobacter pylori. In the current review, we summarize how the gut microbiota contributes in colon carcinogenesis and the potential role of epigenetic mechanism in gene regulation. We discuss microbiota-mediated initiation and progression of colon tumorigenesis and have also touched upon the role of microbial metabolites as an initiator or an inhibitor for procarcinogenic or antioncogenic activities. The hypothesis of gut microbiota associated CRC revealed the dynamic and complexity of microbial interaction in initiating the development of CRC. In the multifaceted processes of colonic carcinogenesis, gradual alteration of microbiota along with their microenvironment and the potential oncopathogenic microbes mediated modulation of cancer therapy and other factors involved in microbiome dysbiosis leading to the CRC have also been discussed. This review provides a comprehensive summary of the mechanisms of CRC development, the role of microbiome or single bacterial infection in regulating the processes of carcinogenesis, and the intervention by novel therapeutics. Epigenetic mechanism involved in CRC is also discussed.

Methylation and MicroRNA Profiling to Understand Racial Disparities of Prostate Cancer.

Prostate cancer is a serious disease in terms of its high incidence and mortality rate in the USA and around the world. The prostate specific antigen (PSA) has been used for prostate cancer diagnosis and follow-up of treatment but a number of challenges remain. Epigenetic biomarkers, especially methylation and microRNA (miR) biomarkers provide an opportunity for diagnosis, prognosis, and recurrence of prostate cancer. Differential global methylation has shown some promising results. In this chapter, the emphasis is given on those biomarkers which can be assayed noninvasively in a prospective study and in a clinic. Challenges in the field, especially the validation of potential biomarkers, and their potential solutions are provided in this chapter.

Core Canonical Pathways Involved in Developing Human Glioblastoma Multiforme (GBM).

Glioblastoma multiforme (GBM) is the most common and aggressive type of the primary brain tumors with pathologic hallmarks of necrosis and vascular proliferation. The diagnosis of GBM is currently mostly based on histological examination of brain tumor tissues, after radiological characterization and surgical biopsy. The ability to characterize tumors comprehensively at the molecular level raises the possibility that diagnosis can be made based on molecular profiling with or without histological examination, rather than solely on histological phenotype. The development of novel genomic and proteomic techniques will foster in the identification of such diagnostic and prognostic molecular markers. We analyzed the global differential gene expression of a GBM cell line HTB15 in comparison to normal human Astrocytes, and established a few canonical pathways that are important in determining the molecular mechanisms of cancer using global gene expression microarray, coupled with the Ingenuity Pathway Analysis (IPA®). Overall, we revealed a discrete gene expression profile in the experimental model that resembled progression of GBM cancer. The canonical pathway analysis showed the involvement of genes that differentially expressed in such a disease condition that included Inositol pathway, Polo like kinases, nNOS signaling, and Tetrapyrrole biosynthesis. Our findings established that the gene expression pattern of this dreaded brain cancer will probably help the cancer research community by finding out newer therapeutic strategies to combat this dreaded cancer type that leads to the identification of high-risk population in this category, with almost hundred percent mortality rate.

Synthesizing a Cellulase like Chimeric Protein by Recombinant Molecular Biology Techniques.

In order to meet the Renewable Fuels Standard demands for 30 billion gallons of biofuels by the end of 2020, new technologies for generation of cellulosic ethanol must be exploited. Breaking down cellulose by cellulase enzyme is very important for this purpose but this is not thermostable and degrades at higher temperatures in bioreactors. Towards creation of a more ecologically friendly method of rendering bioethanol from cellulosic waste, we attempted to produce recombinant higher temperature resistant cellulases for use in bioreactors. The project involved molecular cloning of genes for cellulose-degrading enzymes based on bacterial source, expressing the recombinant proteins in E. coli and optimizing enzymatic activity. We were able to generate in vitro bacterial expression systems to produce recombinant His-tag purified protein which showed cellulase like activity.

