Category: Papers, distilled

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Much Ado About Sleep: the Importance of Getting Adequate Sleep

How was your sleep last night? Were you able to go to bed early and clock in a solid 7 to 9 hours of sleep, or were you tied up with work and had to postpone your bedtime till the draft was written and the email sent?

On average, we human beings spend 8 hours per day sleeping, which amounts to a total of one-third of our lifetime. That is, for a person who spends 75 years on earth, 25 years is spent sleeping. With such a significant amount of time spent in bed, one couldn’t help but wonder, what would happen if we just shift the bedtime later by an hour and a half, while keeping the wake-up time fixed? Surely it will not have much of an impact?

Well, turns out it will.

In a recent study published in Scientific Reports, Columbia postdoc Vikas Malik and colleagues found that for healthy females, after cutting sleep short by an hour and a half for a mere six weeks, cells that protect our blood vessels become negatively impacted. Evidence has shown that sleep restriction introduces a more pronounced risk for females than males, leading the researchers to focus solely on females for this study. With this reduction in sleep, the amount of harmful molecules (oxidants) starts to overpower that of the good molecules (antioxidants) in the cells. Since oxidants are harmful molecules which are responsible for producing the notorious “free radicals” and causing toxic effects in the body, and antioxidants good molecules responsible for detoxifying the body and repairing damages made by oxidants – this imbalance between the amount of oxidants and antioxidants will lead to impaired cell function and detrimental consequences in the form of cardiovascular diseases.

While the significance of sleep is well known, the mechanisms of how lack of sleep could impact human health has remained largely unclear. In fact, this study provides some of the first evidence demonstrating how mild chronic sleep deprivation could impact the health of our heart. In addition, contrary to previous studies that mainly examine sleep deprivation conditions in a compact time frame (e.g., acute sleep deprivation in flies for 10 days), the authors investigated how mild sleep restriction influences vascular cell health in females (i.e., pushing the bedtime 1.5 hours later than what the participants used to, while keeping the wake-up time fixed over the span of 6 weeks). Owing to a more “modern” work/life balance, the results from the authors’ experimental design carry higher relevance to our sleep patterns.

Specifically, the researchers found that after adequate sleep, the imbalance between oxidant (harmful) and antioxidant (good) molecules in the vascular cells can be cleared by a functional antioxidant response. This response is facilitated by a protein called serum response factor (SRF) – when sleep is adequate, the expression level of SRF increases to bring up the expression level of DCUN1D3, another protein which mediates antioxidant response of the cell. After sleep restriction, however, the antioxidant response cannot be turned on because the expression level of SRF is not adequate enough to activate a sequence of transcription of antioxidant genes, therefore hindering the restoration of balance between oxidant and antioxidant molecules in the cells (see illustration below).

Functional vs. impaired antioxidant response under adequate and inadequate sleep. Adequate sleep increases the expression level of SRF, which in turn increases the expression of DCUN1D3, freeing Nrf2 into the nucleus of the cell to activate the transcription of antioxidant genes, which then restores balance between oxidant and antioxidant molecules in the cells. Inadequate sleep, however, perturbs this process and interferes with the activation of antioxidant response. Figure is from the original publication.

These findings carry significant implications on how we should schedule our sleep. While deadlines will always be looming and stress will always be present, maybe we should still make the effort to defend our bedtime. After all, as Shakespeare puts it, sleep is the “balm of hurt minds, great nature’s second course, chief nourisher in life’s feast”. Perhaps, unlike Macbeth, we should all strive to sleep more.

Written by: Linbi Hong

Reviewed by: Vikas Malik, Trang Nguyen, Martina Proietti Onori, Giulia Mezzadri, and Patricia Cooney

 

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When mitochondria get stressed, our brain suffers: Linking mitochondrial dysfunction to neurodegeneration.

Imagine It’s a Saturday morning and you decide to drive upstate for a nice hike. While on the trail, you have a too-close encounter with a too-curious bear, leaving you panting, perplexed. This acute stress response (the famous fight-or-flight response) is extremely useful for us to better react to danger. The main hormones released during a stress response, glucocorticoids (GC), help prepare our body for the adverse situation we may encounter, giving us a better chance of survival.

Chronic stress it’s not so beneficial for us. In fact, it has profound detrimental effects on our bodies, and especially in our brain. There is increasing evidence that it can make our mitochondria (the powerhouse of the cell) function poorly, which can lead to damage in our neurons. Another way chronic stress can damage the brain is by inducing accumulation of the protein Tau, which can lead to neurodegenerative diseases such as Alzheimer’s disease. Tau itself poses an interesting biological conundrum: While it is normally found in the neuron’s microtubules (the cell’s scaffolding) in a healthy setting, it can start to form clumps (i.e, oligomerize) when a neuron becomes stressed or damaged, interfering with the neuron’s basic functions such as synaptic transmission and protein transport.

