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| Status |
Public on Aug 23, 2024 |
| Title |
Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The oviduct is the site of fertilization and preimplantation embryo development in mammals. Evidence suggests that gametes alter oviductal gene expression. To delineate the adaptive interactions between the oviduct and gamete/embryo, we performed a multi-omics characterization of oviductal tissues utilizing bulk RNA-sequencing (RNA-seq), single-cell RNA-sequencing (scRNA-seq), and proteomics collected from distal and proximal at various stages after mating in mice. We observed robust region-specific transcriptional signatures. Specifically, the presence of sperm induces genes involved in pro-inflammatory responses in the proximal region at 0.5 days post-coitus (dpc). Genes involved in inflammatory responses were produced specifically by secretory epithelial cells in the oviduct. At 1.5 and 2.5 dpc, genes involved in pyruvate and glycolysis were enriched in the proximal region, potentially providing metabolic support for developing embryos. Abundant proteins in the oviductal fluid were differentially observed between naturally fertilized and superovulated samples. RNA-seq data were used to identify transcription factors predicted to influence protein abundance in the proteomic data via a novel machine learning model based on transformers of integrating transcriptomics and proteomics data. The transformers identified influential transcription factors and correlated predictive protein expressions in alignment with the in vivo-derived data. In conclusion, our multi-omics characterization and subsequent in vivo confirmation of proteins/RNAs indicate that the oviduct is adaptive and responsive to the presence of sperm and embryos in a spatiotemporal manner.
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| Overall design |
Adult C57B6/J wild-type female mice were mated with either vasectomized or proven breeder males. In some cases, females were superovualted with pregnant mare's serum gonadotropin (PMSG) and human chorionic gonadotrpin (hCG) before mating. The oviduct tissues were collected at 0.5, 1.5, 2.5, and 3.5 days post coitus (dpc) or in some case days of pseudopregnancy (dpp). The oviducts were dissected into infundibulum+ampulla (IA) or isthmus+uterotubal junction (IU) regions. Samples were then processed for bulk RNA-sequencing or single cell RNA-sequencing.
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| Web link |
https://elifesciences.org/reviewed-preprints/100705
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| Contributor(s) |
Finnerty RM, Carulli DJ, Hedge A, Wang Y, Baodu F, Winuthayanon S, Cheng J, Winuthayanon W |
| Citation(s) |
38915688 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HD097087 |
The actions of steroid hormones on oviduct function |
UNIVERSITY OF MISSOURI-COLUMBIA |
Wipawee Winuthayanon |
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| Submission date |
Jun 24, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
Wipawee Winuthayanon |
| Organization name |
University of Missouri
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| Department |
OB/GYN & Women's Health
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| Street address |
1030 Hitt Street
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| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (62)
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| GSM8349393 |
Estrus, IU, Rep1 |
| GSM8349394 |
Estrus, IU, Rep2 |
| GSM8349395 |
Estrus, IU, Rep3 |
| GSM8349396 |
0.5 dpc, IA, Rep1 |
| GSM8349397 |
0.5 dpc, IA, Rep2 |
| GSM8349398 |
0.5 dpc, IA, Rep3 |
| GSM8349399 |
0.5 dpc, IU, Rep1 |
| GSM8349400 |
0.5 dpc, IU, Rep2 |
| GSM8349401 |
0.5 dpc, IU, Rep3 |
| GSM8349402 |
1.5 dpc, IA, Rep1 |
| GSM8349403 |
1.5 dpc, IA, Rep2 |
| GSM8349404 |
1.5 dpc, IA, Rep3 |
| GSM8349405 |
1.5 dpc, IU, Rep1 |
| GSM8349406 |
1.5 dpc, IU, Rep2 |
| GSM8349407 |
1.5 dpc, IU, Rep3 |
| GSM8349408 |
2.5 dpc, IA, Rep1 |
| GSM8349409 |
2.5 dpc, IA, Rep2 |
| GSM8349410 |
2.5 dpc, IA, Rep3 |
| GSM8349411 |
2.5 dpc, IU, Rep1 |
| GSM8349412 |
2.5 dpc, IU, Rep2 |
| GSM8349413 |
2.5 dpc, IU, Rep3 |
| GSM8349414 |
3.5 dpc, IA, Rep1 |
| GSM8349415 |
3.5 dpc, IA, Rep2 |
| GSM8349416 |
3.5 dpc, IA, Rep3 |
| GSM8349417 |
3.5 dpc, IU, Rep1 |
| GSM8349418 |
3.5 dpc, IU, Rep2 |
| GSM8349419 |
3.5 dpc, IU, Rep3 |
| GSM8349420 |
0.5 dpp, IA, Rep1 |
| GSM8349421 |
0.5 dpp, IA, Rep2 |
| GSM8349422 |
0.5 dpp, IA, Rep3 |
| GSM8349423 |
0.5 dpp, IU, Rep1 |
| GSM8349424 |
0.5 dpp, IU, Rep2 |
| GSM8349425 |
0.5 dpp, IU, Rep3 |
| GSM8349426 |
1.5 dpp, IA, Rep1 |
| GSM8349427 |
1.5 dpp, IA, Rep2 |
| GSM8349428 |
1.5 dpp, IA, Rep3 |
| GSM8349429 |
1.5 dpp, IU, Rep1 |
| GSM8349430 |
1.5 dpp, IU, Rep2 |
| GSM8349431 |
1.5 dpp, IU, Rep3 |
| GSM8349432 |
2.5 dpp, IA, Rep1 |
| GSM8349433 |
2.5 dpp, IA, Rep2 |
| GSM8349434 |
2.5 dpp, IA, Rep3 |
| GSM8349435 |
2.5 dpp, IU, Rep1 |
| GSM8349436 |
2.5 dpp, IU, Rep2 |
| GSM8349437 |
2.5 dpp, IU, Rep3 |
| GSM8349438 |
3.5 dpp, IA, Rep1 |
| GSM8349439 |
3.5 dpp, IA, Rep2 |
| GSM8349440 |
3.5 dpp, IA, Rep3 |
| GSM8349441 |
3.5 dpp, IU, Rep1 |
| GSM8349442 |
3.5 dpp, IU, Rep2 |
| GSM8349443 |
3.5 dpp, IU, Rep3 |
| GSM8349444 |
SO_Estrus_IA |
| GSM8349445 |
SO_Estrus_IU |
| GSM8349446 |
SO_0_5_IA |
| GSM8349447 |
SO_0_5_IU |
| GSM8349448 |
SO_1_5_IA |
| GSM8349449 |
SO_1_5_IU |
| GSM8349450 |
SO_2_5_IA |
| GSM8349451 |
SO_2_5_IU |
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| Relations |
| BioProject |
PRJNA1127630 |
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