Deciphering the Finger Prints of Brain Cancer Glioblastoma Multiforme from Four Different Patients by Using Near Infrared Raman Spectroscopy.

To explore the effectiveness of Raman spectra to diagnose brain cancer glioblastoma multiforme (GBM), we investigated the Raman spectra of single cell from four different GBM cell lines developed from four different patients and analyzed the spectra. The Raman spectra of brain cancer (GBM) cells were similar in all these cell lines. The results indicate that Raman spectra can offer the experimental basis for the cancer diagnosis and treatment.

Metabolomic Approaches in Cancer Epidemiology.

Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) that can measure hundreds of thousands of unique chemical entities (UCEs). The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other "omics" include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs). In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them.

Epigenetic inhibitors.

Traditional treatments for cancer include chemotherapy, radiation therapy, and surgery. Recently, epigenetic inhibitors have been found to be very effective in cancer treatment. Epigenetic changes such as DNA methylation, histone deacetylation, and microRNA (miRNA) expression are capable of silencing the expression of tumor suppressor genes and inducing oncogenes, leading to clonal proliferation of tumor cells. Methyltransferase inhibitors and histone deacetylase inhibitors have attracted the attention of researchers and clinicians because they provide an alternative therapeutic regime in some diseases, including cancer.Epigenetic changes are characterized by altered gene expression without any changes in the nucleotide sequences of DNA. In addition, epigenetic changes are dynamic and can be reversed by epigenetic inhibitors. Drugs that inhibit DNA methylation or histone deacetylation have been studied for the reactivation of tumor suppressor genes and repression of cancer cell growth. Epigenetic inhibitors work alone or in combination with other therapeutic agents. To date, several epigenetic inhibitors have been approved for cancer treatment. The main challenge in the field of epigenetic inhibitors is their lack of specificity. Their mechanisms of action and potential in treating cancer are described in this article.

Epigenetic approaches in glioblastoma multiforme and their implication in screening and diagnosis.

Epigenetic modifications have been reported in a number of non-germ-line tumor types. Epigenetic modifications to the genome, especially DNA methylation and histone modifications, affect gene expression causing increased risk for cancers and other diseases. We have summarized information about DNA methylation percentages in Glioblastoma multiforme (GBM) line HTB-12, alveolar cell carcinoma, and acute lymphocytic leukemia samples and determined H3 (K27) methyltransferase activity in GBM and leukemia cells and made comparisons to H3 (K27) methyltransferase activity in normal astrocyte, lung, and lymphocyte cells. GBM and alveolar cell carcinoma gDNA possessed lower gDNA methylation percentages compared to normal cells. Methyl-sensitive cut counting analysis (MSCC) showed fold decreases in GBM CpG methylation sites for genes PBK, KIF23, COL6A3, and LOX. There was no significant difference in CpG DNA methylation, but less histone methyltransferase activity in acute lymphocytic leukemia compared to normal cells. GBM possessed increased histone methyltransferase activity compared to normal samples. Challenges in the field in diagnosis and prognosis for cancer risk especially with regard to the results of this work are discussed.

Identification of death receptors DR4 and DR5 in HTB-12 astrocytoma cell lines and determination of TRAIL sensitivity.

Astrocytomas are tumors which arise from astrocytes, cells that form the blood-brain barrier. There are very few drugs that successfully treat brain tumors. In this study, the cytotoxic effects on the HTB-12 astrocytoma cell line by tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) were studied. The presence of the TRAIL receptors, Death receptor 4 (DR4) and Death receptor 5 (DR5), were detected in HTB-12 cells by Enzyme-Linked Immunosorbent Assay (ELISA). Cytotoxicity assay by Trypan Blue Exclusion Method showed effective cell killing by TRAIL treatment. Thus, the presence of death receptors and TRAIL efficacy raises the therapeutic potential for this type of brain tumor.

Search for a diagnostic/prognostic biomarker for the brain cancer glioblastoma multiforme by 2D-DIGE-MS technique.

