Profiles of alternative splicing in colorectal cancer and their clinical significance: A study based on large-scale sequencing dataResearch in Context

Background: Alternative splicing (AS), as a potent and pervasive mechanism of transcriptional regulatory, expands the genome's coding capacity and involves in the initiation and progression of cancer. Systematic analysis of alternative splicing in colorectal cancer (CRC) is lacking and greatly needed. Methods: RNA-Seq data and corresponding clinical information of CRC cohort were downloaded from the TCGA data portal. Then, a java application, known as SpliceSeq, was used to evaluate the RNA splicing patterns and calculate the Percent Spliced In (PSI) value. Differently expressed AS events (DEAS) were identified based on PSI value between paired CRC and adjacent tissues. DEAS and its splicing networks were further analyzed by bioinformatics methods. Kaplan-Meier, Cox proportional regression and unsupervised clustering analysis were used to evaluate the association between DEAS and patients' clinical features. Results: After strict filtering, a total of 34,334 AS events were identified, among which 421 AS events were found expressed differently. Parent genes of these DEAS play a important role in regulating CRC-related processes such as protein kinase activity (FDR<0.0001), PI3K-Akt signaling pathway (FDR = 0.0024) and p53 signaling pathway (FDR = 0.0143). 37 DEAS events were found to be associated with OS, and 68 DEAS events were found to be associated with DFS. Stratifying patients according to the PSI value of AT in CXCL12 and RI in CSTF3 formed significant Kaplan-Meier curves in both OS and DFS survival analysis. Unsupervised clustering analysis using DEAS revealed four clusters with distinct survival patterns, and associated with consensus molecular subtypes. Conclusions: Large differences of AS events in CRC appear to exist, and these differences are likely to be important determinants of both prognosis and biological regulation. Our identified CRC-related AS events and uncovered splicing networks are valuable in deciphering the underlying mechanisms of AS in CRC, and provide clues of therapeutic targets to further validations. Keywords: CRC, Alternative splicing, RNA-Seq, Prognosi

E-syt1 Re-arranges STIM1 Clusters to Stabilize Ring-shaped ER-PM Contact Sites and Accelerate Ca2+ Store Replenishment

International audienceIn many non-excitable cells, the depletion of endoplasmic reticulum (ER) Ca2+ stores leads to the dynamic formation of membrane contact sites (MCSs) between the ER and the plasma membrane (PM), which activates the store-operated Ca2+ entry (SOCE) to refill the ER store. Two different Ca2+-sensitive proteins, STIM1 and extended synaptotagmin-1 (E-syt1), are activated during this process. Due to the lack of live cell super-resolution imaging, how MCSs are dynamically regulated by STIM1 and E-syt1 coordinately during ER Ca2+ store depletion and replenishment remain unknown. With home-built super-resolution microscopes that provide superior axial and lateral resolution in live cells, we revealed that extracellular Ca2+ influx via SOCE activated E-syt1s to move towards the PM by ~12 nm. Unexpectedly, activated E-syt1s did not constitute the MCSs per se, but re-arranged neighboring ER structures into ring-shaped MCSs (230~280 nm in diameter) enclosing E-syt1 puncta, which helped to stabilize MCSs and accelerate local ER Ca2+ replenishment. Overall, we have demonstrated different roles of STIM1 and E-syt1 in MCS formation regulation, SOCE activation and ER Ca2+ store replenishment

Syntaxin-3 Binds and Regulates Both R- and L-Type Calcium Channels in Insulin-Secreting INS-1 832/13 Cells.

