MYC Rules: Leading Glutamine Metabolism toward a Distinct Cancer Cell Phenotype

Metabolic reprogramming and deregulated cellular energetics are hallmarks of cancer. The aberrant metabolism of cancer cells is thought to be the product of differential oncogene activation and tumor suppressor gene inactivation. MYC is one of the most important oncogenic drivers, its activation being reported in a variety of cancer types and sub-types, among which are the most prevalent and aggressive of all malignancies. This review aims to offer a comprehensive overview and highlight the importance of the c-Myc transcription factor on the regulation of metabolic pathways, in particular that of glutamine and glutaminolysis. Glutamine can be extensively metabolized into a variety of substrates and be integrated in a complex metabolic network inside the cell, from energy metabolism to nucleotide and non-essential amino acid synthesis. Together, understanding metabolic reprogramming and its underlying genetic makeup, such as MYC activation, allows for a better understanding of the cancer cell phenotype and thus of the potential vulnerabilities of cancers from a metabolic standpoint.

Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers

Background Recently, copy number variations (CNV) impacting genes involved in oncogenic pathways have attracted an increasing attention to manage disease susceptibility. CNV is one of the most important somatic aberrations in the genome of tumor cells. Oncogene activation and tumor suppressor gene inactivation are often attributed to copy number gain/amplification or deletion, respectively, in many cancer types and stages. Recent advances in next generation sequencing protocols allow for the addition of unique molecular identifiers (UMI) to each read. Each targeted DNA fragment is labeled with a unique random nucleotide sequence added to sequencing primers. UMI are especially useful for CNV detection by making each DNA molecule in a population of reads distinct. Results Here, we present molecular Copy Number Alteration (mCNA), a new methodology allowing the detection of copy number changes using UMI. The algorithm is composed of four main steps: the construction of UMI count matrices, the use of control samples to construct a pseudo-reference, the computation of log-ratios, the segmentation and finally the statistical inference of abnormal segmented breaks. We demonstrate the success of mCNA on a dataset of patients suffering from Diffuse Large B-cell Lymphoma and we highlight that mCNA results have a strong correlation with comparative genomic hybridization. Conclusion We provide mCNA, a new approach for CNV detection, freely available at https://gitlab.com/pierrejulien.viailly/mcna/ under MIT license. mCNA can significantly improve detection accuracy of CNV changes by using UMI.

IMMUNOHISTOCHEMICAL EXPRESSION OF P53 AND CYCLIN D1 IN SQUAMOUS CELL CARCINOMAAND EPITHELIAL HYPERPLASIA OF ORAL MUCOSA.

Oral cancer is among the top three types of cancers in India. Most invasive oral carcinomas are preceded by a pre-invasive stage, that may last for many years. . Understanding the molecular mechanisms involved in the initiation and progression to malignancy of oral cancer will help to improve its prognosis and in the elaboration of new forms of treatment. The most common genetic alterations, include gene amplication and overexpression of oncogenes such as myc, erbB-2, Epidermal Growth Factor Receptor (EGFR), Cyclin D1 and mutations, deletions and hypermethylation leading to p16 and p53 tumor suppressor gene inactivation. There still remains the problem of differentiating epitheliomatous hyperplasia from squamous cell carcinoma (SCC) especially on biopsies. AIMS: 1. To study and evaluate the expression of p53 and Cyclin D1 in oral SCC and epithelial hyperplasia. 2. To correlate the expression of p53 and Cyclin D1 in different grades of oral SCC. SETTINGS AND DESIGN:Cross-sectional study conducted over a period of 18 months. METHODS AND MATERIAL: 30 cases (n=30) of oral squamous cell carcinoma & 30 cases (n=30) of epithelial hyperplasia diagnosed on H & E were included in this study. All these cases of oral SCC were further classied into different histological grades according to BRODERS' HISTOLOGICALGRADE. STATISTICAL ANALYSIS: The data was collected and the association between different groups was analysed by using Chi square test and quantitative variables were compared using Independent Ttest/Mann-Whitney Test (when the data sets were not normally distributed) between the two groups and ANOVA/Kruskal Wallis test between three groups. Ap value of ≤0.05 was considered statistically signicant. RESULTS: There was a signicant increase in the expression of p53 in oral SCC compared to epithelial hyperplasia. The results were statistically signicant (p value <0.0001). Similarly , Cyclin D1 also showed an increased expression in cases of SCC in contrast to epithelial hyperplasia (p value <0.0001). The expression of p53 signicantly increased with increase in grade of the tumor. The results being statistically signicant, p value=0.004. Similarly, poorly and moderately differentiated SCC also showed an increased expression of Cyclin D1 compared to well differentiated SCC (p value=0.03, statistically signicant). CONCLUSION: Thus the author concludes that the expression of both p53 and Cyclin D1 is increased in oral SCC compared to epithelial hyperplasia of oral mucosa and these markers can be used to differentiate between these two lesion especially on biopsy cases.

Somatic transposition in the Drosophila intestine occurs in active chromatin and is associated with tumor suppressor gene inactivation

Transposable elements (TEs) play a significant role in evolution by contributing to genetic variation through germline insertional activity. However, how TEs act in somatic cells and tissues is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model system. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we map hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, by applying Oxford Nanopore long-read sequencing technology, as well as by mapping germline TE activity, we provide evidence suggesting tissue-specific differences in retrotransposition. By comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are found preferentially in genic regions and open, transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown underlying features of somatic TE mobility in vivo.

VHLSynthetic Lethality Signatures Uncovered by Genotype-specific CRISPR-Cas9 Screens

BackgroundGenome-wide CRISPR-Cas9 essentiality screening represents a powerful approach to identify genetic vulnerabilities in cancer cells. Here, we applied this technology and designed a strategy to identify target genes that are synthetic lethal (SL) withvon Hippel-Lindau(VHL) tumor suppressor gene. Inactivation ofVHLhas been frequently found in clear cell renal cell carcinoma (ccRCC). Its SL partners serve as potential drug targets for the development of targeted cancer therapies.ResultsWe performed parallel genome-wide CRISPR screens in two pairs of isogenic ccRCC cell lines that differ only in theVHLstatus. Comparative analyses of screening results not only confirmed a well-known role for mTOR signaling in renal carcinoma, but also identified DNA damage response and selenocysteine biosynthesis pathways as major SL targets inVHL-inactivated cancer cells. Follow-up studies provided cellular and mechanistic insights into SL interactions of these pathway genes with theVHLgene.ConclusionsUsing isogenic CRISPR screening approach, we uncovered novel biological processes that are SL withVHL, which can be exploited for drug development for ccRCC. Our CRISPR and RNA-seq datasets provide a rich resource for future investigation of the function of the VHL tumor suppressor protein. Our work demonstrates the efficiency of CRISPR-based synthetic lethality screening in human isogenic cell pairs. Similar strategies could be employed to unveil SL partners with other oncogenic drivers.