Biology subjects

Doering, M.

Publications and source records attributed to Doering, M..

4 recordsLinked to original sources

bioRxiv2026

Characterization of the upper epithelial compartment of cervical HSIL

High-grade squamous intraepithelial lesions (HSIL) of the uterine cervix result from transformation by high-risk human papillomavirus (HR-HPV) and are considered precancerous lesions. Depending on the proportion of the epithelium occupied by dysplastic cells, commonly evidenced by a block-like p16INK4a staining pattern, HSIL are subdivided into CIN2 or CIN3. We used immunohistochemistry (IHC) and laser-capture microdissection (LCM) to further characterize these lesions. Broad suprabasal expression of S100A9, a component of the epidermal differentiation complex (EDC), which we had previously found to be up-regulated in genus-beta-HPV-positive skin lesions, was present in the normal exocervix and declined gradually with increasing CIN grade. In CIN2 in particular, the S100A9 staining pattern was nearly complementary to the block-like p16INK4a expression. However, it largely coincided with the expression of CD63, a marker showing strong expression in cervical crypts and in columnar cells within the normal transformation zone, also those overlying reserve cells. We then used LCM to analyze both the p16INK4a- and S100A9/CD63-positive compartments in HSIL separately. Notably, in all samples investigated, we detected the same HR-HPV type (either HPV16, 45 or 51) in both compartments of the same HSIL, while tissue samples dissected from normal exocervix or transformation zone were consistently HR-HPV-negative. Our data suggest that the upper, S100A9-positive maturing compartment of HSILs retaining weak CD63 expression may represent a residual, HR-HPV-infected columnar-cell-derived epithelium, rather than not-yet-transformed squamous epithelium that is progressively being replaced by dysplastic cells. The two-compartment architecture of these HSILs was reminiscent of the staining pattern in the normal transformation zone, where columnar cells overlie reserve cells, and compatible with HR-HPV infection of columnar-derived cells but transformation of reserve cells, the putative origin of cervical squamous cell carcinoma. Our findings have direct clinical implications. Since the upper and lower layers of HSIL appear to form distinct epithelial compartments, our study suggests that the extent and thickness of the HR-HPV-transformed lower compartment itself, rather than the proportion of the epithelium occupied by dysplastic layers, may be the decisive factor in determining the HSIL grade.

Cancer Biology↗

bioRxiv2026

Unraveling Xanthomonas acetyltransferase GumG: decoding catalytic promiscuity, understanding the mechanism, and enhancing enzymatic versatility

Xanthan is a structurally complex exopolysaccharide produced by Xanthomonas campestris and one of the most extensively studied microbial biopolymers. As a sustainable alternative to petroleum-based polymers, its broader application requires precise control of polysaccharide decoration, yet the enzymatic basis of these modifications remains incompletely understood. Here, we characterise the activity and substrate scope of GumG, an AT-3 domain-containing membrane-bound acetyltransferase responsible for xanthan O-acetylation. Using mass spectrometry in combination with in vitro and in vivo assays, we show that GumG mediates non-specific acetylation of the outer mannose residue and displays pronounced substrate promiscuity. GumG also exhibits limited propionyltransferase activity, enabling the biosynthesis of hybrid acetylated-propionylated xanthan at an 8.27:1 ratio. Molecular docking and analysis of 31 xanthan variants identify a cytoplasmic substrate-binding pocket defined by Val67 and Phe71 that governs donor specificity, and an engineered GumG variant (F71L) shows enhanced propionyltransferase activity. In addition, a periplasmic His40-Trp143-Asp246-His297 motif is proposed to constitute the catalytic center. Together, these findings provide mechanistic insight into GumG multifunctionality and establish a framework for engineering xanthan derivatives with tailored physicochemical properties.

microbiology↗

bioRxiv2022

RAFTS: A graphical tool to guide Flux Simulator transcriptome simulation for method development in de novo transcriptome assembly from short reads

Due to complexity of RNA transcripts expressed in any given cell or tissue, the assembly of de novo transcriptomes still represents a computational challenge when compared to genome assemblies. A number of modern transcriptome assembly algorithms have been developed to meet this challenge, and each of them have their own strengths and weaknesses dependent on the transcript abundance and complexity of the biological sample that is sequenced. As such, we are seeking to develop a transcriptome assembly pipeline in which multiple transcriptomes are generated, merged, and then redundancies are filtered out to produce a final transcriptome that should contain full length sequences of all transcripts. However, it is almost impossible to evaluate the efficacies of such novel assembly pipelines using short read sequencing data derived from biological samples due to not knowing a priori the transcript abundance and complexity. Thus, to test our pipelines we developed RAFTS. This tool is used to generate simulated short read sequencing datasets using annotated genomic data from model species.

bioinformatics↗

bioRxiv2019

openPrimeR for multiplex amplification of highly diverse templates

To study the diversity of immune receptors and pathogens, multiplex PCR has become a central approach in research and diagnostics. However, insufficient primer design against highly diverse templates often prevents amplification and therefore limits the correct understanding of biological processes. Here, we present openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers. openPrimeR provides a functional and intuitive interface and uses either a greedy algorithm or an integer linear program to compute the minimal set of primers that performs full target coverage. As proof of concept, we used openPrimeR to find optimal primer sets for the amplification of highly mutated immunoglobulins. Comprehensive analyses on specifically generated immunoglobulin variable gene segment libraries resulted in the composition of highly effective primer sets (oPR-IGHV, oPR-IGKV and oPR-IGLV) that demonstrated to be particularly suitable for the isolation of novel human antibodies.

immunology↗