Applying Precision Medicine to Ovarian Cancer: Proof-of-Principle for a "Molecular Second Look".

OBJECTIVES: The objectives of this study were to assess if targeted investigation for tumor-specific mutations by ultradeep DNA sequencing of peritoneal washes of ovarian cancer patients after primary surgical debulking and chemotherapy, and clinically diagnosed as disease free, provides a more sensitive and specific method to assess actual treatment response and tailor future therapy and to compare this "molecular second look" with conventional cytology and histopathology-based findings. METHODS/MATERIALS: We identified 10 patients with advanced-stage, high-grade serous ovarian cancer who had undergone second-look laparoscopy and for whom DNA could be isolated from biobanked paired blood, primary and recurrent tumor, and second-look peritoneal washes. A targeted 56 gene cancer-relevant panel was used for next-generation sequencing (average coverage, >6500×). Mutations were validated using either digital droplet polymerase chain reaction (ddPCR) or Sanger sequencing. RESULTS: A total of 25 tumor-specific mutations were identified (median, 2/patient; range, 1-8). TP53 mutations were identified in at least 1 sample from all patients. All 5 pathology-based second-look positive patients were confirmed positive by molecular second look. Genetic analysis revealed that 3 of the 5 pathology-based negative second looks were actually positive. In the 2 patients, the second-look mutations were present in either the original primary or recurrent tumors. In the third, 2 high-frequency, novel frameshift mutations in MSH6 and HNF1A were identified. CONCLUSIONS: The molecular second look detects tumor-specific evidence of residual disease and provides genetic insight into tumor evolution and future recurrences beyond standard pathology. In the precision medicine era, detecting and genetically characterizing residual disease after standard treatment will be invaluable for improving patient outcomes.

A beginning of the end: new insights into the functional organization of telomeres.

Ever since the first demonstration of their repetitive sequence and unique replication pathway, telomeres have beguiled researchers with how they function in protecting chromosome ends. Of course much has been learned over the years, and we now appreciate that telomeres are comprised of the multimeric protein/DNA shelterin complex and that the formation of t-loops provides protection from DNA damage machinery. Deriving their name from D-loops, t-loops are generated by the insertion of the 3' overhang into telomeric repeats facilitated by the binding of TRF2. Recent studies have uncovered novel forms of chromosome end-structure that may implicate telomere organization in cellular processes beyond its essential role in telomere protection and homeostasis. In particular, we have recently described that t-loops form in a TRF2-dependent manner at interstitial telomere repeat sequences, which we termed interstitial telomere loops (ITLs). These structures are also dependent on association of lamin A/C, a canonical component of the nucleoskeleton that is mutated in myriad human diseases, including human segmental progeroid syndromes. Since ITLs are associated with telomere stability and require functional lamin A/C, our study suggests a mechanistic link between cellular aging (replicative senescence induced by telomere shortening) and organismal aging (modeled by Hutchinson Gilford Progeria Syndrome). Here we speculate on other potential ramifications of ITL formation, from gene expression to genome stability to chromosome structure.

Eating disorders and sense of self: a learning theory conceptualization.

The learning theory view of sense of self is that problems in one's knowledge about the self arise when: (1) caregivers fail to recognize indicators of a child's private emotional and visceral experiences and (2) subsequently fail to offer appropriate labels that discriminate among those experiences. The purpose of this study was to evaluate the relationship of the process believed to build a sense of self to level of interoceptive awareness (IA) and to risk for eating disorders. One hundred twenty seven undergraduate and graduate students (112 women) completed the Eating Disorders Inventory-3 (EDI-3). Authors assigned (EDI-3) subscales to one of two groups based on their relevance to IA (i.e., IA-relevant and Not IA-relevant.) The classification was supported by factor analysis. Subscales from the EDI-3 were thus used as a measure of a respondent's IAlevel. Students also completed the Experience of Self Scale (EOSS). The EOSS was used as a measure of a respondent's likely exposure to the experiential process believed to build sense of self. Product-moment correlations and multiple regression modeling were used to test the relationships between EOSS and EDI-3 IA-relevant, Not IA-relevant, and Eating Disorder risk scores. With few exceptions, results suggested that IAlevel and sense of selfprocess are related. These findings warrant further exploration of the relationship between IAlevel and sense of selfprocess. A link between the two would inform our understanding of how problems in IA develop and how best to prevent and treat them.

