Re-evaluating the general(ized) roles of AMPK in cellular metabolism.

AMPK is a protein kinase activated by various cellular stresses such as glucose deprivation, hypoxia or exercise. Despite having been studied for decades only a limited number of targets have been well described in tissues as varied as liver, muscle, and adipose tissue. Recent studies have shown that AMPK does not function in a similar manner, or through identical targets, in all cellular situations, posing challenges to some accepted paradigms describing AMPK function. A combination of genetic models and cell biological analysis of AMPK function in specific cell/developmental/environmental contexts will be required to accurately complement our understanding of the role(s) of AMPK in cancer, diabetes and other diseases.

Diverse genomic integration of a lentiviral vector developed for the treatment of Wiskott-Aldrich syndrome.

BACKGROUND: The genomic integration of a lentiviral vector developed for the treatment of Wiskott-Aldrich syndrome (WAS) was assessed by localizing the vector insertion sites (IS) in a murine model of gene therapy for the disease. METHODS: Transduced hematopoietic progenitor cells were transplanted into mice or cultured in vitro. The IS were determined in the genomic DNA from blood, the bone marrow of the animals and from cultured cells. RESULTS: Sequencing vector-genomic DNA junctions yielded more than 150 IS of which 50-70% were located in transcription units. To obtain additional sequences from the population of cultured cells, we used a vector-tag concatenation technique providing 190 additional IS. Altogether, the profiles confirmed the bias for integration in transcription units. The vector did not congregate as hotspots and did not appear to target specific categories of genes. The diversity of the IS reflected the initial marking of a polyclonal population of cells. However, relatively few vector IS were found in vivo because only 30-40 unique IS were identified in each mouse using this approach. Although four to ten IS were shared by the blood and bone marrow, no common IS was found between mice or between any mouse and the cultured cells. CONCLUSIONS: Taken as a whole, the pattern of genomic insertion of the WAS lentiviral vector was diverse and similar to that previously described for other HIV-1-derived lentiviral vectors. Testing cells destined for transplantation is unlikely to predict specific IS to be selected in vivo.

A high throughput method for genome-wide analysis of retroviral integration.

Retroviral and lentiviral vectors integrate their DNA into the host cell genome leading to stable transgene expression. Integration preferentially occurs in the proximity of active genes, and may in some case disturb their activity, with adverse toxic consequences. To efficiently analyze high numbers of lentiviral insertion sites in the DNA of transduced cells, we developed an improved high-throughput method called vector integration tag analysis (VITA). VITA is based on the identification of Genomic Tags associated to the insertion sites, which are used as signatures of the integration events. We use the capacity of MmeI to cleave DNA at a defined distance of its recognition site, in order to generate 21 bp long tags from libraries of junction fragments between vector and cellular DNA. The length of the tags is sufficient in most cases, to identify without ambiguity an unique position in the human genome. Concatenation, cloning and sequencing of the tags allow to obtain information about 20-25 insertion sites in a single sequencing reaction. As a validation of this method, we have characterized 1349 different lentiviral vector insertion sites in transduced HeLa cells, from only 487 sequencing reactions, with a background of <2% false positive tags.