Scientists are still unsure how exactly GC cause Tau to oligomerize. Furthermore, while the impact of GC in mitochondria’s fitness is pretty well studied, the mechanisms driving such dysfunction, and its downstream consequences, are still poorly understood. Overall, to the scientific community, the molecular mechanisms linking GC exposure, mitochondrial dysfunction, and Tau pathology, are still unclear.

 In a recent study published in Brain, Columbia postdocs Dr. Fang Du and Dr. Qing Yu and colleagues investigated the causal relationship between these three important components of brain health, and found that GC directly precipitate mitochondrial dysfunction and drive Tau oligomerization. In a series of elegant experiments in both mouse models (in vivo) and neurons grown in petri dishes ( in vitro),experiments, the group led by Dr. Clarissa Waites demonstrated that found the mechanism by which GC exposure drives mitochondrial dysfunction and Tau oligomerization, and even discovered a potential treatment.

Figure 1- Graphical representation of the findings by Dr Du, Dr Yu, and colleagues. During Chronic stress, Glucocorticoids induce mitochondria dysfunction by increasing its permeability, which turn promotes Tau oligomerization and neurodegeneration. Figure created with Biorender.

 

 First, Dr. Waites’ group established the role of chronic GC exposure in mitochondrial fitness and pathogenic Tau accumulation in vivo. Using the widely used synthetic glucocorticoid dexamethasone (DEX), they demonstrated that GC induce mitochondrial dysfunction (increased permeability and lower respiratory capacity) and oligomeric Tau accumulation. Next, Drs. Du and Yu very cleverly employed in vitro experiments to demonstrate that DEX triggered mitochondrial dysfunction by increasing mitochondrial permeability: their research showed that GC exposure stimulates the opening of the mitochondrial permeability transition pore, a big, non-discriminant, pathological hole in the mitochondrial membrane that when open, greatly compromises its function. Most importantly, they found that GC triggers opening of the pore by activating its key component, the protein cyclophilin D. This key finding led Dr. Waites’ group to block cyclophilin D activation, either genetically (i.e. changing the DNA of the protein) or using drugs, with great success: cells where cyclophilin D activation was prevented were remarkably resilient to GC stress, and showed much lower levels of mitochondrial dysfunction and pathological Tau accumulation.

 Although this was an extremely exciting result by itself, it posed a problem moving forward: neither genetical nor pharmacological inhibition of cyclophilin D are currently viable therapeutic approaches, due to their poor bio-availability or invasive methods required to deliver the treatments. So what other approach could they use to also prevent mitochondrial pore opening, while still being clinically tractable? After some digging, Drs. Du and Yu found apo-cyanin, an orally-available inhibitor of mitochondrial respiration that could tackle GC-driven brain pathology while not directly targeting cyclophilin D. In line with their predictions, this drug was able to restore mitochondrial function and prevent Tau pathology in DEX-treated cells. Most importantly, they were also able to restore neuronal health, neuronal connectivity, and prevent anxious and depressive behavior associated with GC treatment.

 All of these experiments clearly demonstrated that GC-exposure triggers mitochondrial dysfunction and Tau accumulation, which could in turn promote the development of brain pathologies. How could they demonstrate, however, that targeting mitochondrial permeability is a feasible approach to treat common brain pathologies such as Alzheimer’s disease? To tackle this question, Dr Waites’ group made use of an ingenious technique, where they replaced all mitochondria in a test cell with those coming from an Alzheimer’s disease patient. Excitingly, in this model, treatment with mito-apocynin was sufficient to partially reverse mitochondrial dysfunction and Tau oligomerization found in the cells containing mitochondria from Alzheimer’s patients.

 Dr Waites’ group story is a hallmark out-of-the-box thinking, and clinical relevance. While their research clearly highlights mitochondrial damage induced by GC and cyclophilin D activation as a key trigger of Tau accumulation, the implications of this finding could be much broader:  How generalizable is this mechanism to other forms of brain disease such as ischemia, inflammation, or aging? As a matter of fact, cyclophilin D levels are elevated in Alzheimer’s patients, and its inhibition is protective in mouse models of sclerosis, Parkinson’s, and Alzheimer’s disease.

While this story provided incredible insight into the role of mitochondria in controlling brain pathology, many other questions remain unanswered.  For example, What is the exact mechanism by which mitochondrial dysfunction promotes pathogenic Tau accumulation? It is highly likely that these two events are intertwined, and that oligomeric Tau can also drive mitochondrial dysfunction.

