Student Speaker

Holin Zhang

Infection and Immunity - Prof. Thomas Rudel

_{Wednesday, October 8th, 10 am}
From controlling chlamydial protein to controlling Chlamydia – A novel Ctr-AID system based on AID2 system

Targeted protein degradation (TPD) systems are key to functional protein analysis but remain unexplored in obligate intracellular pathogens [1-4]. We address this gap in Chlamydia trachomatis (Ctr), a major cause of sexually transmitted infections linked to severe complications [5-8]. Ctr’s genetically intractable genome hinders mechanistic studies of its life cycle and pathogenesis [2]. Here, we developed Ctr-AID, an AID2-based platform enabling rapid, reversible protein depletion via ligand administration. Using Ctr-AID, we degraded Cdu1, a transmembrane deubiquitinase critical for inclusion membrane integrity and bacterial survival [9-11], demonstrating precise control of pathogenic protein with such system. This system bypasses limitations of traditional knockouts or RNA interference [3, 12], offering a scalable method to study essential Ctr proteins. In conclusion, Ctr-AID establishes a foundational tool for probing pathogen-specific mechanisms, host-pathogen interactions, and therapeutic targets, with broad implications for antimicrobial development.

^{References [1] Schapira, M., et al., Nature Reviews Drug Discovery, 2019. 18(12): p. 949-963. [2] Bastidas, R.J. and R.H. Valdivia, Microbiol Mol Biol Rev, 2016. 80(2): p. 411-27. [3] Békés, M., D.R. Langley, and C.M. Crews, Nat Rev Drug Discov, 2022. 21(3): p. 181-200. [4] Espinoza-Chávez, R.M., et al., ACS Bio & Med Chem Au, 2023. 3(1): p. 32-45. [5] Haggerty, C.L., et al., J Infect Dis, 2010. 201 Suppl 2: p. S134-55. [6] Elwell, C., K. Mirrashidi, and J. Engel, Nat Rev Microbiol, 2016. 14(6): p. 385-400. [7] Rowley, J., et al., Bull World Health Organ, 2019. 97(8): p. 548-562p. [8] Workowski, K.A., et al., MMWR Recomm Rep, 2021. 70(4): p. 1-187. [9] Pruneda, J.N., et al., Nat Microbiol, 2018. 3(12): p. 1377-1384. [10] Misaghi, S., et al., Mol Microbiol, 2006. 61(1): p. 142-50. [11] Bastidas, R.J., et al., 2024, eLife Sciences Publications, Ltd. [12] Jackson, A.L. and P.S., Nat Rev Drug Discov, 2010. 9(1): p. 57-67.}

Deeksha Seetharama

Infection and Immunity - Prof. Wolfgang Kastenmüller

_{Wednesday, October 8th, 10.15 am}
Affinity selection phase during CD8 Tcell priming

T cell priming is initiated by an activation phase marked by stable interactions with dendritic cells (DCs). However, the mechanism by which activated T cells acquire the paracrine signals necessary for their differentiation after detaching from DCs and resuming migration has remained unclear. Using 2-photon Intravital microscopy and other techniques we identified a distinct priming phase that preferentially benefits CD8 T cells expressing high-affinity antigen receptors. This phase requires CXCR3 expression on CD8 T cells, enabling prolonged re-engagement with DCs within specialized sub follicular niches in reactive lymph nodes. There, CD4 T cells provide IL-2 as they transiently pause at sites of CD8 T cell-DC interactions before migrating further. Our findings reveal an unrecognized phase of T cell priming driven by dynamic cell-cell interactions, with direct implications for improving vaccines and to enhance CAR T cell therapies potentially boosting T cell persistence, function, and therapeutic efficacy in cancer treatment.

Lukas Nowak

Biomedicine - Prof. Martin Eilers

_{Wednesday, October 8th, 11.30 am}
MYC/MIZ1 dependent lysosomal flux in pancreatic cancer

Purpose: Pancreatic ductal adenocarcinoma (PDAC) is one of the most devastating tumor entities, with a long-term survival rate of less than 5% and only minor therapeutic improvements over recent decades. PDAC exhibits high levels of the oncoprotein MYC, which interacts with MIZ1 to suppress vesicular transport processes in tumor cells. Depletion of MYC leads to an increased loading of TLR3 with double-stranded RNA. In the absence of MYC/MIZ1 interaction, a variety of genes involved in vesicular transport are upregulated, ultimately resulting in immune signaling via TLR3. In this study, we aimed to identify the pathway responsible for transporting immunogenic double-stranded RNA to TLR3, which is suppressed by MYC/MIZ1 interaction in pancreatic cancer.

