Monday, December 26, 2022

Identifying Mitochondrial Functions by ‘Multiomic’ Profiling

Mitochondria make ATP through oxidative phosphorylation, thus providing energy for nearly all cellular functions. Many human disorders are attributed to mitochondrial dysfunction. Their functions seem narrow and their genomes, known for decades, were reduced to encoding a mere 13 proteins after transferring most to the nuclear genome. However, these authors note that ‘hundreds of mitochondrial proteins lack clear functions’. They previously (Stefely 2016) applied mass spectroscopy (MS) ‘multiomics’ to assign functions to mitochondrial uncharacterized (x) proteins (MXPs) in yeast. Here, they generated using CRISPR over 200 knockout (KO) cell lines, targeting 50 nuclear genes encoded MXPs plus 66 with known functions, and assessed in each line over 8,000 proteins, over 3,000 lipids and over 200 metabolites by MS (epic undertaking!). They found high reproducibility and dynamic range, with ‘many molecules showing regulation over 3-4 orders of magnitude’.

Fig 2e. Relative protein abundance in SLC30A9 KO cells compared to WT (“wild type”, i.e., normal) cells versus statistical significance with noted mitochondrial ribosome (black), OxPhos (blue), and mtDNA-encoded (red) proteins.

Some assessments confirmed expectations or were mild surprises, e.g., the importance of ALDH18A1 or NADK1 in proline synthesis (Fig 2a). Others revealed ‘new biology’, such as a key role for the putative zinc transporter SLC30A9 in mitochondrial ribosome and OxPhos proteins (Fig 2e, shown). They also found that one ’upstream (open) reading frame’ (PYURF) is a chaperone essential for complex I and coQ synthesis, linked a transporter (SLC30A9) to ribosomes, and found a second gene (RAB5IF) contributing to developmental disorders. They offer their “8.3 million distinct biomolecule measurements” online to help others ascribe additional functions, a promising resource.

Rensvold JW, Shishkova E, Sverchkov Y, Miller IJ, Cetinkaya A, Pyle A, Manicki M, Brademan DR, Alanay Y, Raiman J, Jochem A, Hutchins PD, Peters SR, Linke V, Overmyer KA, Salome AZ, Hebert AS, Vincent CE, Kwiecien NW, Rush MJP, Westphall MS, Craven M, Akarsu NA, Taylor RW, Coon JJ, Pagliarini DJ. Defining mitochondrial protein functions through deep multiomic profiling. Nature. 2022 Jun;606(7913):382-388. doi: 10.1038/s41586-022-04765-3. Epub 2022 May 25. PMID: 35614220; PMCID: PMC9310563.
NB PubPeer comment raises concerns regarding the methods, interpretations, and conclusions. 

Friday, December 16, 2022

Seasonal flu vaccination: short term protection, long term risk?

Influenza (flu) sickens millions and kills many thousands of Americans each year. Vaccination is intended to reduce the number cases and severity of illness. The flu virus changes its coat proteins each year, a ‘shape-shifting’ behavior that challenges the timely production of vaccines that are effective against flu variants. The US CDC evaluates vaccine effectiveness (VE) in thousands of outpatient respiratory illness patients, usually finding substantial vaccine protection with little risk Consequently, its Advisory Committee on Immunization Practices (ACIP) as well as the World Health Organization (WHO) recommend annual immunization of everyone over 6 months old unless contraindicated.
Here, the authors surveyed vaccination over 10 years among several thousand Japanese school children and several hundred school staff adults. Of the many forms of flu vaccine, Japan uses a quadrivalent (4 strains; trivalent prior to 2014) “split” vaccine based on influenza hemagglutinin (HA). “Split” vaccine means the virus was ‘disrupted’ by detergent (the equivalent of ‘heat killed’; viruses aren’t alive). The flu viruses used to prepare the vaccine are grown in eggs; alternative quadrivalent preparations are available for those with allergies to eggs, including Flublok and Flucelvax.

They found that morbidity was reduced in vaccinated elementary school students but elevated in middle school students (Fig 1). Most people who had been vaccinated ‘from infancy’ were also vaccinated in the 2019-2020 season (Fig. 2). Moreover, they “found that morbidity was significantly higher among elementary (P < 0.001) and middle (P < 0.05) school students who had been vaccinated since infancy than among those who had not been vaccinated since infancy” (Figure 3, shown).

Fig. 3 Relationship between morbidity and vaccination from infancy.

These data are self-reported via questionnaires, and therefore extra subjective. The authors propose no mechanism for how annual vaccination could cause increased morbidity. It seems probable that the association is not direct, not causative, but indirect through other behavioral or health status factors. This is an intriguing finding that should be analyzed and study that should be repeated.

Kajiume T, Mukai S, Toyota N, Kanazawa I, Kato A, Akimoto E, Shirakawa T. Effectiveness of seasonal influenza vaccine in elementary and middle schools: a 10-year follow-up investigation. BMC Infect Dis. 2022 Dec 6;22(1):909. doi: 10.1186/s12879-022-07898-y. PMID: 36474168; PMCID: PMC9724312.