Sebastiaan (Seb) Vanuytven
@svanuytven.bsky.social
Computational postdoc @cedric-blanpain.bsky.social Lab | Tackling cancer one cell at the time | Science, Coffee, Chess, Running & Bouldering | Views are my own
https://behindthebioinformatics.substack.com/
https://behindthebioinformatics.substack.com/
Finally, we used this dataset to run the first single-cell benchmark of inferCNV, one of the most commonly used tools for inferring CNAs from single-cell transcriptome data, and discovered that these inference methods have limited accuracy. (7/9)
March 27, 2025 at 11:12 AM
Finally, we used this dataset to run the first single-cell benchmark of inferCNV, one of the most commonly used tools for inferring CNAs from single-cell transcriptome data, and discovered that these inference methods have limited accuracy. (7/9)
For the first time, we used matched transcriptome data to study gene dosage effects at single-cell resolution. We found a link between the 22q11.21 amplicon & drug-tolerant cell state plasticity (6/9)
March 27, 2025 at 11:12 AM
For the first time, we used matched transcriptome data to study gene dosage effects at single-cell resolution. We found a link between the 22q11.21 amplicon & drug-tolerant cell state plasticity (6/9)
Using Gtag&T, we uncovered small focal alterations on chromosomes 13 & 22 that were detectable at single-cell resolution. These differences in size, copy-number & structure were specific to different cancer subclones (5/9)
March 27, 2025 at 11:12 AM
Using Gtag&T, we uncovered small focal alterations on chromosomes 13 & 22 that were detectable at single-cell resolution. These differences in size, copy-number & structure were specific to different cancer subclones (5/9)
We applied Gtag&T-seq to a melanoma xenograft model before, during, and after treatment. Our findings reveal important differences in cell state plasticity and treatment response across cancer subclones (4/9)
March 27, 2025 at 11:12 AM
We applied Gtag&T-seq to a melanoma xenograft model before, during, and after treatment. Our findings reveal important differences in cell state plasticity and treatment response across cancer subclones (4/9)
Gtag&T significantly lowers the cost of single-cell genome & transcriptome sequencing while improving coverage uniformity compared to the original G&T-seq. More bang for your research buck! (3/9)
March 27, 2025 at 11:12 AM
Gtag&T significantly lowers the cost of single-cell genome & transcriptome sequencing while improving coverage uniformity compared to the original G&T-seq. More bang for your research buck! (3/9)
In this paper, we present #Gtag&T-seq — a revamped version of G&T-seq that enables simultaneous profiling of genome & transcriptome from the same single cell using direct genomic tagmentation (2/9)
March 27, 2025 at 11:12 AM
In this paper, we present #Gtag&T-seq — a revamped version of G&T-seq that enables simultaneous profiling of genome & transcriptome from the same single cell using direct genomic tagmentation (2/9)
In addition, NP137 therapy in mice transplanted with human lung cancer cells previously treated with TGFB1 (to induce EMT) decreases EMT in cancer cells (20/23)
November 19, 2024 at 1:55 PM
In addition, NP137 therapy in mice transplanted with human lung cancer cells previously treated with TGFB1 (to induce EMT) decreases EMT in cancer cells (20/23)
Finally, we examined the human and clinical relevance of our findings by correlating netrin-1 and UNC5B expression with several EMT signatures in human cancers. Although there was no correlation for netrin-1, there was a strong association for UNC5B expression and EMT (19/23)
November 19, 2024 at 1:55 PM
Finally, we examined the human and clinical relevance of our findings by correlating netrin-1 and UNC5B expression with several EMT signatures in human cancers. Although there was no correlation for netrin-1, there was a strong association for UNC5B expression and EMT (19/23)
A large overlap of genes down- or upregulated in both conditions was revealed by bulk RNA-seq of Ntn1-KD and Unc5b-KD tumour cells, indicating that netrin-1 and UNC5B regulate similar transcriptional programmes and signalling pathways (18/23)
November 19, 2024 at 1:55 PM
A large overlap of genes down- or upregulated in both conditions was revealed by bulk RNA-seq of Ntn1-KD and Unc5b-KD tumour cells, indicating that netrin-1 and UNC5B regulate similar transcriptional programmes and signalling pathways (18/23)
EPCAM+ tumour cells isolated from our mouse model go through EMT in vitro. Ntn1 or Unc5b knockdown significantly reduced this ability. Furthermore, we saw a decrease in cell migration that was not exacerbated by NP137 administration (17/23)
November 19, 2024 at 1:55 PM