Methods: We used a KPC cell model (KRAS^G12D and Trp53^R172H) with doxycycline-inducible shRNA against MYC, as well as cell lines expressing either a doxycycline-dependent MYC wild-type allele or a Myc^VD mutant incapable of MIZ1 binding. We identified genes that are repressed by the cooperative binding of MYC and MIZ1. In a targeted siRNA screen of MYC/MIZ1 repressed genes we used LysoTracker staining to measure an increase in vesicular transport. Results: MYC depletion or disruption of MYC/MIZ1 interaction led to an increased loading of TLR3 with double-stranded RNA. In parallel, LysoTracker staining signal in the perinuclear region increased in the presence of shMYC or MYC^VD mutant. This staining was markedly reduced by siRNA-mediated depletion of Sec24D, GAB2, and RAB33A. Sec24D is a COPII family protein responsible for vesicle budding from the endoplasmic reticulum (ER). RAB33A is a member of the RAB GTPase family, involved in multiple intracellular vesicular transport processes. GAB2 is a scaffold protein primarily known for signaling downstream of tyrosine kinase receptors; its specific role in vesicular transport remains unclear.

Conclusion: Repression of vesicular transport is a key mechanism of immune escape in pancreatic cancer. We provide first evidence that the interaction of MYC/MIZ1 is repressing the transcription of genes critical for lysosomal flux. Targeting the interaction between MYC and MIZ1 might open new ways to target pancreatic cancer by restoring immune surveillance in pancreatic cancer.

Stefan Jungwirth

Biomedicine - Prof. Utz Fischer

_{Wednesday, October 8th, 1.15 pm}
Cooperative Clamp-Mediated Promoter Recognition by Poxviral RNAP and Its TBP/TFIIB-Like Partner

The recruitment of RNA polymerase (RNAP) to gene promoters is a critical step in gene expression. For RNAP II, this process is initiated by the TATA-box binding protein (TBP) and transcription factor IIB (TFIIB), with homologs of these TBP/TFIIB pairs found in all known multi-subunit RNAP systems. Here, we describe a previously unknown mode of promoter recognition by the poxviral intermediate transcription factor 3 (VITF-3). This heterodimeric factor comprises an atypical TBP/TFIIB pair forming a stable ring structure inert towards DNA in the absence of viral RNAP (vRNAP). Promoter recognition instead requires concerted VITF-3 and vRNAP binding, as revealed by cryo-EM analysis of the intermediate pre-initiation complex (iPIC). During iPIC formation, vRNAP facilitates ring opening and loading of VITF-3 onto the promoter, anchoring the polymerase at the transcription start site. Our findings propose vRNAP as a clamp loader for VITF-3 and reveal a thus far unknown transcription initiation mechanism.

Tatiana Saraiva

Neuroscience - Dr. Chi Wang Ip

Wednesday, October 8th, 4 pm
Effects of deep brain stimulation on the entopeduncular and dentate nucleus in a rat model of DYT-TOR1A dystonia

Dystonia is a movement disorder characterized by sustained or intermittent muscle contractions that produce abnormal movements and postures. The most common monogenic form, DYT-TOR1A dystonia, arises from a mutation in the TOR1A gene. However, only about 30% of mutation carriers develop symptoms, implicating environmental factors such as limb overuse in disease manifestation. Deep brain stimulation (DBS) of the globus pallidus internus (GPi) improves symptoms in some patients with dystonia, but therapeutic efficacy remains limited due to the disorder’s heterogeneous aetiology and clinical presentation. To investigate circuit-specific alterations underlying DYT-TOR1A dystonia, we generated a rat model combining overexpression of the human mutated TOR1A gene with repetitive overuse of the right forelimb during a lever-pressing task. Rats were implanted with DBS electrodes targeting either the entopeduncular nucleus (EP, the rodent GPi homologue) or the dentate nucleus (DN) of the cerebellum. The animals performed the overuse task for three weeks without stimulation, followed by two weeks with high-frequency DBS. Previous studies from our group showed that non-implanted DYT-TOR1A animals develop abnormal and more variable lever-press trajectories compared to wildtype controls over the course of overuse. In a preliminary analysis, EP-DBS animals displayed control-like metrics even before stimulation onset, suggesting that electrode implantation itself induces lesion-related changes that mitigate the development of dystonic motor patterns. By contrast, DN-implanted rats developed abnormal trajectories, and high-frequency DN-DBS failed to improve the aberrant motor patterns. Overall, our results reinforce the basal ganglia, specifically the EP/GPi, as a critical node for motor control in DYT-TOR1A dystonia. The pre-stimulation normalization observed in EP-implanted animals highlights the potential influence of lesion effects, which may act as a protective factor against the development of abnormal motor patterns during the overuse task. The lack of improvement with DN-DBS suggests that high-frequency cerebellar modulation alone is insufficient to normalize movement trajectories in this context.

