Transcriptome analysis reveals a high aerobic capacity in the whale brain

A tradeoff evolution between acoustic fat bodies and skull muscles in toothed whales

Toothed whales have developed specialized echolocation abilities that are crucial for underwater activities. Acoustic fat bodies, including the melon, extramandibular fat body, and intramandibular fat body, are vital for echolocation. This study explores the transcriptome of acoustic fat bodies in toothed whales, revealing some insight into their evolutionary origins and ecological significance. Comparative transcriptome analysis of acoustic fat bodies and related tissues in a harbor porpoise and a Pacific white-sided dolphin reveals that acoustic fat bodies possess characteristics of both muscle and adipose tissue, occupying an intermediate position. The melon and extramandibular fat body exhibit specific muscle-related functions, implying an evolutionary connection between acoustic fat bodies and muscle tissue. Furthermore, we suggested that the melon and extramandibular fat body originate from intramuscular adipose tissue, a component of white adipose tissue. The extramandibular fat body has been identified as an evolutionary homolog of the masseter muscle, supported by the specific expression of MYH16, a pivotal protein in masticatory muscles. The intramandibular fat body, located within the mandibular foramen, shows possibilities of the presence of several immune-related functions, likely due to its proximity to bone marrow. Furthermore, this study sheds light on leucine modification in the catabolic pathway, which leads to the accumulation of isovaleric acid in acoustic fat bodies. Swallowing without chewing, a major toothed whale feeding ecology adaptation, makes the masticatory muscle redundant and leads to the formation of the extramandibular fat body. We propose that the intramuscular fat enlargement in facial muscles, which influences acoustic fat body development, is potentially related to the substantial reorganization of head morphology in toothed whales during aquatic adaptation.

Neurotoxic and cytoprotective mechanisms in the ischemic neocortex

Neuronal damage in ischemic stroke occurs due to permanent imbalance between the metabolic needs of the brain and the ability of the blood-vascular system to maintain glucose delivery and adequate gas exchange. Oxidative stress and excitotoxicity trigger complex processes of neuroinflammation, necrosis, and apoptosis of both neurons and glial cells. This review summarizes data on the structural and chemical changes in the neocortex and main cytoprotective effects induced by focal ischemic stroke. We focus on the expression of neurotrophins (NT) and molecular and cellular changes in neurovascular units in ischemic brain. We also discuss how these factors affect the apoptosis of cortical cells. Ischemic damage involves close interaction of a wide range of signaling molecules, each acting as an efficient marker of cell state in both the ischemic core and penumbra. NTs play the main regulatory role in brain tissue recovery after ischemic injury. Heterogeneous distribution of the BDNF, NT-3, and GDNF immunoreactivity is concordant with the selective response of different types of cortical neurons and glia to ischemic injury and allows mapping the position of viable neurons. Astrocytes are the central link in neurovascular coupling in ischemic brain by providing other cells with a wide range of vasotropic factors. The NT expression coincides with the distribution of reactive astrocytes, marking the boundaries of the penumbra. The development of ischemic stroke is accompanied by a dramatic change in the distribution of GDNF reactivity. In early ischemic period, it is mainly observed in cortical neurons, while in late one, the bulk of GDNF-positive cells are various types of glia, in particular, astrocytes. The proportion of GDNF-positive astrocytes increases gradually throughout the ischemic period. Some factors that exert cytoprotective effects in early ischemic period may display neurotoxic and pro-apoptotic effects later on. The number of apoptotic cells in the ischemic brain tissue correlates with the BDNF levels, corroborating its protective effects. Cytoprotection and neuroplasticity are two lines of brain protection and recovery after ischemic stroke. NTs can be considered an important link in these processes. To develop efficient pharmacological therapy for ischemic brain injury, we have to deepen our understanding of neurochemical adaptation of brain tissue to acute stroke.

A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus

Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.

Elevated antioxidant defence in the brain of deep-diving pinnipeds

While foraging, marine mammals undertake repetitive diving bouts. When the animal surfaces, reperfusion makes oxygen readily available for the electron transport chain, which leads to increased production of reactive oxygen species and risk of oxidative damage. In blood and several tissues, such as heart, lung, muscle and kidney, marine mammals generally exhibit an elevated antioxidant defence. However, the brain, whose functional integrity is critical to survival, has received little attention. We previously observed an enhanced expression of several antioxidant genes in cortical neurons of hooded seals (Cystophora cristata). Here, we studied antioxidant gene expression and enzymatic activity in the visual cortex, cerebellum and hippocampus of harp seals (Pagophilus groenlandicus) and hooded seals. Moreover, we tested several genes for positive selection. We found that antioxidants in the first line of defence, such as superoxide dismutase (SOD), glutathione peroxidase (GPX) and glutathione (GSH) were constitutively enhanced in the seal brain compared to mice (Mus musculus), whereas the glutaredoxin and thioredoxin systems were not. Possibly, the activity of the latter systems is stress-induced rather than constitutively elevated. Further, some, but not all members, of the glutathione-s-transferase (GST) family appear more highly expressed. We found no signatures of positive selection, indicating that sequence and function of the studied antioxidants are conserved in pinnipeds.

