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Diagnostics COVID-19, Digital and computational pathology, Microbiology and immunology, Genetics and epigenetics

Bitesize Breakthroughs

Trichoplax adhaerens is one of the three species belonging to the the phylum Placozoa. T. adhaerens is capable of withstanding enormous doses of radiation and is highly resistant to cancer. Researchers hope investigations of such cancer-suppressing mechanisms across the tree of life may advance new methods of cancer prevention and therapy. Credit: Oliver Voigt CC BY-SA 3.0

Benchmarking Exercise

To improve genome sequencing information for diagnosing and treating disease, researchers have used the Genome in a Bottle Consortium’s variant benchmark sets to characterize challenging autosomal genes (1). They found that false duplications in GRCh37 or GRCh38 may lead to missed variants for short- and long-read technologies in relevant genes.

Algorithmic Assistance

Researchers have developed a new tool to predict liver cancer risk in hepatitis C patients using only a single test (2). The team used simple algorithms that incorporate post-treatment liver stiffness, albumin levels, and age to accurately identify at-risk patients. The algorithm can also take into account alpha-fetoprotein levels and alcohol consumption.

Vive la Résistance

Like other multicellular organisms, Trichoplax adhaerens should be vulnerable to cancer – but no cases have yet been reported. Researchers have investigated the organism’s resistance to cancer and found they are able to withstand high levels of radiation damage (3), potentially due to the overexpression of genes involved in DNA repair and apoptosis.

Breaking the Cycle

About 20 percent of patients with human papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) experience recurrence within five years of treatment. New research into a circulating cell-free tumor tissue modified HPV DNA test has demonstrated its clinical validity and utility in predicting and identifying recurrent HPV-driven OPSCC (4).

Anticipating Resistance

Researchers have built machine learning models to predict individuals’ risk of developing resistance to specific antibiotics (5). By combining data from 140,349 urinary tract infections and 7,365 wound infections with whole-genome sequencing of 1,113 pre- and post-treatment bacterial isolates, they identified alternative susceptibility-matched antibiotics with lower predicted resistance risk.

Breakthrough Responses

Researchers have investigated neutralizing antibody responses after breakthrough infection with Omicron and Delta SARS-CoV-2 variants in vaccinated individuals (non-boosted and boosted). They found that infection raised antibody responses overall, but the effect increased with more clinically severe infection (6). Breakthrough Delta infection raised Delta-specific titers to wild-type levels, whereas Omicron breakthroughs induced responses comparable to Delta levels.

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  1. J Wagner et al., Nat Biotechnol, [Online ahead of print] (2022). PMID: 35132260.
  2. G Semmler et al., J Hepatol, [Online ahead of print] (2021). PMID: 34871626.
  3. A Fortunato et al., PLoS Biol, 19, e3001471 (2021). PMID: 34788294.
  4. GJ Hanna et al, “Detection of Occult Recurrence Using Circulating HPV Tumor DNA Among Patients Treated for HPV-driven Oropharyngeal Squamous Cell Carcinoma.” Paper presented at the 2022 Multidisciplinary Head and Neck Cancers Symposium; 24–26 February 2022; Phoenix, USA.
  5. M Stracy et al., Science, 375, 889 (2022). PMID: 35201862.
  6. V Servellita et al., [Preprint] (2022).
About the Author
Liv Gaskill

During my undergraduate degree in psychology and Master’s in neuroimaging for clinical and cognitive neuroscience, I realized the tasks my classmates found tedious – writing essays, editing, proofreading – were the ones that gave me the greatest satisfaction. I quickly gathered that rambling on about science in the bar wasn’t exactly riveting for my non-scientist friends, so my thoughts turned to a career in science writing. At Texere, I get to craft science into stories, interact with international experts, and engage with readers who love science just as much as I do.

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