Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors.

BACKGROUND: Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we compared the proteogenomic analyses of LGSOCs from short- and long-term survivors (defined as < 40 and > 60 months, respectively). Our goal was to identify novel mutations, proteins, and mRNA transcripts that are dysregulated in LGSOC, particularly in short-term survivors. METHODS: Initially, targeted sequencing of 409 cancer-related genes was performed on 22 LGSOC and 6 serous borderline ovarian tumor samples. Subsequently, whole-genome sequencing analysis was performed on 14 LGSOC samples (7 long-term survivors and 7 short-term survivors) with matched normal tissue samples. RNA sequencing (RNA-seq), quantitative proteomics, and phosphoproteomic analyses were also performed. RESULTS: We identified single-nucleotide variants (SNVs) (range: 5688-14,833 per sample), insertion and deletion variants (indels) (range: 880-1065), and regions with copy number variants (CNVs) (range: 62-335) among the 14 LGSOC samples. Among all SNVs and indels, 2637 mutation sites were found in the exonic regions. The allele frequencies of the detected variants were low (median12%). The identified recurrent nonsynonymous missense mutations included KRAS, NRAS, EIF1AX, UBR5, and DNM3 mutations. Mutations in DNM3 and UBR5 have not previously been reported in LGSOC. For the two samples, somatic DNM3 nonsynonymous missense mutations in the exonic region were validated using Sanger sequencing. The third sample contained two missense mutations in the intronic region of DNM3, leading to a frameshift mutation detected in RNA transcripts in the RNA-seq data. Among the 14 LGSOC samples, 7754 proteins and 9733 phosphosites were detected by global proteomic analysis. Some of these proteins and signaling pathways, such as BST1, TBXAS1, MPEG1, HBA1, and phosphorylated ASAP1, are potential therapeutic targets. CONCLUSIONS: This is the first study to use whole-genome sequencing to detect somatic mutations in LGSOCs with matched normal tissues. We detected and validated novel mutations in DNM3, which were present in 3 of the 14 samples analyzed. Additionally, we identified novel indels, regions with CNVs, dysregulated mRNA, dysregulated proteins, and phosphosites that are more prevalent in short-term survivors. This integrated proteogenomic analysis can guide research into the pathogenesis and treatment of LGSOC.

Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.

The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC), which is the most lethal gynecologic malignancy, is not well understood. Here, we perform comprehensive multi-platform omics analyses, including integrated analysis, and immune monitoring on primary and metastatic sites from highly clinically annotated HGSC samples based on a laparoscopic triage algorithm from patients who underwent complete gross resection (R0) or received neoadjuvant chemotherapy (NACT) with excellent or poor response. We identify significant distinct molecular abnormalities and cellular changes and immune cell repertoire alterations between the groups, including a higher rate of NF1 copy number loss, and reduced chromothripsis-like patterns, higher levels of strong-binding neoantigens, and a higher number of infiltrated T cells in the R0 versus the NACT groups.

On the energy landscapes of 3-indole acetic acid and 3-indole propionic acid. A study of side chain flexibilities in their S(0) and S(1) electronic states.

The tandem of 3-indole acetic acid (IAA) and 3-indole propionic acid (IPA) is ideally suited for a detailed study of the intramolecular forces responsible for the conformational properties of species containing side chains. Toward this end, high resolution S(1)<-- S(0) excitation spectra of the three origin bands in IAA and the two origin bands in IPA were recorded and analyzed. Each origin is assigned to a unique conformer. A discussion of the resulting energy landscape is given.

Permanent electric dipole moments of four tryptamine conformers in the gas phase: a new diagnostic of structure and dynamics.

Rotationally resolved electronic spectroscopy in the gas phase, in the absence and presence of an applied electric field, has been used to determine the charge distribution of a cross section of the energy landscape of tryptamine (TRA). We report the magnitude and direction of the permanent electric dipole moments of the four TRA conformers GPyout, GPyup, GPhup, and Antiup in their S0 and S1 electronic states. Each dipole moment is unique, providing a powerful new tool for the conformational analysis of biomolecules in the gas phase. A comparison of the results for the different conformers of TRA reveals that the position and orientation of the ethylamine side chain play a major role in determining both the permanent and induced electric dipole moments of the different species in both electronic states.

Charge redistribution on electronic excitation. Dipole moments of cis- and trans-3-aminophenol in their S(0) and S(1) electronic states.

Rotationally resolved electronic spectroscopy in the gas phase, in the absence and presence of an applied electric field, has been used to distinguish the two conformers of 3-aminophenol (3AP) on the basis of differences in their electric dipole moments. cis-3AP has micro = 2.3 D, and trans-3AP has micro = 0.7 D, in their ground electronic states. The two observed values are approximately equal to those expected on the basis of bond dipole additivity rules. However, these rules fail to predict the large change in both the magnitude and the orientation of micro when the two conformers of 3AP absorb light. cis-3AP has micro = 3.3 D, and trans-3AP has micro = 1.7 D, in their excited S(1) electronic states; the angles of orientation of micro with respect to the a inertial axis change by 13 degrees and 38 degrees, respectively. This effect is attributed to (1)L(b)/(1)L(a) state mixing in the S(1) state.