Syntaxin (Syn)-1A mediates exocytosis of predocked insulin-containing secretory granules (SGs) during first-phase glucose-stimulated insulin secretion (GSIS) in part via its interaction with plasma membrane (PM)-bound L-type voltage-gated calcium channels (Cav). In contrast, Syn-3 mediates exocytosis of newcomer SGs that accounts for second-phase GSIS. We now hypothesize that the newcomer SG Syn-3 preferentially binds and modulates R-type Cav opening, which was postulated to mediate second-phase GSIS. Indeed, glucose-stimulation of pancreatic islet β-cell line INS-1 induced a predominant increase in interaction between Syn-3 and Cavα1 pore-forming subunits of R-type Cav2.3 and to lesser extent L-type Cavs, while confirming the preferential interactions between Syn-1A with L-type (Cav1.2, Cav1.3) Cavs. Consistently, direct binding studies employing heterologous HEK cells confirmed that Syn-3 preferentially binds Cav2.3, whereas Syn-1A prefers L-type Cavs. We then used siRNA knockdown (KD) of Syn-3 in INS-1 to study the endogenous modulatory actions of Syn-3 on Cav channels. Syn-3 KD enhanced Ca2+ currents by 46% attributed mostly to R- and L-type Cavs. Interestingly, while the transmembrane domain of Syn-1A is the putative functional domain modulating Cav activity, it is the cytoplasmic domain of Syn-3 that appears to modulate Cav activity. We conclude that Syn-3 may mimic Syn-1A in the ability to bind and modulate Cavs, but preferring Cav2.3 to perhaps participate in triggering fusion of newcomer insulin SGs during second-phase GSIS

Syn-3 preferentially binds Ca_v2.3 while Syn-1A preferentially binds Ca_v1.3.

<p>Representative blots show HEK293 cells co-transfected with Ca_v1.3 (A) or Ca_v2.3 (C) with either Syn-1A or Syn-3, then subjected to co-IP with anti-Syn-1A or Syn-3 antibody. Co-precipitated proteins were identified with the indicated antibodies. Densitometric analysis of the co-precipitated Ca_v1.3 (B) or Ca_v2.3 (D), expressed as percent recovery of total lysate inputs. Values are means±SEM, n = 3; *p<0.05, **p<0.01.</p

Syn-3 co-immunoprecipitates (IP) distinct Ca_vs than Syn-1A in INS-1 cells.

<p>Syn-3 (A) and Syn-1A (C) interactions with the indicated Ca_vα1 subunits (Ca_v1.2, Ca_v1.3, Ca_v2.3 and Ca_v2.2) and auxiliary subunits (α₂δ-1 and β3) and SNAP25 in INS-1 cells. Densitometric analysis of Syn-3 co-IP (B) and Syn-1A co-IP (D), expressed as percent recovery of total lysate inputs (which showed equal protein loading in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147862#pone.0147862.s001" target="_blank">S1 Fig</a>), shows that high glucose (16.7 mM) plus GLP-1 (10 nM) increased the association of these syntaxins with the respective Ca_vs. Values are means±SEM, n = 3. *p<0.05, ***p<0.001, NS: not significant. As control (E) shows representative blots from five separate co-IP experiments with pre-immune IgG, which did not bring down syntaxins or Ca_vs (<i>left</i> lanes). <i>Righ</i>t lanes show the input lysates. All five experiments probed for the Ca_v α subunits and α₂δ-1, whereas β3, Syn-3 and Syn-1A were probed on two blots from separate experiments.</p

Cytoplasmic Syn-3 domain but not cytoplasmic Syn-1A domain regulates Ca_v currents.

<p>(A) GST-Syn-3 cytoplasmic domain (a.a. 1–263) or GST-Syn-1A cytoplasmic domain (a.a. 1–265) or GST (control) was dialyzed into INS-1 cells, then Ca_v currents recorded. Shown are representative traces in the whole-cell mode with stimulation from −80–60 mV. (B) Current-voltage relationship of Ca_v channels. Currents were normalized to cell capacitance to yield current density. (C) Bar chart showing the maximum current density in INS-1 cells dialyzed with GST control (n = 9), GST-Syn-3 (n = 9), or GST-Syn-1A (n = 8). Values are means±SEM; *p<0.05; NS: no significant difference. (D and E) Representative blots show HEK293 cells transfected with Ca_v1.3 (D) or Ca_v2.3 (E) subjected to pull down with 300 pmol of GST-Syn-1A (a.a. 1–265), GST-Syn-3 (a.a. 1–263) or GST. (F) Summary analysis of four separate experiments. Data was expressed as means ± SEM; *p<0.05.</p