The Expression of the Immunoproteasome Subunit PSMB9 Is Related to Distinct Molecular Subtypes of Uterine Leiomyosarcoma.

BACKGROUND: Uterine leiomyosarcoma (uLMS) are rare and malignant tumors that arise in the myometrium cells and whose diagnosis is based on histopathological features. Identifying diagnostic biomarkers for uLMS is a challenge due to molecular heterogeneity and the scarcity of samples. In vivo and in vitro models for uLMS are urgently needed. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 (MIM:177045) develop spontaneous uLMS. This study aimed to analyze the role of PSMB9 in uLMS tumorigenesis and patient outcome. METHODS: Molecular data from 3 non-related uLMS cohorts were integrated and analyzed by proteotranscriptomic using gene expression and protein abundance levels in 68 normal adjacent myometrium (MM), 66 uterine leiomyoma (LM), and 67 uLMS. RESULTS: the immunoproteasome pathway is upregulated and the gene PMSB9 shows heterogeneous expression values in uLMS. Quartile group analysis showed no significant difference between groups high and low PSMB9 expression groups at 3-years overall survival (OS). Using CYBERSORTx analysis we observed 9 out of 17 samples in the high group clustering together due to high M2 macrophages and CD4 memory resting, and high CD8+/PSMB9 ratio was associated with better OS. The main pathway regulated in the high group is IFNγ and in the low is the ECM pathway dependent on the proto-oncogene SRC. CONCLUSION: these findings suggest 2 subtypes of uLMS (immune-related and ECM-related) with different candidate mechanisms of malignancy.

On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics.

In proteomics, peptide information within mass spectrometry (MS) data from a specific organism sample is routinely matched against a protein sequence database that best represent such organism. However, if the species/strain in the sample is unknown or genetically poorly characterized, it becomes challenging to determine a database which can represent such sample. Building customized protein sequence databases merging multiple strains for a given species has become a strategy to overcome such restrictions. However, as more genetic information is publicly available and interesting genetic features such as the existence of pan- and core genes within a species are revealed, we questioned how efficient such merging strategies are to report relevant information. To test this assumption, we constructed databases containing conserved and unique sequences for 10 different species. Features that are relevant for probabilistic-based protein identification by proteomics were then monitored. As expected, increase in database complexity correlates with pangenomic complexity. However, Mycobacterium tuberculosis and Bordetella pertussis generated very complex databases even having low pangenomic complexity. We further tested database performance by using MS data from eight clinical strains from M. tuberculosis, and from two published datasets from Staphylococcus aureus. We show that by using an approach where database size is controlled by removing repeated identical tryptic sequences across strains/species, computational time can be reduced drastically as database complexity increases.

Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis.

Cancer/testis (CT) genes are excellent candidates for cancer immunotherapies because of their restrict expression in normal tissues and the capacity to elicit an immune response when expressed in tumor cells. In this study, we provide a genome-wide screen for CT genes with the identification of 745 putative CT genes. Comparison with a set of known CT genes shows that 201 new CT genes were identified. Integration of gene expression and clinical data led us to identify dozens of CT genes associated with either good or poor prognosis. For the CT genes related to good prognosis, we show that there is a direct relationship between CT gene expression and a signal for CD8+ cells infiltration for some tumor types, especially melanoma.

Accumulation of prohibitin is a common cellular response to different stressing stimuli and protects melanoma cells from ER stress and chemotherapy-induced cell death.

Melanoma is responsible for most deaths among skin cancers and conventional and palliative care chemotherapy are limited due to the development of chemoresistance. We used proteomic analysis to identify cellular responses that lead to chemoresistance of human melanoma cell lines to cisplatin. A systems approach to the proteomic data indicated the participation of specific cellular processes such as oxidative phosphorylation, mitochondrial organization and homeostasis, as well as the unfolded protein response (UPR) to be required for the survival of cells treated with cisplatin. Prohibitin (PHB) was among the proteins consistently accumulated, interacting with the functional clusters associated with resistance to cisplatin. We showed PHB accumulated at different levels in melanoma cell lines under stressing stimuli, such as (i) treatment with temozolomide (TMZ), dacarbazine (DTIC) and cisplatin; (ii) serum deprivation; (iii) tunicamycin, an UPR inducer. Prohibitin accumulated in the mitochondria of melanoma cells after cisplatin and tunicamycin treatment and its de novo accumulation led to chemoresistance melanoma cell lines. In contrast, PHB knock-down sensitized melanoma cells to cisplatin and tunicamycin treatment. We conclude that PHB participates in the survival of cells exposed to different stress stimuli, and can therefore serve as a target for the sensitization of melanoma cells to chemotherapy.

A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer: PV: A genome browser-like tool, which includes MS data visualization and peptide identification parameters.

