Impaired FHIT expression characterizes serous ovarian carcinoma

HumCFS: a database of fragile sites in human chromosomes

Background

Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearranged in cancer. Rare fragile sites are the archetypal trinucleotide repeats. Fragile sites are known to be involved in chromosomal rearrangements in tumors. Human miRNA genes are also present at fragile sites. A better understanding of genes and miRNAs lying in the fragile site regions and their association with disease progression is required.

Result

HumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites. Protein coding genes in the fragile sites were identified by mapping the coordinates of fragile sites with human genome Ensembl (GRCh38/hg38). Genes present in fragile sites were further mapped to DisGenNET database, to understand their possible link with human diseases. Human miRNAs from miRBase was also mapped on fragile site coordinates. In brief, HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA’s.

Conclusion

User-friendly web-interface of HumCFS and hyper-linking with other resources will help researchers to search for genes, miRNAs efficiently and to intersect the relationship among them. For easy data retrieval and analysis, we have integrated standard web-based tools, such as JBrowse, BLAST etc. Also, the user can download the data in various file formats such as text files, gff3 files and Bed-format files which can be used on UCSC browser.

Database URL:http://webs.iiitd.edu.in/raghava/humcfs/

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5330-5) contains supplementary material, which is available to authorized users.

Mining to find the lipid interaction networks involved in Ovarian Cancers

The role of lipids in cancer during the genesis, progression and subsequent metastasis stages is increasingly discussed in the scientific literature. This information is discussed in a wide range of journals making it difficult for researchers to track the latest developments. A comprehensive assessment and translation of the lipidome of ovarian cancer, originating from literature, has yet to be made. We illustrate the deployment of semantic technologies; lipid ontology and text mining, in the aggregation and coordination of lipid literature. We provide the first report on the roles and types of lipids involved in ovarian cancer based on the mining of literature and identify key lipid-protein interactions that may point to potential drug discovery targets.

A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions

BACKGROUND

The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antigens such as hTERT, PCNA and Ki-67 can be considered as cancer markers, while another set of antigens such as P27KIP1 and FHIT are possible markers for normal tissue. Because more than one marker must be considered to obtain a classification of cancer or no cancer, and if cancer, to classify it as malignant, borderline, or benign, we must develop an intelligent decision system that can fullfill such an unmet medical need.

RESULTS

We have developed an intelligent decision system using machine learning techniques and markers to characterize tissue as cancerous, non-cancerous or borderline. The system incorporates learning techniques such as variants of support vector machines, neural networks, decision trees, self-organizing feature maps (SOFM) and recursive maximum contrast trees (RMCT). These variants and algorithms we have developed, tend to detect microscopic pathological changes based on features derived from gene expression levels and metabolic profiles. We have also used immunohistochemistry techniques to measure the gene expression profiles from a number of antigens such as cyclin E, P27KIP1, FHIT, Ki-67, PCNA, Bax, Bcl-2, P53, Fas, FasL and hTERT in several particular types of neuroendocrine tumors such as pheochromocytomas, paragangliomas, and the adrenocortical carcinomas (ACC), adenomas (ACA), and hyperplasia (ACH) involved with Cushing's syndrome. We provided statistical evidence that higher expression levels of hTERT, PCNA and Ki-67 etc. are associated with a higher risk that the tumors are malignant or borderline as opposed to benign. We also investigated whether higher expression levels of P27KIP1 and FHIT, etc., are associated with a decreased risk of adrenomedullary tumors. While no significant difference was found between cell-arrest antigens such as P27KIP1 for malignant, borderline, and benign tumors, there was a significant difference between expression levels of such antigens in normal adrenal medulla samples and in adrenomedullary tumors.

CONCLUSIONS

Our frame work focused on not only different classification schemes and feature selection algorithms, but also ensemble methods such as boosting and bagging in an effort to improve upon the accuracy of the individual classifiers. It is evident that when all sorts of machine learning and statistically learning techniques are combined appropriately into one integrated intelligent medical decision system, the prediction power can be enhanced significantly. This research has many potential applications; it might provide an alternative diagnostic tool and a better understanding of the mechanisms involved in malignant transformation as well as information that is useful for treatment planning and cancer prevention.

Loss of heterozygosity and microsatellite instabilities of fragile histidine triad gene in gastric carcinoma

AIM: To detect the loss of heterozygosity (LOH) and microsatellite instabilities (MSI) of fragile histidine triad (FHIT) gene in gastric carcinoma and to study their association with the clinical pathological characteristics of gastric carcinoma.

METHODS: LOH and MSI of FHIT gene were detected at four microsatellite loci D3Sl3H, D3S4l03, D3Sl48l and D3S1234 using PCR in matched normal and cancerous tissues from 50 patients with primary gastric cancer.

RESULTS: The average frequency of LOH and MSI of FHIT gene in gastric cancer was 32.4% and 26.4% respectively. LOH and MSI of FHIT gene in gastric cancer had no association with histological, Borrmann, and Lauren’s classification. LOH of FHIT gene in gastric cancer was related to invasive depth. The frequency of FHIT LOH in gastric cancer with serosa-penetration was obviously higher than that in gastric cancer without serosa-penetration (73.5% vs 37.5%, P < 0.05). MSI of FHIT gene in gastric cancer was associated with the lymph node metastasis. The frequency of MSI in gastric cancer without lymph node metastasis was significantly higher than that in gastric cancer with lymph node metastasis (66.7% vs 34.3%, P < 0.05).

