Shengwen Calvin Li

University of California, Irvine | UCI · CHOC Children's Hospital Research Institute

patient-derived xenograft (PDX): Go or No-go model?

Advantage: "The tumour that grows inside will provide cells that can be transferred to more mice - explants for drug screening - personalized mouse model."

However, how do you know it's accurate subcloning of original patient tumor? any beginning and end-point measurement? How do you know you got fresh human tumour fragments? What assays (biomarkers, biochemical, chrmsm, genome) do you assess your PDXs accurately model its original tumour behaviour in patients? Can you use PDXs to test immunotherapies so that you can make a call which immunotheray to go for a patient? How do you know if PDXs change in mice over time? If change occurs, how can you predict which way? Can you manage such change?

Any advice on Cytochromes P450 (CYP) panel on chemotherapy? What's your gene list? Clinically, Roche got an FDA-approved panel but is outdated and limited - do you have an updated list?

Cytochromes P450 (CYP) are a major source of variability in drug pharmacokinetics and response. Of 57 putatively functional human CYPs only about a dozen enzymes, belonging to the CYP1, 2, and 3 families, are responsible for the biotransformation of most foreign substances including 70–80% of all drugs in clinical use. The highest expressed forms in liver are CYPs 3A4, 2C9, 2C8, 2E1, and 1A2, while 2A6, 2D6, 2B6, 2C19 and 3A5 are less abundant and CYPs 2J2, 1A1, and 1B1 are mainly expressed extrahepatically.http://www.sciencedirect.com/science/article/pii/S0163725813000065

Can you recommend me a panel biomarker for B-cell precursor acute lymphoblastic leukemia (ALL)? I'd like to design a panel to check ALL status: ideally predict the time to recurrent/relapse, drug response, etc. Any advice is greatly appreciated. Thx.

Can you tell me how to determine gene copy number without using WGS or Southern blotting? Any thoughts? I's told by a colleague to use array CGH. This is kind of like a microarray designed against specific regions of the genome. You look at the signal generated from a universal pooled reference DNA versus the sample of interest. If the signal for your sample is greater than the reference that means there is a copy number gain, if the value for the sample is less than the reference, that means that you have a loss. However, how can you detect hybrid CNVs?

How can you figure out the copy number of genes in a cancer cell line without using Southern blotting and whole genome sequencing?

Does anybody try any alternative ways? Any advice is greatly appreciated. Thx.

Reading single cell papers made me wonder why researchers use 100 cells, 500 cells, or 1000 cells?  What's criterion to call such numbers? How do you know you got the whole picture by using such a number in your paper? "The population average is a lie." However, those heat maps (clustering) are averaged out of single cells. You call "single cell analysis" - but you still cluster those single cells - sounds you average out of "single cells."

Given cancer heterogeneity is evolving, how do you know the number of single cells  you use at a time point represent or capture the cancer heterogeneity?

What's your thinking?  

Creating an engineered tissue graft is a challenge - concrete detailed protocols are rare and quite welcomed.