 Despite the still-unknowns, it is clear that after this publication from Dr Waite’s lab, we should re-contextualize our middle-school textbooks: The mitochondria is the powerhouse of the cell, and during stress, the gate-keeper of our brain’s health.

Reviewed by: Trang Nguyen, Erin Cullen 

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Make new friends or keep the old? A novel brain circuit explains social novelty preference in mice

Researchers have discovered a pathway in the brain that may dictate whether we decide to interact with a friend versus a stranger. “Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum suppresses interaction with familiar mice”, was published this month in the highly regarded journal Cell. The paper emerged from a collaboration between scientists at the Zuckerman Mind Brain & Behavior Institute at Columbia University and colleagues at the University of Washington in Seattle, Washington and the Instituto de Neurociencias CSIC-UMH in Alicante, Spain. Columbia postdoc Ramon Nogueira contributed to the work. 

A diagram demonstrating Social Novelty Preference in mice. Two mice are in enclosures on opposite sides of an arena. A third mouse, free to explore the arena, chooses to spend more time with a mouse it does not know than a mouse it has met before.
Fig. 1 – Diagram of the task to assess Social Novelty Preference in mice. A mouse with typical social memory and an intact connection between CRH-releasing neurons in the ILA and CRH-receiving neurons in the rLS will spend more time interacting with the novel mouse than the familiar mouse. (Adapted from de León Reyes et al., 2023, Figure 3)

Social novelty preference in mice was first described in the scientific literature 20 years ago, and it is regularly used to assess social memory for research purposes. A typical mouse, when presented with a mouse it knows and a stranger, will spend more time with the familiar mouse (Fig. 1). Until this paper was published, it was unclear what brain regions or pathways influence whether mice choose to interact with novel or familiar mice. Scientists theorized that the lateral septum, a relay center that connects regions of the brain associated with thinking and memory, and the prefrontal cortex, which controls decision-making, might play a part in the social novelty preference. Both regions are also known to be involved in social behavior, and evidence suggested that there may be a neural pathway leading from the infralimbic area (ILA) in the prefrontal cortex to the rostral lateral septum (rLS), a specific region within the lateral septum. The researchers set out to determine how these two regions interact with each other and whether this interaction plays a role in social novelty preference. 

Using a comprehensive and elegant set of experiments to manipulate neuron function in the two regions, the researchers discovered that a population of inhibitory neurons in the ILA connects to the rLS, and that this pathway is crucial for the mice to exhibit the typical social novelty preference. The ILA neurons contain the neurotransmitter corticotropin-releasing hormone (CRH), which is best known for its role in stress and anxiety. Neurons in the rLS have receptors for CRH, but it was previously not known that CRH-containing neurons in the ILA communicate with CRH-receiving neurons in the rLS. When the researchers inactivated the CRH-containing neurons in the ILA, they found that mice failed to exhibit the typical social novelty preference. Next, they asked whether the CRH-receiving neurons in the rLS were also necessary for social novelty preference. They found that removing the CRH receptors from these neurons erased the social novelty preference, just like inactivating the CRH-releasing ILA neurons. Finally, they recorded the activity of CRH-releasing ILA neurons and saw that these neurons were more active when interacting with a familiar mouse than a novel mouse, indicating that these neurons act on the rLS to discourage interactions with familiar mice. 

Graphic showing a pathway through which corticotropin-releasing hormone is sent from the infralimbic area to the rostral lateral septum of the mouse brain. When this pathway is active, mice spend more time with novel rather than familiar mice. When this pathway is inactive, mice spend more time with familiar rather than novel mice.
Fig. 2 – Graphical Abstract of “Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum suppresses interaction with familiar mice” by Noelia Sofia de León Reyes et al., 2023.

To further probe the relevance of this pathway to social dynamics, the researchers assessed whether CRH may be responsible for the social novelty preference appearing in young mice. While adult mice prefer to interact with novel mice, mouse pups less than two weeks old prefer to interact with their mothers and littermates rather than unknown adult females or pups from other litters. During this same developmental time period, the population of CRH-releasing neurons that connect to the rLS steadily grows. When CRH was depleted from these neurons, the young mice failed to exhibit the typical shift from a preference for social familiarity to a preference for social novelty. This may be an evolutionary mechanism that encourages young mice to stay in safe, familiar environments, then emboldens adult mice to explore novel environments, collect food, and procreate. 