EPCAM+ tumour cells isolated from our mouse model go through EMT in vitro. Ntn1 or Unc5b knockdown significantly reduced this ability. Furthermore, we saw a decrease in cell migration that was not exacerbated by NP137 administration (17/23)
Krt15 expression was high in the epithelial-B1 state, and GO term analysis of epithelial-B2 marker genes revealed increased glycolysis and keratinization (15/23)
November 19, 2024 at 1:55 PM
Krt15 expression was high in the epithelial-B1 state, and GO term analysis of epithelial-B2 marker genes revealed increased glycolysis and keratinization (15/23)
In the control tumour, lineage trajectory analysis revealed two distinct lineage trajectories, one from epithelial cells to hybrid EMT and the other from epithelial cells to late full EMT (13/23)
November 19, 2024 at 1:55 PM
In the control tumour, lineage trajectory analysis revealed two distinct lineage trajectories, one from epithelial cells to hybrid EMT and the other from epithelial cells to late full EMT (13/23)
In terms of EMT states, NP137 administration increased the proportion of the epithelial state while inhibiting the occurrence of the late EMT state, thereby blocking EMT progression at the hybrid EMT state (12/23)
November 19, 2024 at 1:55 PM
In terms of EMT states, NP137 administration increased the proportion of the epithelial state while inhibiting the occurrence of the late EMT state, thereby blocking EMT progression at the hybrid EMT state (12/23)
Following netrin-1 inhibition, we found a significant reduction in the expression of genes associated with EMT, hypoxia, angiogenesis, and inflammatory response across all tumour cells (11/23)
November 19, 2024 at 1:55 PM
Following netrin-1 inhibition, we found a significant reduction in the expression of genes associated with EMT, hypoxia, angiogenesis, and inflammatory response across all tumour cells (11/23)
The effect of NP137 treatment on the tumour microenvironment was studied using 10x scRNA-seq. In treated mice, we discovered a significant decrease in tumour cells and an increase in CAFs (10/23)
November 19, 2024 at 1:55 PM
The effect of NP137 treatment on the tumour microenvironment was studied using 10x scRNA-seq. In treated mice, we discovered a significant decrease in tumour cells and an increase in CAFs (10/23)
NP137 treatment in combination with cisplatin and 5-FU decreased the resistance to chemotherapy in tumours with EMT (9/23)
November 19, 2024 at 1:55 PM
NP137 treatment in combination with cisplatin and 5-FU decreased the resistance to chemotherapy in tumours with EMT (9/23)
Furthermore, this pharmacological inhibition of netrin-1 reduced the number of metastasis, demonstrating that NP137 treatment directly inhibits metastasis formation (8/23)
November 19, 2024 at 1:55 PM
Furthermore, this pharmacological inhibition of netrin-1 reduced the number of metastasis, demonstrating that NP137 treatment directly inhibits metastasis formation (8/23)
Administration of NP137, a blocking antibody targeting Netrin-1 treatment reduced the number of tumours per mouse as well as the proportion of tumour cells that underwent EMT (7/23)
November 19, 2024 at 1:55 PM
Administration of NP137, a blocking antibody targeting Netrin-1 treatment reduced the number of tumours per mouse as well as the proportion of tumour cells that underwent EMT (7/23)
We first tested the role of Netrin-1 in promoting EMT by overexpressing it in our mouse model. Netrin1 overexpression results in an increase in the number of tumours per mouse and the proportion of tumour cells undergoing EMT (6/23)
November 19, 2024 at 1:55 PM
We first tested the role of Netrin-1 in promoting EMT by overexpressing it in our mouse model. Netrin1 overexpression results in an increase in the number of tumours per mouse and the proportion of tumour cells undergoing EMT (6/23)
Our primary focus was on secreted factors predominantly expressed by mesenchymal tumour cells, with specific therapies already in use for human cancer treatment. Our most promising discovery was Netrin-1 (Ntn1) and its receptor Unc5b. (4/23)
November 19, 2024 at 1:55 PM
Our primary focus was on secreted factors predominantly expressed by mesenchymal tumour cells, with specific therapies already in use for human cancer treatment. Our most promising discovery was Netrin-1 (Ntn1) and its receptor Unc5b. (4/23)
In our quest for potential novel therapies, we performed RNA-seq on tumour cells from the skin squamous cell carcinoma model, previously characterised in the ground-breaking work of the fantastic Prof. Pastushenko and the 'bioinfomagician' Prof. Sifrim in 2018 (3/23)
November 19, 2024 at 1:55 PM
In our quest for potential novel therapies, we performed RNA-seq on tumour cells from the skin squamous cell carcinoma model, previously characterised in the ground-breaking work of the fantastic Prof. Pastushenko and the 'bioinfomagician' Prof. Sifrim in 2018 (3/23)