Methane-derived stromatolitic carbonate crust from an active fluid seepage in the western basin of the Sea of Marmara: Mineralogical, isotopic and molecular geochemical characterization

Cold seeps along the North Anatolian fault in the Sea of Marmara (Turkey) were explored during submersible dives of the Marsite cruise in November 2014 when sediments, pore waters and carbonate crusts were sampled at active fluid seeping sites. In this study, we investigate the mineralogy, carbon and oxygen isotopic compositions and the lipid biomarkers of a carbonate crust from the western Tekirdağ basin of the Sea of Marmara. This crust exhibits a laminated domal structure that resembles stromatolite. The mineralogy of authigenic seep-carbonate is mostly represented by aragonite associated with minor amounts of high-magnesian calcite. The abundance of pyrite associated with the authigenic seep-carbonate points to very intense bacterial sulfate reduction. The carbon (−42.6‰ to −34.4‰) and oxygen (−1.5‰ to +1.1‰) isotopic compositions of the authigenic seep-carbonate crust indicate that carbonate precipitation was related to anaerobic oxidation of methane and occurred in mixtures of bottom seawater with brackish water expelled from the underlying sediments. Abundant microbial lipid biomarkers with negative δ13C values (−121‰ to −96‰), confirm that anaerobic oxidation of methane (AOM) coupled with sulfate reduction, was mediated by methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB). Diagnostic lipid fingerprints indicate that ANME-2 archaea and associated SRB were the prevalent AOM-mediating consortia, which characterize moderate to high methane flow at this site. Moreover, changes in microbial lipid distribution within the carbonate crust suggest a variation in the intensity of methane emission

Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes

<div><p>Background</p><p>Breast cancer patients who are resistant to neoadjuvant chemotherapy (NeoCT) have a poor prognosis. There is a pressing need to develop <i>in vivo</i> models of chemo resistant tumors to test novel therapeutics. We hypothesized that patient-derived breast cancer xenografts (BCXs) from chemo- naïve and chemotherapy-exposed tumors can provide high fidelity <i>in vivo</i> models for chemoresistant breast cancers.</p><p>Methods</p><p>Patient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, reverse phase protein arrays, molecular inversion probe arrays, and next generation sequencing.</p><p>Results</p><p>Forty-eight breast cancers (24 post-chemotherapy, 24 chemo-naïve) were implanted and 13 BCXs were established (27%). BCX engraftment was higher in TNBC compared to hormone-receptor positive cancer (53.8% vs. 15.6%, p = 0.02), in tumors from patients who received NeoCT (41.7% vs. 8.3%, p = 0.02), and in patients who had progressive disease on NeoCT (85.7% vs. 29.4%, p = 0.02). Twelve patients developed metastases after surgery; in five, BCXs developed before distant relapse. Patients whose tumors developed BCXs had a lower recurrence-free survival (p = 0.015) and overall survival (p<0.001). Genomic losses and gains could be detected in the BCX, and three models demonstrated a transformation to induce mouse tumors. However, overall, somatic mutation profiles including potential drivers were maintained upon implantation and serial passaging. One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.</p><p>Conclusions</p><p>BCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT. Future studies will determine the potential of <i>in vivo</i> models for identification of genotype-phenotype correlations and individualization of treatment.</p></div

Tumor characteristics and engraftment rate.

<p>NeoCT: Neoadjuvant chemotherapy</p><p>*P value by Fisher exact analysis, comparing BCX engraftment in TNBC to HR+ breast cancer.</p><p>**P value by Fisher exact analysis, comparing BCX engraftment in NeoCT to no NeoCT implantations.</p><p>***P value by Fisher exact analysis, comparing BCX engraftment in tumors that progressed on NeoCT vs. those that had stable disease/partial response.</p><p>Tumor characteristics and engraftment rate.</p

Generating and maintaining patient-derived breast cancer xenografts (BCXs) and their time to passage.

<p>(A) After surgery, patient tumors (P0) were implanted into nude mice, creating a patient-derived BCX, passage 1 (P1). When tumors reached 1.5 cm diameter, they were harvested and implanted into 5 new mice (P2), and subsequent passages respectively. Patient tumors and BCXs were evaluated by STR and selected passages underwent molecular and histologic characterization. (B) Y-axis depicts time to reach 1.5 cm with each passage. The graph shows thirteen BCXs that were serially passage. (C) Time to passage (in months) at from implantation to first passage (P1), P1 to P2 (P2), and P1 to P3 (P3). Time to passage at P2 and P3 were compared to time to passage at from implantation to first passage (P1).</p