CONCLUSION: LOH of FHIT gene is correlated with invasive depth of gastric carcinoma. MSI of FHIT gene is correlated with lymph node metastases. LOH and MSI of FHIT gene play an important role in carcinogenesis of gastric cancer.

Prognostic significance of p53 mutation in suboptimally resected advanced ovarian carcinoma treated with the combination chemotherapy of paclitaxel and carboplatin

The prognostic significance of p53 mutation, microsattelite instability and DNA mismatch protein hMLH1 expression in suboptimally resected advanced ovarian carcinoma treated with the combination chemotherapy of paclitaxel and carboplatin was evaluated. The overall combination chemotherapy response rate and the complete remission rate were significantly higher among patients with mutant p53 tumors than those with wild-type p53 tumors (35/42 (83%) vs. 32/58 (55%); P=0.003 and 18/42 (43%) vs. 16/58 (28%); P=0.03, respectively). This tendency apparently existed in non-serous carcinoma, but not in serous carcinoma. Univariate analysis showed that the risk of death due to disease and risk of progression was significantly lower among patients with p53 mutation (P=0.0357 and 0.0281, respectively). However, the presence of microsattelite instability or loss of hMLH1 expression was not associated with either the clinical response or prognosis. Determining p53 mutational status can be useful in predicting therapeutic response to drugs in ovarian carcinoma, especially in non-serous tumors.

Abnormal fragile histidine triad expression in advanced cervical cancer and evaluation of its utility as a prognostic factor

OBJECTIVE

The relationship between the abnormal expression of fragile histidine triad (FHIT) and the prognosis in advanced cervical cancer was investigated, focusing on the relation with radiosensitivity.

METHODS

A retrospective study was performed in 54 patients with stage IIIb cervical squamous cell carcinoma who received radiation therapy as the initial treatment. Formalin-fixed paraffin-embedded tissues were immunohistochemically stained using anti-FHIT antibody. The survival curve for patients with abnormal FHIT expression (low expression) was prepared and the prognosis was compared with that for the normal expression group. The decrease rate of the serum squamous cell carcinoma antigen (SCC) levels (SCC index = SCC level after radiotherapy/SCC level before radiotherapy) was calculated.

RESULTS

Abnormal FHIT expression was observed in 25 patients (46%). There were no significant differences in clinical backgrounds between the abnormal and normal FHIT expression groups. The 5-year survival rate was 72% in the abnormal expression group, showing no significant difference from that in the normal expression group (64%). The SCC indices were 0.21 +/- 0.14 and 0.29 +/- 0.19 in the abnormal and normal expression groups, respectively, showing no significant difference between the two groups.

CONCLUSIONS

Abnormal FHIT expression was not correlated with radiosensitivity in patients with stage IIIb cervical cancer, showing that abnormal FHIT expression cannot be used as a prognostic factor.

Genetic alterations in ovarian carcinoma: with specific reference to histological subtypes

Multiple genetic changes including activation of proto-oncogenes and inactivation of tumor suppressor gene are involved in the development of human ovarian cancer. We describe such genetic alterations with specific reference to histological subtypes. K-ras activation is specific for mucinous tumors including adenomas. Borderline tumors and carcinomas, suggesting that K-ras activation may be associated with the mucinous differentiation rather than malignant transformation. Inactivation of p53 is detected in 30-40% of ovarian carcinoma. Mutations are more frequently observed in serous carcinomas, but not found in adenomas or rarely found in borderline tumors, suggesting that p53 mutations may be directly involved in malignant transformation. TGFbeta-2 mutations are found in 50% of endometrioid carcinoma, but rarely in other type. Loss of DCC mRNA expression is found in 50% of serous carcinomas but less frequently in other type. Loss of DCC expression is rare in borderline tumors and adenomas, suggesting that inactivation of DCC may be directly involved in malignant transformation. Microsatellite instability (MI) is found in 17% of ovarian carcinomas, and is frequently found in endometrioid carcinomas. Although inactivation of p16 by point mutation or deletion is rare, p16 inactivation by loss of expression is relatively common.

Down-regulation of fragile histidine triad expression in prostate carcinoma

BACKGROUND

The fragile histidine triad (FHIT) gene is a tumor suppressor gene that belongs to the histidine triad family of nucleoside binding proteins. The gene encompasses the common human chromosomal fragile site, the FRA3B locus at chromosome 3p14.2, and is expressed in most normal adult tissues and tumor cell lines. Numerous studies have indicated that the FHIT gene on chromosome 3p may play an important role in human neoplasia, although very few studies have investigated the FHIT gene in prostate carcinoma.

METHODS

Using immunohistochemical analyses, the authors studied the expression of FHIT in prostate tumors from 84 radical prostatectomy specimens to determine whether there were any correlations between FHIT expression and various clinicopathologic characteristics.

RESULTS

The percentages of cells stained with antibody to FHIT were significantly lower overall for tumor cells compared with normal cells (P = 0.0001). FHIT immunostaining intensity also was significantly lower for tumor cells compared with normal cells (P = 0.0001). A weak but statistically significant correlation (P = 0.045) was demonstrated with the presence of extraprostatic extension in the patient samples. No other significant correlation was seen between the percentage of cells stained for FHIT or FHIT immunostaining intensity and Gleason grade, tumor stage, tumor size, lymph node metastasis, surgical margins, vascular invasion, perineural invasion, or the presence of high-grade prostatic intraepithelial neoplasia.

CONCLUSIONS

The data presented indicate a down-regulation of the FHIT tumor suppressor gene in prostate carcinoma and, thus, propose a potential target for therapeutic intervention.