Anna Schapiro

Jonathan Roiser

eLife assessment
This important work, leveraging state-of-the-art whole-night sleep EEG-fMRI methods, advances our understanding of the brain states underlying sleep and wakefulness. Despite a small sample size, the authors present convincing evidence for substates within N2 and REM sleep stages, with reliable transition structure, supporting the perspective that there are more than the five canonical sleep/wake states.

anonymous

Reviewer #1 (Public Review):
Summary:
The study made fundamental findings in investigations of the dynamic functional states during sleep. Twenty-one HMM states were revealed from the fMRI data, surpassing the number of EEG-defined sleep stages, which can define sub-states of N2 and REM. Importantly, these findings were reproducible over two nights, shedding new light on the dynamics of brain function during sleep.
Strengths:
The study provides the most compelling evidence on the sub-states of both REM and N2 sleep. Moreover, they showed these findings on dynamics states and their transitions were reproducible over two nights of sleep. These novel findings offered unique information in the field of sleep neuroimaging.
Weaknesses:
The only weakness of this study has been acknowledged by the authors: limited sample size.

Reviewer #2 (Public Review):
Summary:
Yang and colleagues used a Hidden Markov Model (HMM) on whole-night fMRI to isolate sleep and wake brain states in a data-driven fashion. They identify more brain states (21) than the five sleep/wake stages described in conventional PSG-based sleep staging, show that the identified brain states are stable across nights, and characterize the brain states in terms of which networks they primarily engage.
Strengths:
This work's primary strengths are its dataset of two nights of whole-night concurrent EEG-fMRI (including REM sleep), and its sound methodology.
Weaknesses:
The study's weaknesses are its small sample size and the limited attempts at relating the identified fMRI brain states back to EEG.
General appraisal:
The paper's conclusions are generally well-supported, but some additional analyses and discussions could improve the work.
The authors' main focus lies in identifying fMRI-based brain states, and they succeed at demonstrating both the presence and robustness of these states in terms of cross-night stability. Additional characterization of brain states in terms of which networks these brain states primarily engage adds additional insights.
A somewhat missed opportunity is the absence of more analyses relating the HMM states back to EEG. It would be very helpful to the sleep field to see how EEG spectra of, say, different N2-related HMM states compare. Similarly, it is presently unclear whether anything noticeable happens within the EEG time course at the moment of an HMM class switch (particularly when the PSG stage remains stable). While the authors did look at slow wave density and various physiological signals in different HMM states, a characterization of the EEG itself in terms of spectral features is missing. Such analyses might have shown that fMRI-based brain states map onto familiar EEG substates, or reveal novel EEG changes that have so far gone unnoticed.
It is unclear how the presently identified HMM brain states relate to the previously identified NREM and wake states by Stevner et al. (2019), who used a roughly similar approach. This is important, as similar brain states across studies would suggest reproducibility, whereas large discrepancies could indicate a large dependence on particular methods and/or the sample (also see later point regarding generalizability).
More justice could be done to previous EEG-based efforts moving beyond conventional AASM-defined sleep/wake states. Various EEG studies performed data-driven clustering of brain states, typically indicating more than 5 traditional brain states (e.g., Koch et al. 2014, Christensen et al. 2019, Decat. et al 2022). Beyond that, countless subdivisions of classical sleep stages have been proposed (e.g., phasic/tonic REM, N2 with/without spindles, N3 with global/local slow waves, cyclic alternating patterns, and many more). While these aren't incorporated into standard sleep stage classification, the current manuscript could be misinterpreted to suggest that improved/data-driven classifications cannot be achieved from EEG, which is incorrect.
More discussion of the limitations of the current sample and generalizability would be helpful. A sample of N=12 is no doubt impressive for two nights of concurrent whole-night EEG-fMRI. Still, any data-driven approach can only capture the brain states that are present in the sample, and 12 individuals are unlikely to express all brain states present in the population of young healthy individuals. Add to that all the potentially different or altered brain states that come with healthy ageing, other demographic variables, and numerous clinical disorders. How do the authors expect their results to change with larger samples and/or varying these factors? Perhaps most importantly, I think it's important to mention that the particular number of identified brain states (here 21, and e.g. 19 in Stevner) is not set in stone and will likely vary as a function of many sample- and methods-related factors.

Reproducible, data-driven characterization of sleep based on brain dynamics and transitions from whole-night fMRI

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