Gene expression using the PALM system

LCM-Seq for Retinal Cell Layer-Specific Responses During Optic Nerve Regeneration

LCM-seq is a powerful tool for gene expression analysis from individual or groups of cells that can be spatially isolated. Within the visual system, retinal ganglion cells (RGCs), the cells that connect the eye to the brain through the optic nerve, reside in the retinal ganglion cell layer of the retina. This well-defined location provides a unique opportunity to harvest RNA by laser capture microdissection (LCM) from a highly enriched cell population. Using this method, it is possible to explore transcriptome-wide changes in gene expression following optic nerve injury. In the zebrafish model, this method can be used to identify molecular events driving successful optic nerve regeneration in contrast to mammals that fail to regenerate axons in the central nervous system. Here we provide a method for LCM from the different retinal layers of zebrafish following optic nerve injury and during the process of optic nerve regeneration. Purified RNA from this protocol is sufficient for RNA-seq or other downstream analysis.

Laser capture microdissection protocol for gene expression analysis in the brain

Laser capture microdissection (LCM) allows the isolation of specific cell populations from complex tissues that can be then used for gene expression studies. However, there are no reproducible protocols to study RNA in the brain and, particularly, in the substantia nigra. RNA is a very labile biomolecule that is easily degraded during manipulation. LCM studies use low amounts of material and special precautions must be taken to preserve RNA yield and integrity, which are decisive for PCR analysis. The RNA yield and/or integrity can be affected negatively by tissue manipulation, LCM process and RNA extraction. We have optimized these three critical steps using nigral tissue sections, and developed a LCM protocol to obtain high-quality RNA for gene expression analysis. The optimal LCM protocol requires the use of 20 µm-thick tissue sections mounted on glass slides and processed for rapid tyrosine hydroxylase immunofluorescence. Additionally, a total microdissected tissue area of 1 mm² and a column-based RNA extraction method were used to obtain a high RNA yield and integrity. In the rat substantia nigra, we demonstrated the expression of RNA for the angiotensin type 1 and type 2 receptors using this optimized LCM protocol. In conclusion, the LCM protocol reported here can be used to study the expression of both scarcely or abundantly expressed genes in the different brain regions of mammals under both physiological and pathological conditions.

Glomerular and tubulointerstitial miR-638, miR-198 and miR-146a expression in lupus nephritis

AIM

MicroRNAs (miRNAs) play important roles in the pathogenesis of autoimmune diseases. We studied the intra-renal expression of miRNA targets that were reported to be differentially expressed in peripheral blood or urine between lupus nephritis (LN) patients and normal controls.

METHODS

We quantified the expression of in glomerulus and tubulointerstitium of miR-146a, miR-155, miR-198 miR-638 and miR-663 in 42 patients with LN and 10 healthy controls.

RESULTS

As compared with controls, LN patients had lower glomerular expression of miR-638 (P < 0.001) but higher tubulointerstitial expression of this target (P = 0.001). Both glomerular and tubulointerstitial expression of miR-198 were higher in LN patients than controls (P < 0.001). For miR-146a, LN patients only had higher expression in glomerulus (P = 0.005) but not in tubulointerstitium. Tubulointerstitial miR-638 expression was significantly correlated with proteinuria (r = 0.404; P = 0.022) and disease activity score (r = 0.454; P = 0.008), while glomerular miR-146a expressions were correlated with estimated GFR (r = 0.453; P = 0.028) and histological activity index (r = 0.494; P = 0.027).

CONCLUSION

We found that intra-renal expression of miR-638, miR-198 and miR-146a are differentially expressed between LN patients and normal controls. Furthermore, the degree of change in glomerular miR-146a and tubulointerstitial miR-638 expression correlated with clinical disease severity. The results suggested that these miRNA targets may play a role in the pathogenesis of lupus nephritis.