While the social novelty preference in mice does not have a direct analogue in humans, this research may provide clues for understanding and treating social anxiety disorders and social phobias. The human prefrontal cortex and septal regions also respond to social information, and CRH is known to be involved in anxiety disorders including social phobias. The researchers suggest that low CRH levels in the prefrontal cortex may prevent people from seeking social novelty, and that this mechanism could be responsible for social anxiety disorders. The field of neuroscience is just beginning to understand the biological underpinnings of social interaction, and new methods give scientists ever expanding ability to learn about this exciting field. 

Reviewed by: Trang Nguyen and Martina Proietti Onori

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When Numbers Play Tricks: Unraveling The Brain’s Biases

Imagine living in a dark cave, with your entire understanding of the world based on shadows on the wall. Sounds unrealistic and terrifying, right? However, this allegory presented by Plato is an apt metaphor for our brain’s perception of the real world. While we might believe we perceive reality in its entirety, our brain can only provide a shadowy representation of the variables in our environment, and our decisions are based on these shadowy representations.

A comforting thought might be that numbers are a universal language for Western countries and, specifically, for those who use Arabic numerals. For instance, when the price of a good is marked as $14, it conveys an unambiguous and specific value, meaning that one would unequivocally expect to pay exactly that amount. However, experiments show that people make mistakes when dealing with Arabic numerals. For instance, under time constraints, the closer two numbers are in value, the more challenging it becomes for us to rapidly and accurately pinpoint the larger one. These mistakes are very similar to those made in psychophysics tasks involving physical stimuli, such as comparing the length of segments or averaging the orientation of tilted lines. These results, together with neurobiological studies, suggest the existence of a representation system for numbers that is similar to how we interpret physical stimuli.

A popular idea in theoretical neuroscience is that while the brain’s computational abilities have inherent limits, leading to imprecise representations, these representations are optimal within those constraints. This theory, called “efficient coding”, suggests that our brain’s perceptions are influenced by how often these magnitudes are encountered (i.e., the prior). For example, vertical and horizontal orientations are perceived with more clarity than oblique ones, likely because they’re more common in our environment.

A recent study (https://www.nature.com/articles/s41562-022-01352-4), led by Columbia postdoc Arthur Prat-Carrabin and published in Nature Human Behaviour, delves into whether our brain treats numbers the same way it treats physical stimuli. In their experiment, participants were asked to determine which series of numbers, red or green, had a higher average value. For instance, as shown in Figure 1, the number 79.60 would flash in red on the computer screen, followed by 44.92 in green, and so forth. Participants were tasked with rapidly and intuitively calculating the average of the red and green numbers to determine which sequence had the greater average. To investigate how the frequency at which numbers were encountered impacts their representation, numbers were drawn from different distributions: one, in which smaller numbers were more frequent (Downward prior); another, in which all numbers had equal chances (Uniform prior); and a third, in which larger numbers were more frequent (Upward prior).

Figure 1: Example trial of the task. Participants were presented with 5 red and 5 green numbers and had to choose the color with the higher average.

To analyze the participants’ decisions, the researchers compared their answers with multiple computational models characterized by two components: first, whether or not the numbers are encoded with a bias that depends on the value of the number, and second, whether or not the imprecision (the noise) with which numbers are represented varies with the number. Their results showed that the model that best aligned with the participants’ answers had to include both components. Notably, less common numbers are fuzzier in their perception. So, when using the Downward prior, bigger numbers are encoded with more noise, while with the Upward prior, the smaller numbers are the noisiest ones.

This discovery not only supports the “efficient coding” theory, which posits that the brain encodes and represents information in the most efficient way possible, but also showcases its applicability beyond just physical perceptions. Whether we’re assessing the speed of a car, the talent of a dancer, or the sweetness of a cake, our brain might use a universal mechanism to represent these variables. This mechanism dynamically adjusts to the statistical distribution of numbers that are expected or experienced, which implies that our understanding of numbers and magnitudes isn’t static but can be influenced by our prior experiences and expectations. In the near future, we might be able to design environments that help people refine their perceptions (such as by crafting digital games to enhance the consumer’s responsiveness to certain prices), allowing them to better discern specific value ranges and improve their decision-making.

Reviewed by: Emily Hokett, Trang Nguyen, Martina Proietti Onori

 

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Revealing How Cancer Cells Balance Immune Signals

The immune system constitutes a complex network of biological processes that serves to safeguard organisms from various diseases. An important role of the immune system is its ability to distinguish between normal cells in the body and foreign cells such as germs and cancer cells. This discrimination empowers the immune system to target foreign agents while preserving normal cellular integrity. If the immune system malfunctions, it mistakenly attacks healthy cells, tissues, and organs which is called autoimmune disease. These attacks can affect any part of the body, weakening bodily function and even turning life-threatening. Therefore, it is very critical to maintain a balance between combating tumor cells and avoiding autoimmune disease in the body. The immune system maintains such balance by using checkpoint proteins on immune cells. The checkpoints act like switches that need to be turned on (or off) to ensure an optimal immune response. However, cancer cells sometimes find ways to use these checkpoints to avoid being attacked by the immune system.