In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry-based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non-coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation. Also see the video abstract here: http://youtu.be/5NzyRvuk4Ac.

Concomitant cisplatin plus radiotherapy and high-dose-rate brachytherapy versus radiotherapy alone for stage IIIB epidermoid cervical cancer: a randomized controlled trial.

PURPOSE: The benefits of chemoradiotherapy (CRT) for cervical cancer compared with radiation (RT) alone seem to diminish in later-stage disease. However, these modalities have not been directly compared for disease-free interval (DFI) and overall survival (OS) of women with stage IIIB cervical cancer. PATIENTS AND METHODS: We conducted a randomized controlled clinical trial comparing DFI and OS of 147 women with stage IIIB squamous cervical cancer who received either cisplatin plus RT (CRT) or RT alone (72 patients in the CRT group and 75 patients in the RT-only group). RESULTS: The CRT group had significantly better DFI (hazard ratio [HR], 0.52; 95% CI, 0.29 to 0.93; P = .02). However, patients in the CRT group did not have significantly better OS than those in the RT-only group (HR, 0.67; 95% CI, 0.38 to 1.17; P = .16). Toxicity was graded according to criteria of the Radiation Therapy Oncology Group. The organs affected (excluding hematologic effects) did not differ significantly between groups. Also, late toxicity events and organs affected were not significantly disproportionate between the study groups. CONCLUSION: For stage IIIB cervical cancer, the addition of cisplatin offers a small but significant benefit in DFI, with acceptable toxicity.

[Postoperative adverse effects in gynaecological and breast surgeries]. / Efeitos adversos no pós-operatório de cirurgias ginecológicas e mamárias.

OBJECTIVES: To analyze the occurrence of adverse effects in the first 24-hour postoperative/postanesthetic period in women undergoing minor gynecologic or minor breast surgeries and to identify main associated factors. METHODS: A cross-sectional study was conducted with 159 women who underwent minor gynecologic or breast surgeries. The women were admitted to the hospital one day before surgery and remained hospitalized for at least 24 hours after surgery. The anesthetic techniques performed were intercostal nerve blockade, spinal anesthesia, and general anesthesia. RESULTS: The most frequent adverse effects were vomiting, nausea and pain that occurred in 40.3% of women. Of these effects, 60% were observed in the first four hours and 80% were observed in up to six hours after surgical intervention. Women submitted to intercostal blockade received earlier postanesthetic release. Spinal anesthesia was most frequently associated with postoperative pain, although with a lower incidence of nausea and vomiting when compared to general anesthesia and intercostal blockade. The incidence of pain was higher in women who smoked. CONCLUSIONS: A six-hour period of postoperative observation appeared to be adequate for assessment of most complications and adverse effects occurring in women who undergo minor gynecologic or minor breast surgeries.

Uterine artery embolization for the treatment of symptomatic myomas in Brazilian women.

CONTEXT: Uterine myomas are benign tumors that mostly occur in women of reproductive age at a frequency ranging from 20 to 25%. The symptoms are increased menstrual flow, pain and compressive signs. New treatments have been proposed and uterine artery embolization is one of them. OBJECTIVE: To evaluate the effects of treatment by embolization of the uterine artery, in women with symptomatic myomas. Uterine and dominant myoma volumes and the major symptoms were evaluated before treatment and 12 weeks later. TYPE OF STUDY: Open clinical trial. SETTING: A tertiary-care women's hospital. PARTICIPANTS: The study was conducted on 32 women with symptomatic single or multiple myomas of the uterine body, seen at the outpatient unit from May 2000 to September 2001. MAIN MEASUREMENTS: The patients were submitted to gynecological examination and abdominal and endovaginal pelvic ultrasonography, and the examinations were repeated 12 weeks after the first procedure. Uterine artery embolization using PVA (polyvinyl alcohol) particles of 355-700 was performed by catheterization of the right femoral artery in 30 women and by bilateral catheterization in two. RESULTS: Before embolization, the mean uterine volume of the 32 women was 455 cm and the mean volume of the dominant myoma was 150 cm . Twelve weeks after embolization, the mean uterine volume was 256 cm and the mean volume of the dominant myoma was 91 cm , with p < 0.01 in both cases. Twelve weeks after the treatment, all the women answered a questionnaire, which showed that 71% had improvement in menstrual regularity, 90% decreased menstrual volume and 81% shortened menstrual duration. The most frequent immediate post-procedure symptoms, established as complications, were pain (100%) and fatigue (34%). One woman had myoma degeneration and was submitted to myomectomy. CONCLUSION: The significant reduction in uterine and dominant myoma volume confirms the validity of the treatment of symptomatic myomas by the technique of uterine artery embolization in Brazilian women. There was significant reduction in menstrual flow and duration, as well as better cycle regularity in the women studied. The few adverse effects observed in the sample studied mainly involved pain immediately after embolization.