Biology subjects

Lapierre, J.

Publications and source records attributed to Lapierre, J..

4 recordsLinked to original sources

bioRxiv2025

SRRM1 coordinates an alternative splicing program that promotes expression of oncogenic protein isoforms.

The alternative splicing of the adapter protein NUMB is dysregulated in multiple cancer types, regulating its functional divergence towards either tumor suppression or oncogenesis in an isoform-dependant manner. Here we utilized a NUMB exon 9 (E9) splicing reporter in a genome-wide CRISPR screen to identify splicing regulators SRRM1 and SRSF11 that promote NUMB oncogenic splicing in colorectal, lung and breast cancer cell lines. We show that SRRM1 and SRSF11 share common protein interactors, RNA targets and effects on an oncogenic splicing program which favors the expression of pro-tumorigenic isoforms. In addition to NUMB E9, SRRM1 regulates cancer-associated splicing events in genes encoding signaling proteins, transcription factors and actin cytoskeleton regulators, many of which are also developmentally regulated, including CD44, MKNK2, ECT2, DIAPH1, KAT5, TCF7L2, FOXM1 and TBX3. Loss of SRRM1 in colorectal and lung cancer cells reduces cell proliferation, colony formation and invasion capabilities, as well as expression of tumour promoters Cyclin D1, Notum, and PRDX2. Our data indicate that SRRM1 regulation of alternative splicing represents a node to target multiple properties of malignant cells, with broad effects on cellular signaling, proliferation, EMT, apoptosis resistance and stemness.

cancer biology↗

bioRxiv2023

Converging PMF calculations of antibiotic permeation across an outer membrane porin with sub-kilocalorie per mole accuracy

The emergence of multi-drug resistant pathogens led to a critical need for new antibiotics. A key property of effective antibiotics against Gram-negative bacteria is their ability to permeate through the bacterial outer membrane via transmembrane porin proteins. Molecular dynamics (MD) simulations are in principle capable of modeling antibiotic permeation across outer membrane porins (OMPs). However, owing to sampling problems, it has remained challenging to obtain converged potentials of mean force (PMFs) for antibiotic permeation across OMPs. Here, we investigated the convergence of PMFs obtained with three advanced flavors of the umbrella sampling (US) technique aimed to quantify the permeation of the antibiotic fosmidomycin across the OprO porin: (i) Hamiltonian replica-exchange with solute tempering in combination with US, (ii) simulated tempering-enhanced US, and (iii) replica-exchange US. To quantify the PMF convergence and to reveal hysteresis problems, we computed several independent sets of US simulations started from pulling simulations in outward and inward permeation directions. We find that replica-exchange US in combination with well-chosen restraints is highly successful for obtaining converged PMFs of fosmidomycin permeation through OprO, reaching PMFs converged to sub-kilocalorie per mole accuracy. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/534415v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1ecfd61org.highwire.dtl.DTLVardef@1ef1445org.highwire.dtl.DTLVardef@11be702org.highwire.dtl.DTLVardef@db6202_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

DNA opening during transcription initiation by RNA polymerase II in atomic detail

RNA polymerase II (RNAP II) is a macro-molecular complex that synthesizes RNA by reading the DNA code, a process called transcription. During transcription initiation, RNAP II opens the double-stranded DNA to expose the DNA template to the active site. The molecular interactions driving and controlling the DNA opening are not well understood. We used all-atom molecular dynamics (MD) simulations to obtain a continuous atomistic pathway for the DNA opening process in human RNAP II. To achieve such large-scale and highly nonlinear transition, we steered the MD simulations along a combination of collective variables involving a guided DNA rotation and a set of path collective variables. The simulations reveal extensive interactions of the DNA with three protein loops near the active site, namely the rudder, fork loop 1, and fork loop 2. According to the simulations, these DNA-protein interactions support DNA opening by attacking Watson-Crick hydrogen bonds, and they stabilize the open DNA bubble by the formation of a wide set of DNA-protein salt bridges.

biophysics↗

bioRxiv2019

ZIKA VIRUS INFECTION DURING PREGNANCY AND INDUCED BRAIN PATHOLOGY IN BECLIN1-DEFICIENT MOUSE MODEL

We investigated the role of the autophagy protein, Beclin1, in the replication and disease of Zika virus (ZIKV) in pregnant dams and their offspring using Beclin1-deficient (Atg6+/-) and wild-type (Atg6+/+) mouse model infected with the Honduran (R103451), Puerto Rican (PRVABC59), and the Uganda (MR766) strains of ZIKV. Pregnant dams infected subcutaneously at embryonic stage (E)9 showed viral RNA in serum harvested at E13 and in various organs removed postmortem at E17. Subcutaneous infections with ZIKV also showed the vertical transmission of ZIKV from the placenta to embryos removed postmortem at E17. From the three isolates, R103451-infected Atg6+/- dams had the lowest mortality rate while 30 % of their offspring containing the hemizygous beclin1 allele (Atg6+/-) were smaller in size and had smaller and underdeveloped brain. Growth impairment in the pups became noticeable after two weeks post-birth. After 21-days, pups were sacrificed and brain tissues removed postmortem showed expression of the envelope (E) and the non-structural (NS)-1 proteins, along with signs of neuronal injury, despite an absence in viral RNA detection. A significant decrease in the mRNA expression levels of the insulin-like growth factor-1 (IGF-1) by 8-fold and a decrease in the mRNA expression levels of several microcephaly related genes along with an increase in the secretion of several inflammatory molecules may have contributed to the observed phenotype. Since autophagy regulates cytokines and chemokines production, a dysregulation in this pathway may have further exacerbated the pathology of ZIKV. IMPORTANCEPups delivered from ZIKV-infected dams showed significant growth impairments in the body and the brain. We believe that the reduction in insulin growth factor together with the increase secretion of inflammatory molecules may have triggered neuronal injury and the downregulation of the microcephalic genes, while reduced expression of the autophagy protein, Beclin1 further exacerbated the pathology. Although the mechanism is still unknown, the autophagy pathway seems to play a key role in ZIKV pathology. It is therefore of great significance to study the role of autophagy during viral infection with the goal to identify potential targets for anti-ZIKV therapeutic intervention.

immunology↗