Multi-Omics Immune Interaction Networks in Lung Cancer Tumorigenesis, Proliferation, and Survival.

There are currently no effective biomarkers for prognosis and optimal treatment selection to improve non-small cell lung cancer (NSCLC) survival outcomes. This study further validated a seven-gene panel for diagnosis and prognosis of NSCLC using RNA sequencing and proteomic profiles of patient tumors. Within the seven-gene panel, ZNF71 expression combined with dendritic cell activities defined NSCLC patient subgroups (n = 966) with distinct survival outcomes (p = 0.04, Kaplan-Meier analysis). ZNF71 expression was significantly associated with the activities of natural killer cells (p = 0.014) and natural killer T cells (p = 0.003) in NSCLC patient tumors (n = 1016) using Chi-squared tests. Overexpression of ZNF71 resulted in decreased expression of multiple components of the intracellular intrinsic and innate immune systems, including dsRNA and dsDNA sensors. Multi-omics networks of ZNF71 and the intracellular intrinsic and innate immune systems were computed as relevant to NSCLC tumorigenesis, proliferation, and survival using patient clinical information and in-vitro CRISPR-Cas9/RNAi screening data. From these networks, pan-sensitive and pan-resistant genes to 21 NCCN-recommended drugs for treating NSCLC were selected. Based on the gene associations with patient survival and in-vitro CRISPR-Cas9, RNAi, and drug screening data, MEK1/2 inhibitors PD-198306 and U-0126, VEGFR inhibitor ZM-306416, and IGF-1R inhibitor PQ-401 were discovered as potential targeted therapy that may also induce an immune response for treating NSCLC.

A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells.

Loss of photoreceptors due to retinal degeneration is a major cause of untreatable visual impairment and blindness. Cell replacement therapy, using retinal stem cell (RSC)-derived photoreceptors, holds promise for reconstituting damaged cell populations in the retina. One major obstacle preventing translation to the clinic is the lack of validated markers or strategies to prospectively identify these rare cells in the retina and subsequently enrich them. Here, we introduce a microfluidic platform that combines nickel micromagnets, herringbone structures, and a design enabling varying flow velocities among three compartments to facilitate a highly efficient enrichment of RSCs. In addition, we developed an affinity enrichment strategy based on cell-surface markers that was utilized to isolate RSCs from the adult ciliary epithelium. We showed that targeting a panel of three cell surface markers simultaneously facilitates the enrichment of RSCs to 1 : 3 relative to unsorted cells. Combining the microfluidic platform with single-cell whole-transcriptome profiling, we successfully identified four differentially expressed cell surface markers that can be targeted simultaneously to yield an unprecedented 1 : 2 enrichment of RSCs relative to unsorted cells. We also identified transcription factors (TFs) that play functional roles in maintenance, quiescence, and proliferation of RSCs. This level of analysis for the first time identified a spectrum of molecular and functional properties of RSCs.

Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells.

During development, multipotent progenitors undergo temporally-restricted differentiation into post-mitotic retinal cells; however, the mechanisms of progenitor division that occurs during retinogenesis remain controversial. Using clonal analyses (lineage tracing and single cell cultures), we identify rod versus cone lineage-specific progenitors derived from both adult retinal stem cells and embryonic neural retinal precursors. Taurine and retinoic acid are shown to act in an instructive and lineage-restricted manner early in the progenitor lineage hierarchy to produce rod-restricted progenitors from stem cell progeny. We also identify an instructive, but lineage-independent, mechanism for the specification of cone-restricted progenitors through the suppression of multiple differentiation signaling pathways. These data indicate that exogenous signals play critical roles in directing lineage decisions and resulting in fate-restricted rod or cone photoreceptor progenitors in culture. Additional factors may be involved in governing photoreceptor fates in vivo.