Medicines known as monoclonal antibodies can be designed to target these checkpoint proteins. These drugs are called immune checkpoint inhibitors. Checkpoint inhibitors don’t kill cancer cells directly, but they help the immune system to better find and attack the cancer cells in the body. Immune checkpoint inhibitors such as anti-PD-1 antibodies, are now used to treat some types of cancers such as metastatic melanoma or brain tumors due to their ability to boost the immune response against cancer cells. It normally acts as a type of “off switch” that helps keep the T cells from attacking other cells in the body. It does this when it attaches to PD-L1, a protein on some normal (and cancer) cells. When PD-1 binds to PD-L1, it basically tells the T cell to leave the other cell alone. Some cancer cells have large amounts of PD-L1, which helps them hide from an immune attack (Figure 1).

 

Figure 1: The interaction between tumor cells and T cells. Tumor cells contain PD-L1 receptors that bind to PD-1 in T cells to hide an immune attack from T cells (left panel). However, through the application of an immune checkpoint inhibitor (anti-PD-L1 or anti-PD-1), this binding is hindered, empowering T cells to eliminate tumor cells (right panel). Image is created via Biorender.

The Izar group at Columbia University Medical Center, led by Patricia Ho identified a mechanism by which CD58 loss or downregulation contributes to cancer immune evasion and immune checkpoint inhibitor (ICI) therapy. CD58 is known as an adhesion molecule facilitating the initial binding of effector T cells. By sequencing the whole genome of patient samples, specifically those who underwent anti-PD-1 antibody treatment and later developed drug resistance, they illuminated the role of CD58. Notably, CD58 facilitates early T-cell infiltration into tumors within a tumor differentiation. Moreover, the study shed light on CD58 loss potentially expediting tumor progression by upregulation of PD-L1, consequently intensifying resistance to ICI therapies.

To better understand the CD58/PD-L1 co-regulation, the research group performed a genome-wide knock out screen to identify the regulator of CD58. Among the top hits of cell population with low CD58 protein, authors identified CMTM6 as an important regulator for the T cell activation and antitumor responses. CMTM6 binds to CD58 and promotes its recycling from cell surface to endosomes, thus preventing its lysosomal degradation (Figure 2). Interestingly, CMTM6 is also known as an important regulator of PD-L1 maintenance. Thus, loss of CD58 results in increased PD-L1 levels by stabilizing CMTM6-PD-L1 interactions and therefore reducing lysosomal PD-L1 degradation (Figure 2).


Figure 2: Both CD58 and PD-L1 require and directly bind to CMTM6. CD58 forms a direct binding with CMTM6, enhancing recycling and curtailing lysosomal degradation (left). CD58 knockout fosters PD-L1 up-regulation by interacting with CMTM6 (right). Figure is adopted from the original paper.

This work provides a molecular basis for clinically relevant roles of CD58 to facilitate initial infiltration into the tumor. Loss of CD58 confers resistance to immune checkpoint inhibitors which may provide important insights and inform rationale for the next generation of combinations of cancer immunotherapies.

Read more about this novel finding here: The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity.

Reviewed by: Martina Proietti Onori and Carlos Diaz Salazar Albelda

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Masters of disguise: unlocking the secrets of color-changing cuttlefish

Cuttlefish, octopus, and squid are fascinating marine creatures that have perfected the art of camouflage underwater. With uncanny speed, these soft-bodied cephalopods can change the color, pattern, and texture of their skin to blend seamlessly into their surroundings, impressively adapting to their environment. Unlike many animals, cuttlefish don’t rely on fur or feathers to hide in the background. Instead, they actively manipulate thousands of pigment cells in their skin to acquire the color of the environment around them. This intricate disguise process starts in their brains, as camouflage is a response to the animal’s perception of the external world. To conceal their bodies, cephalopods convert visual inputs into neural representations within their brain, ultimately transmitting signals all the way to the skin, where thousands of tiny structures called chromatophores adjust to allow color changes. However, camouflage is just one captivating aspect of cuttlefish biology. These marine animals present a rich repertoire of signaling behaviors for mating and communication and they are proficient learners, with memory capabilities not often seen in invertebrates. Collectively, these attributes position cephalopods as extraordinarily captivating subjects within the realm of biological studies.

