Abstract DP-005: RNA-SEQUENCING OF FALLOPIAN TUBE – FIMBRIA AND HGSC FROM BRCA MUTATION CARRIERS
Bibliographic record
Abstract
Abstract Inheritance of a deleterious mutation in the BRCA1/2 genes increases the risk of the disease by up to 40%. The origin of the disease is still debated; however considerable evidence suggests the fallopian tube as the primary site of disease origin. The fallopian tube epithelium changes morphologically and genomically with the ovulatory cycle. To further understand the transcriptomic profile of the fallopian tube epithelium amongst patients with and without a BRCA mutation who have undergone prophylactic surgery, samples with clinically annotated ovulatory cycle status were analyzed by next-generation sequencing (RNA-Seq). The results from this study will provide an understanding of the origins of the disease and how new therapeutic and preventative interventions can be applied early in the development of the disease. METHODS: In total a cohort of 68 archival formalin fixed paraffin embedded (FFPE) fallopian tube -fimbria was amassed: FTE-BRCA1 (n=32), FTE-BRCA2 (n=4), chemonaive HGSC-BRCA1 (n=9), FTE-nonBRCA (n=26). The pre-menopausal fallopian tube specimens were sub-divided by ovulatory cycle: normal-Follicular, normal-Luteal, BRCA-Follicular, BRCA-Luteal. The majority of the FTE specimen were obtained from pre-menopausal women (post-menopausal n=2). Laser capture microdissection was performed on the distal end of the fallopian tubes – the fimbria. Six-twelve, 10um FFPE sections were cut and stained with hematoxylin prior to LCM. RNA was extracted using the Roche High Pure FFPE Micro Kit and samples were processed using Illumina Tru-Seq Stranded Total RNA Kit with RiboGold ready and sequenced on the Illumina Hi-seq 2000 V3. Raw results, in FASTQ format, were then processed through the RNA sequencing pipeline to generate results including gene expression data. RESULTS: Gene expression differences between carriers and non-carriers (FTE-BRCA1/2 and FTE-nonBRCA) revealed genes involved in metabolic pathways namely: oxidative phosphorylation, mitochondrial functions, glycolysis/gluconeogenesis and glycan biosynthesis and metabolism: UGT2A1, ST6GALNNAC6, Complex 1 (ND1, ND2, ND4, NDL4, ND5), ATP6/ATP8, and COX1-3. A comparison between the tumor and fimbria cases showed increased activity in the HMGBI Signaling (increase in HAT1, KAT2B, LIF, JAK3 and PIK3CA and decrease in RAP1A/B, ATM and HMGB1). CONCLUSION: These results highlight BRCA1/2 distinct unique preneoplastic processes not previously identified. The fallopian tube epithelial in the fimbria in BRCA1 and BRCA2 mutation carriers have increased metabolic activity, indicated by their gene expression profiles. HGSC developed BRCA1 germline mutation carriers have an increased histone acetyltransferase activity shown to be involved in BRCA mediated DNA damage repair. Further analysis is required to understand how the ovulatory cycle influences the fallopian tube epithelium transcriptome, but preliminary results suggest that pathways altered include: metabolic pathways, apoptosis pathways, p53 pathways and mismatch repair pathways. These results support previous findings in addition to providing new insight into the early development of the disease. Citation Format: Ramlogan Sowamber, Leah Dodds, Anca Milea, Iru Paudel, Michael Considine, Leslie Cope, Patricia A Shaw and Sophia HL George. RNA-SEQUENCING OF FALLOPIAN TUBE – FIMBRIA AND HGSC FROM BRCA MUTATION CARRIERS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr DP-005.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".