Dr Daniel Humphreys

Department of Biomedical Science

UKRI Future Leaders Research Fellow

d.humphreys@sheffield.ac.uk
+44 114 222 4632

Full contact details

Dr Daniel Humphreys
Department of Biomedical Science
Florey Building
Western Bank
Sheffield
S10 2TN
Profile

My research focusses on the host cell biology underlying infectious diseases with the aim of discovering new ways to combat globally important bacterial pathogens. I am a UKRI Future Leaders Research Fellow studying DNA damage responses and senescence in typhoid fever and its transmission by chronic bacterial carriage.

I obtained my PhD and gained postdoctoral training at the University of Cambridge before being appointed as a lecturer in 2016 at the Department of Biomedical Science, University of Sheffield, where I received an MRC New Investigator Research Grant. Before that I studied Microbiology at the University of Liverpool (BSc) and Biological Sciences at the University of Manchester (Masters).

  • 2019 - present: UKRI Future Leaders Research Fellow
  • 2016 - present: Lecturer, Department of Biomedical Science, University of Sheffield
  • 2014 - 2016: Research Fellow, Department of Pathology, University of Cambridge
  • 2008 - 2013: Postdoctoral Research Associate, University of Cambridge
  • 2003 - 2007: PhD in Cellular Microbiology, Department of Pathology, University of Cambridge
  • 2002 - 2003: Masters of Biological Research, University of Manchester
  • 1999 - 2002: BSc in Microbiology, University of Liverpool
Research interests

Typhoid fever and its transmission by chronic bacterial carriage

Typhoid fever is a major disease in low- and middle-income countries resulting in ~11 million cases and ~128,000 deaths each year. Typhoid is caused by the human-restricted pathogen Salmonella Typhi that has evolved antibiotic-resistance with multi- and extremely-resistant strains causing current epidemics.

S.Typhi causes disease through a wide repertoire of toxins and virulence effectors that mediate bacterial invasion of human cells, intracellular survival and immune evasion. A major focus of our laboratory is a key virulence determinant called the typhoid toxin that enters human cells where it causes breaks in our DNA, which activates a cellular alarm system known as the DNA damage response.

Illustration of Dan Humphreys Lifecycle talks

S.Typhi is transmitted via the faecal-oral route (yellow in Figure), a problem which is exacerbated in impoverished countries that lack access to clean water and good sanitation. Following ingestion, S.Typhi infects cells of the intestine before establishing a systemic, often fatal, infection underlying typhoid fever (pink in Figure).

Our research also investigates how S.Typhi and its typhoid toxin cause chronic infections in humans - ‘chronic carriage’ (turquoise in Figure). S.Typhi establishes chronic carriage by evading immune responses and causing an asymptomatic infection (yellow arrow), or following typhoid fever in 5% of cases (pink arrow). Chronic carriers transmit the pathogen in the population and are difficult to diagnose due to the lack of obvious clinical symptoms. The most infamous ‘chronic carrier’ was a household cook called Typhoid Mary who caused numerous outbreaks of typhoid between 1900-1906. Chronic carriage is a stealth strategy of S.Typhi that continues today and helps perpetuate the infection cycle (turquoise arrow), which impedes global efforts to eradicate typhoid. By studying decisive disease mechanisms, our research contributes to global efforts combatting multidrug-resistant typhoid with the aim of improving the health and wealth of vulnerable communities in low- and middle-income countries.

Read more about the typhoid problem here:
https://naturemicrobiologycommunity.nature.com/users/295084-daniel-humphreys/posts/53817-typhoid-fever-an-age-old-problem

For more information on typhoid, please visit Take on Typhoid:
https://www.coalitionagainsttyphoid.org

Research projects on typhoid and chronic infection

Pathogenic bacteria manipulate the host DNA damage response (DDR) to execute virulence strategies and establish infections. This is exemplified by Salmonella Typhi that causes typhoid fever and fuels the infection cycle by chronic bacterial carriage. Upon infection, S.Typhi deploys the typhoid toxin, which is endocytosed by target host cells where the toxin activates the DDR.

How the toxin hijacks the DDR and how this contributes to typhoid and chronic carriage is unclear. Understanding the toxin is especially important as related toxins are encoded by diverse bacterial pathogens that cause disease in humans and food-chain animals worldwide.

DNA damage responses underlying typhoid and chronic Salmonella carriage

We discovered a novel disease mechanism revealing that the typhoid toxin hijacks the activities of Replication Protein A (RPA), a key component of the DNA replication fork, which elicits DNA damage and cellular senescence.

Normally, RPA coats and protects single-stranded DNA (ssDNA) generated at DNA replication forks, thus acting as a cellular safeguard against DNA damage and permitting cell cycle progression (diagram in turquoise box). Remarkably, we found that the typhoid toxin hijacks this RPA mechanism to induce DNA replication stress and senescence. By inducing ssDNA breaks, toxin nuclease activity sequesters RPA and exhausts the pool of free RPA needed for DNA replication.

This causes irreparable DNA damage observed as signature accumulation of the DNA damage marker γH2AX at the nuclear periphery - Response Induced by a bacterial Genotoxin (RING). We found that the novel RING phenotype marks replication catastrophe and cellular senescence (pink box). Investigating this novel virulence mechanism is providing new information on disease while revealing potential therapeutic targets.

Read the paper

Illustration of Dan Humphreys Ring Mechanism talks

Investigating how pathogens accelerate the ageing of human host cells

We are investigating the significance of pathogen subversion of cellular ageing in typhoid and chronic Salmonella carriage. Understanding how chronic infection develops, and identifying effective diagnostic, treatment and prevention strategies is vital to typhoid elimination efforts.

Infections are often harder to combat and recover from as we age, which is partly due to senescence, and the idea that bacterial pathogens target this phenomenon could be important to infection and contribute to age-related pathologies such as cancer. We find that the typhoid toxin of S.Typhi induces chronic DNA replication stress via the RING phenotype, which results in cellular senescence, thus accelerating cellular ageing (diagram in yellow box).

Interestingly, proteins are secreted from cells with the RING phenotype that induce senescence in neighbouring cells. These senescent cells are rendered more susceptible to intracellular Salmonella infections (see yellow bacteria in grey cells). We are currently investigating the mechanisms of senescence in the host-pathogen interaction.

Read the paper

Illustration of Toxic Chronic Carriage talks
Publications

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Grants
  • UKRI Future Leaders Research Fellowship (2019)
  • HIC-Vac GCRF Grant (2019)
  • Royal Society Research Grant (2017)
  • MRC New Investigator Research Grant (2016)
  • Pathology Research Fellowship (2014)
Teaching activities

I am undergraduate module co-ordinator for Pathobiology BMS106/BMS109 in which I teach infection and immunity. I also lecture on the MSc for Molecular Medicine and the MSc for Antimicrobial Resistance.

Opportunities

Enquires for postdoc, fellowship and PhD positions are welcome.

We advertise PhD opportunities (Funded or Self-Funded) on FindAPhD.com

For further information and details of other projects on offer, please see the department PhD Opportunities page.