Researchers at Columbia University’s Zuckerman Institute, led by Dr. Richard Axel, have made significant progress in comprehending the shape-shifting abilities of cuttlefish. In a recent article published in Current Biology, they generated a detailed neuroanatomical brain map, revealing insights into how their skin transformation is controlled. Tessa Montague, PhD and colleagues focused on the dwarf cuttlefish (Sepia bandensis), a small tropical species found around coral reefs in the Indo-Pacific Ocean (Figure 1A). The dwarf cuttlefish is an intriguing model for neuroscience research with its rich array of dynamic social behaviors and camouflage. Through an advanced imaging technique called MRI (magnetic resonance imaging), computer programming and web design they constructed a 3D atlas illustrating the dwarf cuttlefish’s brain anatomy (Figure 1B).

Figure 1. (A) Adult dwarf cuttlefish. (B) 3D template brain, based on magnetic resonance imaging (MRI) of 8 cuttlefish brains, (i) anterior view, (ii) right view, and (iii) posterior view. The abbreviations in color indicate the different brain structures that were identified and mapped.  Modified from T. G. Montague et al., 2023

By scanning the bodies and brains of male and female cuttlefish, the researchers identified 32 distinct lobes or functional units within the cuttlefish brain (Figure 1B). Each lobe is densely packed with neurons and performs specialized tasks. The two largest lobes, making up 75% of the total brain volume, are the optic lobes (O in Figure 1B). They receive direct projections from the eyes and process visual information, a crucial step in enabling cuttlefish camouflage. Notably, other key lobes in the camouflage pathway include those controlling the chromatophores, the pigment-filled saccules in cuttlefish skin that provide the color. When the lobes send signals to the chromatophores, these rapidly expand or contract to alter skin shades on a millisecond timescale. The lateral basal lobe (LB in Figure 1B) for example, is the lobe involved in establishing the most appropriate skin pattern components for camouflage. Another brain area highlighted by the atlas is the vertical lobe complex (V and surrounding lobes in Figure 1B), which previous studies suggest plays a key role in learning and memory. Unlocking the functions of this lobe could reveal the neural basis for complex behaviors like camouflage.

While past studies have mapped the brains of related cephalopods like squid and octopus, this is the first complete atlas for a cuttlefish species and it provides the neuroscience field with a valuable comparative perspective.  The researchers found strong similarities in the anatomy of the dwarf cuttlefish with the common cuttlefish, despite differences in size and camouflage strategies between the species. This suggests that fundamental aspects of brain organization are conserved, at least among close cephalopod relatives. It also highlights how flexible cuttlefish brains are: they can generate very different camouflage patterns using essentially the same basic circuit layout. Exploring what accounts for such flexibility on the microscopic scale will be the next challenge.

To maximize the utility of the brain atlas, for both educational and research purposes, the authors built an interactive freely available web tool, called Cuttlebase, where users can identify specific brain regions in the histological 2D atlas (that shows the cellular components in the cuttlefish brain)  and use the 3D model of the brain to explore the different lobes (Figure 2).

Figure 2. Cuttlebase is an interactive scientific web toolkit for the dwarf cuttlefish that includes a histological brain atlas in 2D and a 3D body and brain atlas to visualize and explore the different organs and brain lobes. Obtained and modified from https://www.cuttlebase.org/

This atlas serves as an invaluable tool for the scientific community to explore the basic anatomical components of complex behaviors and can give us insight into how brains are capable of representing information. It also offers an invaluable anatomy lesson, giving scientists a privileged peek inside the ingenious brains of these undersea masters of disguise. With a detailed understanding of their sophisticated neural systems, unraveling cuttlefish mysteries seems closer than ever.

Reviewed by: Trang Nguyen, Maaike Schilperoort

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Copy & Paste – an essential mechanism to repair damaged DNA

Maintaining genome integrity is crucial for cell survival and genome instability is one of the hallmarks of cancer. The genomes of many living organisms including humans are composed of different numbers of DNA molecules that are folded into structures called chromosomes. Each chromosome represents one double stranded DNA molecule. Most of our cells harbor two sets of each chromosome, which are denoted as homologous chromosomes (Figure 1, left panel). The homologous chromosome pairs can contain identical or different versions (alleles) of the genes that they carry since they are inherited from each parent. In this sense homologous chromosomes are genetically non-identical.

Most of the cells in our body are constantly renewed and replaced in a process that involves cellular division. During cell division the genome needs to be duplicated so that each of the newly formed daughter cells receives a genome copy. The process of DNA duplication is called DNA replication. During replication, each of the two strands of the DNA double helix serves as a template for the synthesis of a new complementary DNA strand. These chromosome copies that are produced during cell division are named sister chromatids (Figure 1, right panel), and they are found transiently in the cells just before the division. Unlike the homologous chromosomes, the alleles of the genes in the sister chromatids are genetically identical since they are produced by DNA replication.

