WMS » Publications (tag [Preprint])

Good clocks in breast tumours are bad news for patients

Wed, 18 Mar 2026 20:55:00 GMT

Vadim's magnum opus now online as a preprint. 7 years after the initial preprint, 2 PhD students working on it. A coolaboration with David Rand and also including input Francis Lévi and with data from George Bjarnasson and Tami Martino.

We show in over 1200 patients that TimeTeller predicted functional tumour clocks have a negative effect on 10-year survival in breast cancer patients. Also, the tumour clocks are "off" compared to wall clock time, which we speculate might be a feature of tumour evading detection by the patients immune system.

Machine learning assisted classification of cell and brain penetrating peptides

Fri, 29 Aug 2025 11:28:00 GMT

Great collaboration with Seb Perrier and Gabriele Sosso from Warwick Chemistry. Vito's first paper from his PhD work in the IBR MRCDTP.

Crossing the blood-brain barrier (BBB) remains a major obstacle for central nervous system therapeutics. Short peptides have emerged as promising vectors, including cell-penetrating peptides (CPPs) and brain-penetrating peptides (BPPs). However, the structural and physicochemical features that distinguish CPPs from BPPs remain poorly understood, limiting rational design. Here, we systematically analysed their amino acid composition, sequence distribution, and physicochemical descriptors. Our findings suggest that BBB penetration is not a simple extension of cell penetration but requires finely tuned physicochemical properties. This study provides mechanistic insights into BPP design and highlights machine learning as a valuable tool for engineering next-generation BBB-penetrating peptides and peptide-mimetic materials.

A clock in mammalian cells modulates bacterial cellular entry

Tue, 06 May 2025 21:10:00 GMT

Title:

The cellular mammalian clock regulates Staphylococcus aureus invasion in epithelial cells

Authors:

Pooja Agarwal, Giridhar Chandrasekharan, Jaspreet Grewal, Robert Dallmann, and Meera Unnikrishnan

An endogenous biological clock, the circadian clock, coordinates life with the 24-hour day/night cycle of the environment. The unit of this circadian clock is the cell but in multicellular organisms, such as mammals, a circadian timing system (CTS) with a central pacemaker orchestrates peripheral clocks and the overall finely tuned temporal order. For example, the CTS changes immune responses to infections depending on time-of-day, however, its role in controlling bacterial infections at a cellular level is not understood.

In this study, we investigated the role of the host cellular clock during infection by Staphylococcus aureus, a highly drug-resistant, facultatively intracellular human pathogen. Our findings revealed that S. aureus invasion into epithelial cells is dependent on the cellular circadian phase. Interestingly, in BMAL1, an essential clock protein, deficient cells bacterial uptake was significantly higher compared to parental A549 cells. RNA sequencing of BMAL1 knockdown (KD) cells showed a significant upregulation of GP340, coding for the receptor of SraP, an S. aureus adhesin. An S. aureus mutant lacking SraP did not exhibit a circadian rhythm of uptake into A549 cells nor an increased uptake into BMAL1 KD compared to the parental A549 cells. Of note, bacterial mutants for other adhesins continued to show a rhythmic and higher uptake in BMAL1 KD cells.

Hence, we report that S. aureus invasion of epithelial cells is clock-modulated and mediated through S. aureus SraP, suggesting potential for host clock-directed therapy against this pathogen.

Cationic antimicrobial copolymers reveal immunomodulatory properties in LPS stimulated macrophages in vitro

Wed, 09 Apr 2025 18:41:00 GMT

Great collaboration with Seb Perrier's group characterising the anti-inflammatory properties of anti-microbial polymers led by Sophie Laroque.

Antimicrobial polymers, which have emerged as a promising alternative to antibiotics in the fight against antimicrobial resistance, are based on the design of cationic host defence peptides (CHDPs). Being a part of the mammalian innate immune system, CHDPs possess both antimicrobial and immunoregulatory effects to manage bacterial infections. However, the immunomodulatory effects of antimicrobial polymers remain largely unexplored. Within this work, a library of 15 copolymers were synthesised by reversible addition-fragmentation chain transfer (RAFT) polymerisation and their abilities to modulate pro-inflammatory pathways in LPS-activated murine and human macrophages were investigated. We found that two diblock copolymers with cationic units copolymerised with either apolar or hydrophilic comonomers appeared to have anti-inflammatory activity through suppression of the activation of the NF-κB signalling pathway, scavenging of reactive oxygen species and reduced production of the pro-inflammatory cytokine IL-6. Furthermore, the cationic-apolar copolymer exhibits
significant antimicrobial activity against P. aeruginosa. Thus, this promising copolymer holds potential as a dual-action therapeutic, effectively combating bacterial infections while curbing prolonged inflammation and thereby preventing sepsis at the site of infection.

Zinc finger homeobox-3 (ZFHX3) orchestrates genome-wide daily gene expression in the suprachiasmatic nucleus

Mon, 01 Jul 2024 22:34:00 GMT

New preprint from Pat Nolan's lab by Akaknsha Bafna looks at the contribution of the ZFHX3 deletion in adult mice for SCN transcriptome and cistrome. Vadim contributed TimeTeller analysis of SCN data suggesting a significant phase advance in entrained SCN of mutant mice.

