ItemeIF2α controls memory consolidation via excitatory and somatostatin neurons(Nature Research, 2020-10-07) Sharma, Vijendra; Sood, Rapita; Khlaifia, Abdessattar; Eslamizade, Mohammad Javad; Hung, Tzu-Yu; Lou, Danning; Asgarihafshejani, Azam; Lalzar, Maya; Kiniry, Stephen J.; Stokes, Matthew P.; Cohen, Noah; Nelson, Alissa J.; Abell, Kathryn; Possemato, Anthony P.; Gal-Ben-Ari, Shunit; Truong, Vinh T.; Wang, Peng; Yiannakas, Adonis; Saffarzadeh, Fatemeh; Cuello, A. Claudio; Nader, Karim; Kaufman, Randal J.; Costa-Mattioli, Mauro; Baranov, Pavel V.; Quintana, Albert; Sanz, Elisenda; Khoutorsky, Arkady; Lacaille, Jean-Claude; Rosenblum, Kobi; Sonenberg, Nahum; International Development Research Centre; Azrieli Foundation; Canadian Institutes of Health Research; Israel Science Foundation; National Institutes of Health; Ministerio de Ciencia, Innovación y Universidades; European Research Council; Ministerio de Economía y Competitividad; Agència de Gestió d’Ajuts Universitaris i de Recerca; National Institute of Neurological Disorders and Stroke; Richard and Edith Strauss FoundationAn important tenet of learning and memory is the notion of a molecular switch that promotes the formation of long-term memory1,2,3,4. The regulation of proteostasis is a critical and rate-limiting step in the consolidation of new memories5,6,7,8,9,10. One of the most effective and prevalent ways to enhance memory is by regulating the synthesis of proteins controlled by the translation initiation factor eIF211. Phosphorylation of the α-subunit of eIF2 (p-eIF2α), the central component of the integrated stress response (ISR), impairs long-term memory formation in rodents and birds11,12,13. By contrast, inhibiting the ISR by mutating the eIF2α phosphorylation site, genetically11 and pharmacologically inhibiting the ISR kinases14,15,16,17, or mimicking reduced p-eIF2α with the ISR inhibitor ISRIB11, enhances long-term memory in health and disease18. Here we used molecular genetics to dissect the neuronal circuits by which the ISR gates cognitive processing. We found that learning reduces eIF2α phosphorylation in hippocampal excitatory neurons and a subset of hippocampal inhibitory neurons (those that express somatostatin, but not parvalbumin). Moreover, ablation of p-eIF2α in either excitatory or somatostatin-expressing (but not parvalbumin-expressing) inhibitory neurons increased general mRNA translation, bolstered synaptic plasticity and enhanced long-term memory. Thus, eIF2α-dependent mRNA translation controls memory consolidation via autonomous mechanisms in excitatory and somatostatin-expressing inhibitory neurons. ItemVanadium isotope fractionation of alkali basalts during mantle melting(Elsevier B.V., 2023-02-22) Chen, Zhenwu; Ding, Xin; Kiseeva, Ekaterina S.; Lin, Xiaobao; Huang, Jian; National Key Research and Development Program of China; Chinese Academy of Sciences; Natural Environment Research Council; Irish Research Council; Youth Innovation Promotion Association of the Chinese Academy of SciencesIt is well known that vanadium (V) is redox-sensitive during magmatism, but whether V isotopes can be used as a mantle oxygen fugacity (fO2) sensor remains controversial. Before using V isotopes as a redox proxy, it is crucial to understand the fractionation behavior and controlling factors of V isotopes during mantle melting. This study reports high-precision V isotopic data for alkali basalts with high fO2 in eastern China, which were derived from carbonated mantle by a low degree of partial melting. Our results show that their δ51V values (−0.85‰ to −0.61‰) are higher than those of bulk silicate Earth (BSE) and mid-ocean ridge basalts (MORBs). Chemical alteration, crustal contamination or fractional crystallization negligibly affect the δ51V values of alkali basalts. Although subducted carbonates are involved in the mantle source region under eastern China, mass balance calculations show that the incorporation of carbonates did not significantly increase the δ51V values of alkali basalts. In contrast, the observed high δ51V values probably reflect that mantle melting controls the V isotopic compositions of mantle-derived melts. The relative abundances of V5+, V4+ and V3+ in silicate melt are influenced by the variation of fO2 and/or the degree of partial melting. Basaltic melts tend to be enriched in V with high valence at the condition of high fO2 during mantle melting, which contributes to the enrichment of 51V in alkali basalts because of the affinity of high valence V and 51V. Because mantle minerals are overall more compatible of V with low valence, the valence states of V in silicate melt tend to be higher at low degree of partial melting, resulting in more significant fractionation of V isotopes. Therefore, this study validates discernable V isotope fractionation during partial melting of the mantle and examines the potential of using V isotopes to trace the redox state of magmatic systems. ItemInvestigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints(Springer Nature, 2022-11-23) Keane, Jonathan M.; Walsh, Calum J.; Cronin, P.; Baker, Kevin J.; Melgar, Silvia; Cotter, Paul D.; Joyce, Susan A.; Gahan, Cormac G. M.; Houston, Aileen M.; Hyland, Niall P.; Science Foundation IrelandBackground: Distinct sets of microbes contribute to colorectal cancer (CRC) initiation and progression. Some occur due to the evolving intestinal environment but may not contribute to disease. In contrast, others may play an important role at