Giorgia Danti

Biomedicine - Dr. Hans Maric

_{Thursday, Ocotber 9th, 9 am}
Targeted Chemical Modifications Improve Antisense Antibiotic Efficacy

Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes have great potential as antibiotics with programmable and species-specific action [1]. Traditionally, full mRNA blockade and antimicrobial potency required antisense constructs of eight or more canonical building blocks. Taking advantage of our high-throughput parallel synthesis combined with mRNA hybridization and direct minimal inhibitory concentration (MIC) determination [2], we identified unprecedentedly short but highly potent antisense PNAs. Specifically, we screened shorter sequences with synergistic action on one or more essential genes and systematically explored the effects of various chemical modifications and their positioning within the antisense construct in terms of target sequence hybridization strength and bacterial growth inhibition. This integrated approach revealed specific modifications and positional effects that significantly boost potency, enabling the design of antisense constructs with minimal length and maximal activity. Taken together, we demonstrate the potential of chemical optimization to improve antisense antibiotic design and broaden the chemical space for future programmable antibacterial agents.

^{References: [1] Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics, Nucleic Acids Research, Volume 49, Issue 8, 7 May 2021, Pages 4705–4724, https://doi.org/10.1093/nar/gkab242 [2] Danti, G., Popella, L., Vogel, J. & Maric, H. M. High-Throughput Tiling of Essential mRNAs Increases Potency of Antisense Antibiotics (Adv. Sci. 28/2025). Advanced Science 12, 2570223 (2025), https://doi.org/10.1002/advs.202570223}

Pratheeba Pandiaraj

Biomedicine - Prof. Andreas Brunschweiger

_{Thursday, October 9th, 9.45 am}
barTrack: An R-Based Framework for Barcode Analysis of DNA-Encoded Libraries

Barcoding entities with DNA oligomers are the fundamentals of technologies such as DNA-encoded libraries (DEL) technology and it aids in in-vivo optimization of modalities such as nanoparticles. In DEL screening, barcodes uniquely identify chemical compounds, while in nanoparticle development they track accumulation of nanoparticles in organs. Here, we present barGenerate and barTrack, an R-based computational framework designed for robust barcode generation and statistical analysis of DEL screening and in vivo enrichment experiments. The barGenerate tool employs combinatorial algorithms to design unique DNA barcode sequences Hamming distance-optimized for NGS compatibility. These barcodes are generated with the option to select AGCT content, avoid secondary structure, and achieve maximal sequence diversity either based on Hamming or Levenshtein distance and maximum homo-oligomer length. barTrack consists of two core modules: (1) a barcode identification module and (2) an enrichment analysis module. The barcode identification module employs advanced sequence alignment and error-correction algorithms to accurately map NGS reads to their corresponding molecular entities, handling sequencing errors. The enrichment analysis tool quantifies barcode abundance across different conditions, identifying significantly enriched barcodes in DEL selections or biological compartments. Key features of barTrack include: • High-accuracy barcode identification using fuzzy matching and machine learning-based error correction (allowing 1-2 nucleotide error per barcode) and counting of barcodes. • Comprehensive visualization tools to assess barcode enrichment Implemented in R, barTrack leverages robust statistical and bioinformatics capabilities to provide a modular solution for barcode-based tracking. The framework enhances the efficiency and accuracy of molecular tracking in both DEL screening and in vivo nanoparticle optimization.