Transcriptomes Suggest That Pinniped and Cetacean Brains Have a High Capacity for Aerobic Metabolism While Reducing Energy-Intensive Processes Such as Synaptic Transmission

The mammalian brain is characterized by high energy expenditure and small energy reserves, making it dependent on continuous vascular oxygen and nutritional supply. The brain is therefore extremely vulnerable to hypoxia. While neurons of most terrestrial mammals suffer from irreversible damage after only short periods of hypoxia, neurons of the deep-diving hooded seal (Cystophora cristata) show a remarkable hypoxia-tolerance. To identify the molecular mechanisms underlying the intrinsic hypoxia-tolerance, we excised neurons from the visual cortices of hooded seals and mice (Mus musculus) by laser capture microdissection. A comparison of the neuronal transcriptomes suggests that, compared to mice, hooded seal neurons are endowed with an enhanced aerobic metabolic capacity, a reduced synaptic transmission and an elevated antioxidant defense. Publicly available whole-tissue brain transcriptomes of the bowhead whale (Balaena mysticetus), long-finned pilot whale (Globicephala melas), minke whale (Balaenoptera acutorostrata) and killer whale (Orcinus orca), supplemented with 2 newly sequenced long-finned pilot whales, suggest that, compared to cattle (Bos taurus), the cetacean brain also displays elevated aerobic capacity and reduced synaptic transmission. We conclude that the brain energy balance of diving mammals is preserved during diving, due to reduced synaptic transmission that limits energy expenditure, while the elevated aerobic capacity allows efficient use of oxygen to restore energy balance during surfacing between dives.

A drastic shift in the energetic landscape of toothed whale sperm cells

Mammalian spermatozoa are a notable example of metabolic compartmentalization.¹ Energy in the form of ATP production, vital for motility, capacitation, and fertilization, is subcellularly separated in sperm cells. While glycolysis provides a local, rapid, and low-yielding input of ATP along the flagellum fibrous sheath, oxidative phosphorylation (OXPHOS), far more efficient over a longer time frame, is concentrated in the midpiece mitochondria.² The relative weight of glycolysis and OXPHOS pathways in sperm function is variable among species and sensitive to oxygen and substrate availability.^3-5 Besides partitioning energy production, sperm cell energetics display an additional singularity: the occurrence of sperm-specific gene duplicates and alternative spliced variants, with conserved function but structurally bound to the flagellar fibrous sheath.^6,7 The wider selective forces driving the compartmentalization and adaptability of this energy system in mammalian species remain largely unknown, much like the impact of ecosystem resource availability (e.g., carbohydrates, fatty acids, and proteins) and dietary adaptations in reproductive physiology traits.⁸ Here, we investigated the Cetacea, an iconic group of fully aquatic and carnivorous marine mammals, evolutionarily related to extant terrestrial herbivores.⁹ In this lineage, episodes of profound trait remodeling have been accompanied by clear genomic signatures.^10-14 We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends on endogenous fatty acid β-oxidation, but not carbohydrates. Such unique energetic rewiring substantiates the observation of large mitochondria in toothed whale spermatozoa and emphasizes the radical physiological reorganization imposed by the transition to a carbohydrate-depleted marine environment.

Convergent Cortistatin losses parallel modifications in circadian rhythmicity and energy homeostasis in Cetacea and other mammalian lineages

The ancestors of Cetacea underwent profound morpho-physiological alterations. By displaying an exclusive aquatic existence, cetaceans evolved unique patterns of locomotor activity, vigilant behaviour, thermoregulation and circadian rhythmicity. Deciphering the molecular landscape governing many of these adaptations is key to understand the evolution of phenotypes. Here, we investigate Cortistatin (CORT), a neuropeptide displaying an important role in mammalian biorhythm regulation. This neuropeptide is a known neuroendocrine factor, stimulating slow-wave sleep, but also involved in the regulation of energy metabolism and hypomotility inducement. We assessed the functional status of CORT in 359 mammalian genomes (25 orders), including 30 species of Cetacea. Our findings indicate that cetaceans and other mammals with atypical biorhythms, thermal constraints and/or energy metabolism, have accumulated deleterious mutations in CORT. In light of the pleiotropic action of this neuropeptide, we suggest that this inactivation contributed to a plethora of phenotypic adjustments to accommodate adaptive solutions to specific ecological niches.

Functional Studies with Primary Cells Provide a System for Genome-to-Phenome Investigations in Marine Mammals

Marine mammals exhibit some of the most dramatic physiological adaptations in their clade and offer unparalleled insights into the mechanisms driving convergent evolution on relatively short time scales. Some of these adaptations, such as extreme tolerance to hypoxia and prolonged food deprivation, are uncommon among most terrestrial mammals and challenge established metabolic principles of supply and demand balance. Non-targeted omics studies are starting to uncover the genetic foundations of such adaptations, but tools for testing functional significance in these animals are currently lacking. Cellular modeling with primary cells represents a powerful approach for elucidating the molecular etiology of physiological adaptation, a critical step in accelerating genome-to-phenome studies in organisms in which transgenesis is impossible (e.g., large-bodied, long-lived, fully aquatic, federally protected species). Gene perturbation studies in primary cells can directly evaluate whether specific mutations, gene loss, or duplication confer functional advantages such as hypoxia or stress tolerance in marine mammals. Here, we summarize how genetic and pharmacological manipulation approaches in primary cells have advanced mechanistic investigations in other non-traditional mammalian species, and highlight the need for such investigations in marine mammals. We also provide key considerations for isolating, culturing, and conducting experiments with marine mammal cells under conditions that mimic in vivo states. We propose that primary cell culture is a critical tool for conducting functional mechanistic studies (e.g., gene knockdown, over-expression, or editing) that can provide the missing link between genome- and organismal-level understanding of physiological adaptations in marine mammals.