Figure 1: Schematic representation of the homologous chromosomes and the sister chromatids produced during cellular division. Created with BioRender.com

During DNA replications, as well as under the influence of diverse environmental and endogenous agents, lesions constantly occur on DNA. These DNA “injuries” can trigger mutations, compromise the genome integrity, or even cause cell death. DNA double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions that can lead to gross chromosome rearrangements. Similar rearrangements are very common in cancer.  One of the major mechanisms for DNA DSBs repair is homologous recombination (HR), a process explained below. Mutations in different genes from the HR pathway have been associated with diseases like cancer of Fanconi anemia, as well as to hypersensitivity to DNA-damaging agents which increase mutation accumulation.

One of the versions of HR involves the use of the intact sister chromatid as donor of information. Since the sister chromatid has an identical sequence to the damaged DNA molecule, this repair system faithfully restores the genetic information and is considered as being error free. Homologous recombination can also occur between the homologous chromosome pairs in the case of non-dividing cells. In HR, the DNA DSB ends are processed and a long single-stranded DNA (ssDNA) overhang is left to serve as platform for the assembly of the protein machinery mediating the repair (Figure 1, a). This ssDNA is coated by the protein RPA to prevent degradation and folding. Subsequently RPA is replaced by RAD51, into a structure termed the presynaptic nucleoprotein filament. This filament is capable of searching for a homologous undamaged DNA molecule that will serve as a template for repair. This exchange between RPA and RAD51 on ssDNA in the presynaptic filament assembly is facilitated by mediators of HR. One of those mediators is a complex of four proteins that are paralogues of RAD51: the BCDX2 complex. However, the exact mechanism of action of the BCDX2 complex in HR remained elusive.

Figure 2. Double-strand breaks (DSBs) can be repaired by several homologous recombination (HR)-mediated pathways. Represented is a simplified version of the “synthesis-dependent strand annealing HR pathway”. In all pathways, the repair is initiated by resection of a DSB to provide 3′ single-stranded DNA (ssDNA) overhangs (a and b). The ssRNA is rapidly coated with RPA to prevent damage and folding (c). RPA is exchanged with RAD51 with the help of HR mediator complexes, which are composed from different RAD51 paralogues, one of which is four protein complex BCDX2 (d). RAD51 coated DNA can search for the non-damaged homologous chromosome / sister chromatid pair and invade that intact DNA duplex (e). After strand invasion and “copying” of the information from the intact DNA on one of the damaged strands from the blue DNA duplex, the reaction can proceed to hybridization to the ssDNA on the other break end of the blue DNA duplex, followed by DNA synthesis (f) and restoring  of blue DNA molecule (g). Created with BioRender.com

Recent studies from Columbia postdoc Aviv Meir and colleagues revealed the structure of the human BCDX2 complex. Cryogenic electron microscopy, a technique that allows the high-resolution structure determination of biomolecules in solution, was used to resolve both the  free and single-strand DNA-bound states of BCDX2. This provided the first structural information of one of the RAD51 paralogues complexes. This structural information provides insight into how the complex assembles and disassembles, which in turn is linked to the regulation of its function. The scientists also discovered by single molecule analysis that the association of BCDX2 with RPA–ssDNA enhances the rate of assembly of the RAD51–ssDNA filament. In humans, BCDX2 binds the RPA–ssDNA prior to the arrival of RAD51 and then promotes the RAD51 filament assembly. This novel mode of action for the proteins of the BCDX2 complex is different from what was previously observed in other organisms, where BCDX2 only transiently associates with the ssDNA. The work by Dr. Meir and colleagues, recently published in the prestigious journal Nature, not only elucidates how BCDX2 mediates RPA–RAD51 exchange on ssDNA but also provides a foundation for deciphering how alterations in BCDX2 subunits that were found in patients with cancer can impact genome repair and can lead to the pathogenesis. This valuable information opens the doors for future targeting of those “defectuous” BCDX2 parts for therapeutic developments.

Reviewed by: Maaike Schilperoort, Apurva Limaye, Giulia Mezzadri , Trang Nguyen

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What will capture your attention?