The prognosis of patients with glioblastoma multiforme, the most malignant adult glial brain tumor, remains poor in spite of advances in treatment procedures, including surgical resection, irradiation, and chemotherapy. Genetic heterogeneity of glioblastoma warrants extensive studies to gain a thorough understanding of the biology of this tumor. While there have been several studies of global transcript profiling of glioma with the identification of gene signatures for diagnosis and disease management, translation into clinics is yet to happen. In the present study, we report a novel proteomic approach by using two-dimensional difference gel electrophoresis followed by spot picking and analysis of proteins/peptides by Mass spectrometry. We report at least ten different novel proteins/peptides as identified by this technique which are differentially expressed in this cancer and could be of further importance for diagnostic, therapeutic, and prognostic approaches.

C-6 Ceramide Induces p53 Dependent Apoptosis in Human Astrocytoma Grade4 (Glioblastoma Multiforme) Cells.

Ceramide is composed of sphingosine and a fatty acid found in large concentration within the cell membrane and often acts as a signaling molecule for various functions including programmed cell death. In the present investigation, we observed that C6-ceramide induces p53-dependent apoptosis and effectively killed the Astrocytoma grade4 (Glioblastoma Multiforme) HTB12 cell lines. Ceramide-induced cell death was confirmed by Trypan blue assay which showed about 65% cells dying from ceramide treatment. Apoptosis was confirmed by Caspase3 ELISA assay and DNA fragmentation assay. The p53 induction was confirmed by immunoblot studies. Since C6 Ceramide induces apoptosis in Glioblastoma cells, it may be employed in chemotherapeutic strategy to treat this highly malignant brain cancer.

Molecular Diagnosis of Helicobacter Pylori Strain by 16S rDNA PCR Amplification and Direct Sequencing.

AIM: Rapid detection of H.pylori strains by PCR-Sequencing. METHODS: 16S rDNA amplification by PCR from template genomic DNA, confirmation of amplicon size by agarose gel electrophoresis, sequencing of amplicons by automated sequencer, analysis of sequences by NCBI -BLAST software. RESULTS: The PCR -Sequencing and analysis of the sequence data by BLAST resulted in detection of the strain to be of H.pylori strain#26695. CONCLUSION: The pathogenicity of H.pylori depends on the strain of the bacteria, PCR-Sequencing and analysis of the sequence data by BLAST can be a very quick and useful diagnostic method of the pathogen.

Depletion of a single nucleoporin, Nup107, induces apoptosis in eukaryotic cells.

Nuclear pores are large protein complexes that cross the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus. There are about on average 2,000 nuclear pore complexes (NPCs) in the nuclear envelope of a vertebrate cell, but it varies depending on cell type and the stage in the life cycle. The proteins that make up the NPC are known as nucleoporins. In mammalian cells, Nup107 is the homolog of yeast Nup84p nucleoporin. Nup107 contains a leucine zipper motif in its carboxyl-terminal region and numerous kinase consensus sites, but does not contain FG repeats. Previously it was reported that NUP88 and NUP107 are over expressed in many types of cancers including colon, breast, prostrate, etc. In this study, we were interested in investigating the role of NUP107 in grade 4 Astrocytoma, i.e., Glioblastoma multiforme cultured cell line. We transfected human Astrocytoma cells with Nup107-specific siRNA duplexes. The level of mRNA for Nup107 was monitored by RT-PCR, 24, 48, and 72 h after the initial transfection. Nup107 mRNA was significantly diminished by 24 h after transfection and we took that as our incubation time. Next we studied the effect of this inhibition on cell viability. We did a Trypan Blue cell viability assay and it showed increased cell death in NUP107 transfected cells than untreated control. We further tried to analyze the nature of the cell death whether apoptotic or necrotic by doing apoptosis assays like ssDNA ELISA assay, Caspase-3, and Caspase-8 assays. All the assays showed that siRNA transfected cells are undergoing increased apoptosis than control.