TRF2 and lamin A/C interact to facilitate the functional organization of chromosome ends.

Telomeres protect the ends of linear genomes, and the gradual loss of telomeres is associated with cellular ageing. Telomere protection involves the insertion of the 3' overhang facilitated by telomere repeat-binding factor 2 (TRF2) into telomeric DNA, forming t-loops. We present evidence suggesting that t-loops can also form at interstitial telomeric sequences in a TRF2-dependent manner, forming an interstitial t-loop (ITL). We demonstrate that TRF2 association with interstitial telomeric sequences is stabilized by co-localization with A-type lamins (lamin A/C). We also find that lamin A/C interacts with TRF2 and that reduction in levels of lamin A/C or mutations in LMNA that cause an autosomal dominant premature ageing disorder--Hutchinson Gilford Progeria Syndrome (HGPS)-lead to reduced ITL formation and telomere loss. We propose that cellular and organismal ageing are intertwined through the effects of the interaction between TRF2 and lamin A/C on chromosome structure.

A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function.

The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.

Regulation of chromatin organization and inducible gene expression by a Drosophila insulator.

Insulators are multiprotein-DNA complexes thought to affect gene expression by mediating inter- and intrachromosomal interactions. Drosophila insulators contain specific DNA-binding proteins plus common components, such as CP190, that facilitate these interactions. Here, we examine changes in the distribution of Drosophila insulator proteins during the heat-shock and ecdysone responses. We find that CP190 recruitment to insulator sites is the main regulatable step in controlling insulator function during heat shock. In contrast, both CP190 and DNA-binding protein recruitment are regulated during the ecdysone response. CP190 is necessary to stabilize specific chromatin loops and for proper activation of transcription of genes regulated by this hormone. These findings suggest that cells may regulate recruitment of insulator proteins to DNA to activate insulator activity at specific sites and create distinct patterns of nuclear organization that are necessary to achieve proper gene expression in response to different stimuli.

The effects of temperature on the physiological response to low oxygen in Atlantic sturgeon.

Atlantic sturgeon (Acipenser oxyrhynchus), which are bottom dwelling and migratory fish, experience environmental hypoxia in their natural environment. Atlantic sturgeon, acclimated to either 5 or 15°C, were subjected to a 1 h severe (<10 mm Hg) hypoxia challenge in order to document their physiological responses. We measured hematological parameters, including O(2) transport (hemoglobin, hematocrit), ionic (chloride, osmolality), and metabolic (glucose, lactate) variables under normoxic conditions (~160 mm Hg), immediately following a 1 h exposure to hypoxic water, and following a further 2 h of recovery from this challenge in normoxic water. In a second experiment, we assessed the opercular beat frequency before, during, and after hypoxic exposure. Hemoglobin concentrations and hematocrit were significantly different between fish held at 5°C vs. 15°C and also significantly different between normoxia prior to hypoxia and following recovery. Plasma lactate concentrations increased following hypoxia at both temperatures, indicative of an increase in anaerobic metabolism. In contrast, a significant increase in plasma glucose concentrations in response to hypoxia only occurred at 5°C, suggesting different fuel demands under different temperatures. Changes in opercular beat frequency (OBF) were dependent on temperature. At 5°C, OBF increased upon exposure to hypoxia, but returned to pre-exposure levels within 35 min for the remainder of the experiment. During hypoxia at 15°C, OBF increased very briefly, but then rapidly (within 20 min) decreased to levels below control values. Following a return to normoxia, OBF quickly increased to control levels. Overall, these findings suggest that Atlantic sturgeons are relatively tolerant to short-term and severe hypoxic stress, and the strategies for hypoxia tolerance may be temperature dependent.