Identification Of Expression Profiles Research Articles

Identification of expression profiles and transcription factors during EGFR‐TKI acquired resistance in LUAD

Identification of expression profiles and transcription factors during <scp>EGFR</scp>‐<scp>TKI</scp> acquired resistance in <scp>LUAD</scp>

Identification of expression profiles and prognostic value of RFCs in colorectal cancer

Colorectal cancer (CRC) ranks among the most prevalent cancers globally, with its incidence closely tied to DNA damage. The Replication Factor C (RFC) complexes comprises five protein subunits: RFC1, RFC2, RFC3, RFC4, and RFC5. These RFC complexes play crucial roles in DNA replication, repair pathways, activities post DNA damage, and ATP-dependent processes during DNA synthesis. However, the impact of RFC complexes proteins on CRC prognosis remains unclear. To explore this, we employed a computational analysis approach, utilizing platforms such as the DepMap portal, GEPIA, DAVID Bioinformatics for KEGG pathway analysis, Human Protein Atlas (HPA), STRING, and TIMER. Our results indicate that the mRNA levels of RFC1 and RFC5 were the least expressed among CRC cell lines compared to other RFC complex subunits. Notably, low RFC1 and RFC5 expression was correlated with poor prognosis in terms of CRC patients' overall survival (OS). Immunohistochemical results from the Human Protein Atlas demonstrated medium staining for RFC1, RFC2, and RFC5 in CRC tissues. Furthermore, the low expression of RFC1 and RFC5 showed a significant correlation with high expression levels of miR-26a-5p and miR-636, impacting cell proliferation through mismatch repair, DNA replication, and the nucleotide excision repair pathway. Although the precise functions of RFC1 in cancer are still unknown, our findings suggest that the small-molecule single target, CHEMBL430483, and multiple target molecules could be potential treatments for CRC. In conclusion, the elevated expression of miR-26a-5p and miR-636 targeting RFC1 and RFC5 expression holds promise as a potential biomarker for early-stage CRC detection. These insights provide novel directions and strategies for CRC therapies.

Epigenetic Effects of Endocrine Disrupting Chemicals

Recently, there is increasing evidences supported by animal studies emphasizing that exposure to environmental factors, nutritional conditions, xenobiotic chemicals, reproductive factors and low dose exposure to radiations can alter epigenetic programming and concomitantly enhance the risk of developing diseases. Endocrine disrupting chemicals (EDCs) can influence organization of developing brain, which may appear in expression of species typical social behaviors. Environmental exposures to EDCs are shown to increase the susceptibility against many kind of diseases. Currently, there are already several articles, books and journals about the epigenetic effects of EDCs available in media and internet. The aim of this thesis is to review these articles and to evaluate the possible consequences of being exposed to these agents in our daily life for the process of risk assessment of these chemicals. Epigenetic effects do not change the gene sequence. They affect the gene expression and therefore identification of expression profile in sensitive genes to epigenetic effects may be used as a biomarker for disease and environmental exposure. In the future, theses epigenetic biomarkers may help for early diagnosis of sensitivity of an individual for adult onset disease or maybe used to prevent the disease before the disease’s symptoms develop. When an organism grows and develops, precisely organized chemical reactions activate or deactivate parts of the genome at specific time and locations. The study of these chemical reactions and factors influencing them is called epigenetics. It has been observed that, transgenerationally modified progenies in their life are more prone to different kinds of diseases, such as mammary tumors, prostate disease, kidney disease, testis abnormalities and immune abnormalities. Our health depends on our normal development and reproductive ability. Healthy endocrine system is needed to have normal development and normal reproduction. Few years ago we thought that our life starts with the DNA we receive from our parents, but currents studies have shown that we receive more than just DNA from our parents. Famine, stress, fear and even drug use could all leave chemical marks on parent’s genetic material. Environmental exposure to EDCs during early development and pregnancy can modify epigenomes and induce trans-generationally asthma, autism, cancer, cardiovascular dysfunctions, diabetes, obesity, schizophrenia, infertility, reproductive diseases and dysfunction later in life. There is evidence showing that EDCs can induce epigenetic gene alterations by which these altered genes can be transferred into subsequent generations.

MicroRNA signature analysis in colorectal cancer: identification of expression profiles in stage II tumors associated with aggressive disease

Colorectal cancer (CRC) is a clinically diverse disease whose molecular etiology remains poorly understood. The purpose of this study was to identify miRNA expression patterns predictive of CRC tumor status and to investigate associations between microRNA (miRNA) expression and clinicopathological parameters. Expression profiling of 380 miRNAs was performed on 20 paired stage II tumor and normal tissues. Artificial neural network (ANN) analysis was applied to identify miRNAs predictive of tumor status. The validation of specific miRNAs was performed on 102 tissue specimens of varying stages. Thirty-three miRNAs were identified as differentially expressed in tumor versus normal tissues. ANN analysis identified three miRNAs (miR-139-5p, miR-31, and miR-17-92 cluster) predictive of tumor status in stage II disease. Elevated expression of miR-31 (p = 0.004) and miR-139-5p (p < 0.001) and reduced expression of miR-143 (p = 0.016) were associated with aggressive mucinous phenotype. Increased expression of miR-10b was also associated with mucinous tumors (p = 0.004). Furthermore, progressively increasing levels of miR-10b expression were observed from T1 to T4 lesions and from stage I to IV disease. Association of specific miRNAs with clinicopathological features indicates their biological relevance and highlights the power of ANN to reliably predict clinically relevant miRNA biomarkers, which it is hoped will better stratify patients to guide adjuvant therapy.

Using mRNA expression profiling to determine anticancer drug efficacy.

Pharmacogenomics is a fast-growing field of investigations that aims to further elucidate the inherited nature of interindividual differences in drug disposition and effects, with the ultimate goal of providing a stronger scientific basis for selecting the optimal drug therapy. Providing the right drug for the right patient is an important problem in the treatment of cancer. This is mainly due to the lack of information about the sensitivity of the tumor for a specific treatment modality, such as either chemotherapy or radiation treatment. This presentation highlights two approaches to identify responsiveness to treatment. Both approaches are based on the identification of expression profiles. The first approach concentrates on drug resistance and the second on the signaling pathways leading up to the death of the cell. Both approaches provide expression profiles; however, the more dynamic expression profiling as used to determine the signaling in damage cells promises to be a better determinant for the pharmacogenomic changes in expression profiles and, consequently, a potential better determinant for drug efficacy.