Biology subjects

Krawczyk, P.

Publications and source records attributed to Krawczyk, P..

6 recordsLinked to original sources

bioRxiv2025

Post-transcriptional control of enamel matrix mineralization by TENT5A-mediated cytoplasmic polyadenylation

Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis. TeaserTENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.

developmental biology↗

bioRxiv2024

Terminal nucleotidyltransferase Tent2 microRNA tailing regulates excitatory/inhibitory balance in the hippocampus

One of the post-transcriptional mechanisms regulating the stability of RNA molecules involves the addition of non-templated nucleotides to their 3 ends, a process known as RNA tailing. To systematically investigate the physiological consequences of terminal nucleotidyltransferase TENT2 absence on RNA 3 end modifications in the mouse hippocampus we developed a new Tent2 knockout mouse. Electrophysiological measurements revealed increased excitability in Tent2 KO hippocampal neurons, and behavioral analyses showed decreased anxiety and improved fear extinction in these mice. At the molecular level, we observed a significant contribution of TENT2 to the monoadenylation of various classes of miRNAs, but found no effect of the enzymes loss on the total poly(A) tail length of mRNAs, as measured by Direct Nanopore RNA sequencing. Alterations in monoadenylation of a large population of microRNAs affected the overall mRNA abundance, particularly transcripts related synaptic transmission, which were downregulated in the hippocampus of Tent2 knockout mice. These changes explain the observed behavioral and electrophysiological alterations. Our data thus establish a link between TENT2-dependent microRNA tailing and the balance of inhibitory and excitatory neurotransmission.

neuroscience↗

bioRxiv2023

Polyadenylation of mRNAs encoding secreted proteins by TENT5 family of enzymes is essential for gametogenesis in mice.

Cytoplasmic polyadenylation plays a vital role in gametogenesis, however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of 4 TENT5 poly(A) polymerases in mice fertility and gametogenesis. TENT5B and TENT5C play crucial, but redundant roles in oogenesis, with double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display gain-of-function infertility effect with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, shown by sterility of males with either genes knockout mutation. Finally, Tent5a knockout significantly lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through Direct RNA sequencing we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motives analysis and reporter mRNA assay revealed that the presence of endoplasmic reticulum-leader represents the primary determinant of TENT5-mediated regulation.

developmental biology↗

bioRxiv2023

mRNA decay can be uncoupled from deadenylation during stress response

The polyadenosine tail (pA-tail) regulates mRNA nuclear export, stability, and translatability. Based on reporter constructs, the prevailing model suggests that pA-tail removal mediated by Ccr4-NOT or PAN2/3 deadenylases is required for mRNA decapping and degradation. Here, we use direct RNA sequencing to track mRNA deadenylation and decay at steady-state and in stress conditions to show a global correlation between deadenylation and decay. Interestingly, codon optimality, previously postulated to dictate mRNA stability, only strongly affects decay of conserved and abundant transcripts, such as coding for ribosomal protein subunits. Degradation of those mRNAs is also accelerated in response to stress. Still, the in-depth analysis revealed that deadenylation is a factor that contributes to degradation but is not indispensable for decapping. We further demonstrate that deadenylation is the fastest for newly made tails depending on polyA-binding protein Pab1. Unexpectedly, decapping initiates on mRNAs of pA-tails of 20-35 adenosines presumably bound by Pab1.

molecular biology↗

bioRxiv2021

Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer

Despite the fact that tumor microenvironment (TME) and gene mutations are the main determinants of progression of the deadliest cancer in the world - lung cancer - their interrelations are not well understood. Digital pathology data provide a unique insight into the spatial composition of the TME. Various spatial metrics and machine learning approaches were proposed for prediction of either patient survival or gene mutations from these data. Still, these approaches are limited in the scope of analyzed features and in their explainability and as such fail to transfer to clinical practice. Here, we generated 23,199 image patches from 55 hematoxylin-and-eosin (H&E)-stained lung cancer tissue sections and annotated them into 9 different tissue classes. Using this dataset, we trained a deep neural network ARA-CNN, achieving per-class AUC ranging from 0.72 to 0.99. We applied the trained network to segment 467 lung cancer H&E images downloaded from The Cancer Genome Atlas (TCGA) database. We used the segmented images to compute human interpretable features reflecting the heterogeneous composition of the TME, and successfully utilized them to predict patient survival (c-index 0.723) and cancer gene mutations (largest AUC 73.5% for PDGFRB). Our approach can be generalized to different cancer types to inform precision medicine strategies.

bioinformatics↗

bioRxiv2020

Cytoplasmic polyadenylation by TENT5A is required for proper bone formation

Osteoblasts orchestrate bone formation by secreting dense, highly cross-linked type I collagen and other proteins involved in osteogenesis. Mutations in Col11, Col12, or collagen biogenesis factors lead to the human genetic disease, osteogenesis imperfecta (OI). Herein, we show that the TENT5A gene, whose mutation is responsible for poorly characterized type XVIII OI, encodes an active cytoplasmic poly(A) polymerase regulating osteogenesis. TENT5A is induced during osteoblast differentiation and TENT5A KO osteoblasts are defective in mineralization. The TENT5A KO mouse recapitulates OI disease symptoms such as bone fragility and hypomineralization. Direct RNA sequencing revealed that TENT5A polyadenylates and increases expression of Col11 and Col12 RNAs, as well as those of other genes mutated in OI, resulting in lower production and improper folding of collagen chains. Thus, we have identified the specific pathomechanism of XVIII OI and report for the first time a biologically relevant post-transcriptional regulator of collagen production. We further postulate that TENT5A, possibly together with its paralogue TENT5C, is responsible for the wave of cytoplasmic polyadenylation of mRNAs encoding secreted proteins occurring during bone mineralization.

genetics↗