Weekly reads: CTCF, Sox transcription factors, Clinic fires back, more

I’m taking a short break today from working on a big grant to put out this weekly reads post including on Sox transcription factors, cord blood paper controversy, and other interesting papers such as one on CTCF and chromatin domains after mitosis that really struck me.

I can actually see blue sky today here in Northern California, which is a relief from days of air full of smoke and ash from all the California fires.

We reached another milestone on our Stem Cell Channel on YouTube with more than 200 subscribers. Please check it out.

SOX transcription factors in stem cells and disease

Insights into the mechanisms underlying aberrant SOX11 oncogene expression in mantle cell lymphoma, Lymphoma. Sox11 is a transcription factor that regulates stem cells and certain aspects of development. It fits into the category of oncodevelopmental transcription factors that are an interest of mine.

SOX10 ablation severely impairs the generation of postmigratory neural crest from human pluripotent stem cells, Cell Death & Disease. Here’s an example of another related SOX family factor functioning in stem cells.

You can see a movie of the structure of Sox factors bound to DNA above.

Clinic fires back on criticism of Stem Cells Translational Medicine pub

Addressing concerns regarding associated costs, transparency, and integrity of research in recent stem cell trial, Stem Cells Translational Medicine. Here we have a stem cell clinic responding to criticism of their recent Stem Cells Translational Medicine paper, including from Jeremy Snyder and Leigh Turner.

For instance, the clinic authors claim in this new piece that they do not charge trial participants for the experimental therapy, but that the $7,000+ that families pay is for incidental expenses. Thus, they argue, their study is not “pay-for-play.” I’m curious what others think. The clinic here is The Stem Cell Institute in Panama I reviewed The Stem Cell Institute here on The Niche recently. In my fact checking I found numerous reasons for concern.

The clinic authors also note their cautious tone in discussing their trial results. Part of the challenge for a clinic in publishing a paper like the one at the heart of this discussion is that the clinic is already selling this unproven treatment. In that case, is simply declaring your COI sufficient?

Stem Cells Translational Medicine has had more than its share of controversy over the last few years, mostly related to publication of papers on cord blood studies.

Other notable papers

• CTCF and transcription influence chromatin structure re-configuration after mitosis, Nat Comm. How can cells possibly reestablish their vast arrays of epigenetic and chromatin configurations after each mitosis? It seems CTCF is central to this process, which makes sense given its role in defining chromatin domain boundaries.

• State‐of‐play for cellular therapies in cardiac repair and regeneration, Stem Cells. At present it seems the general consensus in the field is that there are not meaningful populations of endogenous heart stem cells that can mediate repair in the adult heart. So can that be countered by cell transplants? If so, the two main mechanisms appear to be  cell replacement via engraftment and paracrine functions. See model by the authors above.

• The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms, Cell Reports

• De novo DNA methyltransferases DNMT3A and DNMT3B are essential for XIST silencing for erosion of dosage compensation in pluripotent stem cells, Stem Cell Reports

• Aspartate availability limits hematopoietic stem cell function during hematopoietic regeneration, Cell Stem Cell
• OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human, Nat Comm.