particular times during the tumorigenic process. Here, we describe changes in the microbiota and host over the course of azoxymethane (AOM)-induced tumorigenesis. Methods: Mice were administered AOM or PBS and were euthanised 8, 12, 24 and 48 weeks later. Samples were analysed using 16S rRNA gene sequencing, UPLC-MS and qRT-PCR. Results: The microbiota and bile acid profile showed distinct changes at each timepoint. The inflammatory response became apparent at weeks 12 and 24. Moreover, significant correlations between individual taxa, cytokines and bile acids were detected. One co-abundance group (CAG) differed significantly between PBS- and AOM-treated mice at week 24. Correlation analysis also revealed significant associations between CAGs, bile acids and the bile acid transporter, ASBT. Aberrant crypt foci and adenomas were first detectable at weeks 24 and 48, respectively. Conclusion: The observed changes precede host hyperplastic transformation and may represent early therapeutic targets for the prevention or management of CRC at specific timepoints in the tumorigenic process. ItemA bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset(Elsevier, 2020-03-17) Zaheed, Oza; Samson, Julia; Dean, Kellie; University College CorkBreast cancer research has traditionally centred on genomic alterations, hormone receptor status and changes in cancer-related proteins to provide new avenues for targeted therapies. Due to advances in next generation sequencing technologies, there has been the emergence of long, non-coding RNAs (lncRNAs) as regulators of normal cellular events, with links to various disease states, including breast cancer. Here we describe our bioinformatic analyses of a previously published RNA sequencing (RNA-seq) dataset to identify lncRNAs with altered expression levels in a subset of breast cancer cell lines. Using a previously published RNA-seq dataset of 675 cancer cell lines, a subset of 18 cell lines was selected for our analyses that included 16 breast cancer lines, one ductal carcinoma in situ line and one normal-like breast epithelial cell line. Principal component analysis demonstrated correlation with well-established categorisation methods of breast cancer (i.e. luminal A/B, HER2 enriched and basal-like A/B). Through detailed comparison of differentially expressed lncRNAs in each breast cancer sub-type with normal-like breast epithelial cells, we identified 15 lncRNAs with consistently altered expression, including three uncharacterised lncRNAs. Utilising data from The Cancer Genome Atlas (TCGA) and The Genotype Tissue Expression (GETx) project via Gene Expression Profiling Interactive Analysis (GEPIA2), we assessed clinical relevance of several identified lncRNAs with invasive breast cancer. Lastly, we determined the relative expression level of six lncRNAs across a spectrum of breast cancer cell lines to experimentally confirm the findings of our bioinformatic analyses. Overall, we show that the use of existing RNA-seq datasets, if re-analysed with modern bioinformatic tools, can provide a valuable resource to identify lncRNAs that could have important biological roles in oncogenesis and tumour progression. ItemMolecular and cellular characterization of two patient-derived ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010(BMC, part of Springer Nature, 2021-07-08) Samson, Julia; Derlipanska, Magdalina; Zaheed, Oza; Dean, Kellie; University College Cork; Boehringer Ingelheim; Boehringer Ingelheim Fonds; Deutsche Forschungsgemeinschaft; Bundesministerium für Bildung und ForschungBackground: Currently it is unclear how in situ breast cancer progresses to invasive disease; therefore, a better understanding of the events that occur during the transition to invasive carcinoma is warranted. Here we have conducted a detailed molecular and cellular characterization of two, patient-derived, ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010. Methods: Human DCIS cell lines, ETCC-006 and ETCC-010, were compared against a panel of cell lines including the immortalized, breast epithelial cell line, MCF10A, breast cancer cell lines, MCF7 and MDA-MB-231, and another DCIS line, MCF10DCIS.com. Cell morphology, hormone and HER2/ERBB2 receptor status, cell proliferation, survival, migration, anchorage-independent growth, indicators of EMT, cell signalling pathways and cell cycle proteins were examined using immunostaining, immunoblots, and quantitative, reverse transcriptase PCR (qRT-PCR), along with clonogenic, wound-closure and soft agar assays. RNA sequencing (RNAseq) was used to provide a transcriptomic profile. Results: ETCC-006 and ETCC-010 cells displayed notable differences to another DCIS cell line, MCF10DCIS.com, in terms of morphology, steroid-receptor/HER status and markers of EMT. The ETCC cell lines lack ER/PR and HER, form colonies in clonogenic assays, have migratory capacity and are capable of anchorage-independent growth. Despite being isogenic, less than 30% of differentially expressed transcripts overlapped between the two lines, with enrichment in pathways involving receptor tyrosine kinases and DNA replication/cell cycle programs and in gene sets responsible for extracellular matrix organisation and ion transport. Conclusions: For the first time, we provide a molecular and cellular characterization of two, patient-derived DCIS cell lines, ETCC-006 and ETCC-010, facilitating future investigations into the molecular basis of DCIS to invasive ductal carcinoma transition.