I have arrange the Sox2 KO/ control RNA-seq data to study the shift in cellular plasticity. These Sox2 KO allograft (of Apc/Kras/Tp53/Tgfbr2 mutated mouse organoids) showed increase growth rate compar
I have arrange the Sox2 KO/ control RNA-seq data to study the shift in cellular plasticity. These Sox2 KO allograft (of Apc/Kras/Tp53/Tgfbr2 mutated mouse organoids) showed increase growth rate compared to the Cas9 control. i have to add that while in DMSO condition, sox2 KO allografts grow much faster than cas9; but in 5FU condition, they grow equally. So the 5FU is actually inhibiting Sox2 KO growth. I want to understand what exact cell state the Sox2 ko organoids are shifting to in DMSO and 5FU condition. Based on the results, can the absorptive colonocyte explain the difference in growth and steroid biosynthesis?
Here's my results:
Cell state Sox2 KO/Cas9 (DMSO)
Enteroendocrine Displayed downregulation trend but not significant.
Steroid biosynthesis Displayed very strong upregulation. Key targets include Sc5d, Mvk, Lipa, Soat1.
Lgr5-stem cell Strong downregulation of stem cell, including Olm4, Lgr5, Smoc2 and Prom1.
Paneth-like Overall, show downregulation but none statistically significant.
Quiescent Ambiguous. Nrf21, Nanog, Bhlhe41, Zeb2, Hif1a, Pou5f1 show downregulation; Klf4, Cdkn1a, Cdkn1b and Fbxo8 show upregulation. But none are statistically significant. Sox2 is significantly downregulated as it’s KO.
Secretory-Goblet Overall, show downregulation but none statistically significant.
Tuft-cell Overall, show downregulation but none statistically significant except Trpm5.
Transit-Amplifying Very mild down trend, but not statistically significant.
Absorptive-colonocyte Strong upregulation. Alpi, Fabp2, Krt20, Vil1 are significantly upregulated. Fabp1 and Aqp8 are also up but not significant. Apoa1 and Otop2 show mild but not significant downregulation.
Fetal-like revival Ambiguous. Ankrd1, Clu, Basp1, Tacstd1 show downregulation; ly6d, msln, anxa1, cscl12 show upregulation. But none are statistically significant.
EMT Very ambiguous. Only Mmp9 is statistically downregulated.
Cell state Sox2 KO/Cas9 (5FU)
Enteroendocrine Displayed downregulation trend but not significant. Except Arx, Gcg, Sct, Syp which are upregulated but also not significant.
Steroid biosynthesis Displayed even strong upregulation. In addition, the ones in DMSO, Hmgcr, Sqle, Hmgcs1, Lss, Fdps, Nsdhl, Idi1 are upregulated.
Lgr5-stem cell Displayed similar trend as DMSO, but only Smoc2 significantly downregulated.
Paneth-like Overall, show downregulation but none statistically significant.
Quiescent Ambiguous. Nrf21, Nanog, Bhlhe41, Zeb2, Hif1a show downregulation; Pou5f1, Klf4, Cdkn1a, Cdkn1b and Fbxo8 show upregulation. But only Cdkn1a is statistically significant. Sox2 is significantly downregulated as it’s KO.
Secretory-Goblet Overall, show downregulation but none statistically significant.
Tuft-cell Overall, show downregulation but none statistically significant.
Transit-Amplifying Mild uptrend, but only Ube2c is significantly upregulated.
Absorptive-colonocyte Milder upregulation. Krt20 and Vil1 are significantly upregulated. Fabp1 and Aqp8 are also up but not significant. Apoa1 and Otop2 show mild but not significant downregulation.
Fetal-like revival Ambiguous. Ankrd1, Clu, Msln, Basp1, Tacstd1 show downregulation; ly6d, , anxa1, cscl12 show upregulation. But none are statistically significant.
EMT Show downregulation but none are statistically significant.
Here's my results:
Cell state Sox2 KO/Cas9 (DMSO)
Enteroendocrine Displayed downregulation trend but not significant.
Steroid biosynthesis Displayed very strong upregulation. Key targets include Sc5d, Mvk, Lipa, Soat1.
Lgr5-stem cell Strong downregulation of stem cell, including Olm4, Lgr5, Smoc2 and Prom1.
Paneth-like Overall, show downregulation but none statistically significant.
Quiescent Ambiguous. Nrf21, Nanog, Bhlhe41, Zeb2, Hif1a, Pou5f1 show downregulation; Klf4, Cdkn1a, Cdkn1b and Fbxo8 show upregulation. But none are statistically significant. Sox2 is significantly downregulated as it’s KO.
Secretory-Goblet Overall, show downregulation but none statistically significant.
Tuft-cell Overall, show downregulation but none statistically significant except Trpm5.
Transit-Amplifying Very mild down trend, but not statistically significant.
Absorptive-colonocyte Strong upregulation. Alpi, Fabp2, Krt20, Vil1 are significantly upregulated. Fabp1 and Aqp8 are also up but not significant. Apoa1 and Otop2 show mild but not significant downregulation.
Fetal-like revival Ambiguous. Ankrd1, Clu, Basp1, Tacstd1 show downregulation; ly6d, msln, anxa1, cscl12 show upregulation. But none are statistically significant.
EMT Very ambiguous. Only Mmp9 is statistically downregulated.
Cell state Sox2 KO/Cas9 (5FU)
Enteroendocrine Displayed downregulation trend but not significant. Except Arx, Gcg, Sct, Syp which are upregulated but also not significant.
Steroid biosynthesis Displayed even strong upregulation. In addition, the ones in DMSO, Hmgcr, Sqle, Hmgcs1, Lss, Fdps, Nsdhl, Idi1 are upregulated.
Lgr5-stem cell Displayed similar trend as DMSO, but only Smoc2 significantly downregulated.
Paneth-like Overall, show downregulation but none statistically significant.
Quiescent Ambiguous. Nrf21, Nanog, Bhlhe41, Zeb2, Hif1a show downregulation; Pou5f1, Klf4, Cdkn1a, Cdkn1b and Fbxo8 show upregulation. But only Cdkn1a is statistically significant. Sox2 is significantly downregulated as it’s KO.
Secretory-Goblet Overall, show downregulation but none statistically significant.
Tuft-cell Overall, show downregulation but none statistically significant.
Transit-Amplifying Mild uptrend, but only Ube2c is significantly upregulated.
Absorptive-colonocyte Milder upregulation. Krt20 and Vil1 are significantly upregulated. Fabp1 and Aqp8 are also up but not significant. Apoa1 and Otop2 show mild but not significant downregulation.
Fetal-like revival Ambiguous. Ankrd1, Clu, Msln, Basp1, Tacstd1 show downregulation; ly6d, , anxa1, cscl12 show upregulation. But none are statistically significant.
EMT Show downregulation but none are statistically significant.
Want to take this research further?
Sign up free and the thread will land in your workspace so you can refine the question, ask follow-ups, or branch into related searches.