Adenosine Kinase regulates Sleep Timing and the Homeostatic Sleep Response through Distinct Molecular Pathways

Thu, 14 Dec 2023 14:49:50 GMT

A follow up on the actions of adenosine kinase in collaboration with Aarti Jagannath's group.

Sleep behaviour is broadly regulated by two drives, the circadian (Process C), which is orchestrated by the suprachiasmatic nuclei (SCN), and controls sleep timing, and the homeostatic (Process S), which controls sleep amount and the response to sleep deprivation (Borbély et al., 2016). However, the molecular pathways that mediate their independent effects, and their interactions remain unclear. Adenosine is an important integrator of both processes (Bjorness & Greene, 2009; Jagannath et al., 2021, 2022), such that adenosine levels track and modulate wakefulness, whilst adenosine signalling inhibits the circadian response to light. Therefore, we studied the sleep/circadian behaviour, and cortical and SCN transcriptomic profiles of a mouse model overexpressing Adenosine Kinase (Adk-Tg) (Fedele et al., 2005), (Palchykova et al., 2010). We found that overall, the Adk-Tg mouse slept less and showed lower amplitude circadian rhythms with an altered sleep/wake distribution across the 24h day, which correlated with changes in transcription of synaptic signalling genes that would shift the excitatory/inhibitory balance. In addition, the Adk-Tg mouse showed a reduced level of ERK phosphorylation, and attenuation of DNA repair related pathways. After sleep deprivation, however, the Adk-Tg mouse significantly increased relative to wildtype, immediate early gene expression levels including of Arc, but paradoxically reduced ERK phosphorylation. Thus, baseline sleep levels and timing are regulated by ERK signalling, whereas the response to sleep loss is mediated by the alteration of the transcriptomic landscape independently of ERK.

TimeTeller: a tool to probe the circadian clock as a multigene dynamical system

Wed, 15 Mar 2023 10:45:00 GMT

Great collaboration started by David Rand and Francis Lévi with contributions from many including MRC DTP PhD students Laura Usselmann and Vadim Vasilyev, we describe a novel tool to interrogate the circadian clock from a single sample's transcriptome. We show in many examples how this can deliver useful information not only on the phase of the biological clock in the sample, but also give an estimate on the functionality of the clock. Furthermore, we show how this has potential as a biomarker to stratify data-sets from human tissues as well as inform research in experimental models. The TimeTeller algorithm will be available for use to any interested colleague soon.

Flow Rate Independent Multiscale Liquid Biopsy for Precision Oncology

Thu, 21 Jul 2022 08:21:00 GMT

Collaborative work with Jerome Charmet and Holosensor Medical Technology Ltd.

Immunoaffinity-based liquid biopsies of circulating tumour cells (CTCs) hold great promise for cancer management, but typically suffer from low throughput, relative complexity and post-processing limitations. Here we address these issues simultaneously by decoupling and independently optimising the nano-, micro- and macro-scales of a CTC enrichment device that is both simple to fabricate and operate. Our device achieved an 80% positive match in the identification of HER2+ breast cancer (n=26) compared to clinical standard FISH on solid biopsy. The results suggest that our approach, which overcomes major limitations previously associated with affinity-based liquid biopsies, could provide a versatile tool to improve cancer management.

First Preprint: Cell-type specific circadian bioluminescence rhythms recorded from Dbp reporter mice reveal circadian oscillator misalignment

Wed, 07 Apr 2021 10:53:00 GMT

Circadian rhythms are endogenously generated physiological and molecular rhythms with a cycle length of about 24 h. Bioluminescent reporters have been exceptionally useful for studying circadian rhythms in numerous species. Here, we report development of a reporter mouse generated by modification of a widely expressed and highly rhythmic gene encoding D-site albumin promoter binding protein (Dbp). In this line of mice, firefly luciferase is expressed from the Dbp locus in a Cre-recombinase-dependent manner, allowing assessment of bioluminescence rhythms in specific cellular populations. A mouse line in which luciferase expression was Cre-independent was also generated. The Dbp reporter alleles do not alter Dbp gene expression rhythms in liver or circadian locomotor activity rhythms. In vitro and In vivo studies show the utility of the reporter alleles for monitoring rhythmicity. Our studies reveal cell-type specific characteristics of rhythms among neuronal populations within the suprachiasmatic nuclei in vitro. In vivo studies show stable Dbp-driven bioluminescence rhythms in the liver of Albumin-Cre;DbpKI/+ liver reporter mice. After a shift of the lighting schedule, locomotor activity achieved the proper phase relationship with the new lighting cycle more rapidly than hepatic bioluminescence did. As previously shown, restricting food access to the daytime altered the phase of hepatic rhythmicity. Our model allowed assessment of the rate of recovery from misalignment once animals were provided with food ad libitum. These studies provide clear evidence for circadian misalignment following environmental perturbations and reveal the utility of this model for minimally invasive, longitudinal monitoring of rhythmicity from specific mouse tissues.