Ever wonder how your brain directs your attention to certain stimuli or events? For example, if you are walking into a crowded restaurant you will likely direct your attention to finding an empty seat or finding your friends rather than the color of the tablecloths or the number of tables and chairs in the restaurant. Our brains have to navigate and distinguish what is important in complex environments. The term “salience” is defined as a noticeable or important object that stands out from the surroundings or background. Salience processing has been studied in neuroscience and psychology in order to understand how our brains distinguish important stimuli. This phenomenon involves two general mechanisms: bottom-up processing in which sensory information can be amplified or filtered, or top-down processing which focuses on goal-directed behaviors and cognitive control. Prior research has identified areas of the brain that are involved in salience processing using functional magnetic resonance imaging (fMRI) studies. FMRI is a technique that measures brain activity by measuring minute changes in blood flow. The regions identified include the regions in the cortex: dorsal attention network (DAN), salience network (SN), sensory cortex, primary somatosensory cortex (S1), and subcortex (Figure 1). However, understanding how these regions communicate with one another in salience processing is still unknown. In addition to these cortical networks, the locus coeruleus (LC), which is the primary source of the neurotransmitter norepinephrine (NE) and located in the brain stem (Figure 1), is also associated with salience processing. 

Figure 1. Cortical and non-cortical regions of the brain involved in salience processing.

Researchers commonly use MRI or FMRI (functional magnetic resonance imaging) as a technique to detect active areas of the brain while performing an activity. This is complemented with EEG (electroencephalogram) scans to measure electrical activity in the brain while performing different tasks.  One of the widely used experimental designs to evaluate salience processing includes the oddball task. For these experiments, subjects are instructed to detect infrequent target stimuli (a sound of a laser gun)  in a stream of standard stimuli (standard tones). FMRI and EEG measurements were obtained to determine activation of the different areas of the brain while hearing the sound of the target laser gun as compared to hearing the consistent standard tone. Columbia postdoc Linbi Hong and colleagues in their study, published in PLOS Computational Biology on May 2023, wanted to further understand the interaction between the non-cortical, LC-NE system and the cortical networks using simultaneous recordings of pupillometry which measures changes in pupil diameter and has been used as a marker for LC activity, electroencephalography (EEG) and fMRI in an oddball experiment. 

The study first utilized EEG-informed fMRI analysis to map the neural cascade underlying salience processing and identify the order of specific regions which are activated during the oddball task. The researchers defined areas in the brain to understand the organization of regions involved in salience processing. Next, the researchers wanted to understand the functional connectivity between the distinct cortex regions and the LC-complex (non-cortex regions) during salience processing by analyzing EEG signals at different times during the oddball experiment. It was determined that the prefrontal cortex and dorsal attention network are the main players in processing salient stimuli. 

Next, the researchers characterized the directional interactions between the functional network regions including the cortical and non-cortical regions. Specifically, they determined that non-cortical regions showed significant functional connectivity with dorsal auditory attention networks and salience networks. These results indicate that the non-cortical regions (LC network) are involved in switching between the different cortical networks during salience processing.

Overall, this study identified spatiotemporally the connectivity of different cortical regions to the non-cortical regions (LC complex) in salience processing. The study also provides insights into utilizing noninvasive pupillary response, which measures non-cortical region (LC) activity, in combination with EEG and fMRI signals, which measure cortical activity, as a valid approach to understand connectivity within the different regions in the brain. As a result, these methods could be used to determine any decline in connectivity of the cortical and non-cortical regions which can provide further understanding in neurological diseases such as Alzhiemers in which the LC network is the first region affected. Future studies from this group can provide additional input to how our brains can distinguish important information such as finding your friends in a crowded restaurant and whether this information is captured the same way in diseased conditions. So, next time you look around in a crowded restaurant, you can think, what captures your attention?

Reviewed by: Trang Nguyen, Martina Proietti Onori, Maaike Schilperoort

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How many candles on the cake this year?

Every year as we celebrate our birthdays, we mark the addition of a year to our lives. Our birthdays determine our chronological age measured in days, months and years since the day we were born. Biological aging on the other hand is another measure of aging that accounts for the gradual accumulation of cellular and tissue damage that occurs in the body as we grow older. Aging is a natural process and various factors contribute to biological aging, including our chronological age, genetics, lifestyle, nutrition, and physical activity. Research has shown poor nutrition and low physical activity can accelerate biological aging. Accelerated biological aging is marked by increased levels of certain hallmarks of cellular damage, leading to chronic diseases. Poor nutritional habits and sedentary lifestyles have been associated with increased risk of heart diseases, high blood pressure, cholesterol and type 2 diabetes. Additionally, over 60% of the aging population (>65 years) is expected to be affected by more than one chronic disease by 2030. Research has also shown that lifestyle interventions may reduce or delay the progress of biological aging. In this regard, Aline Thomas and colleagues obtained real life data from a large cohort of US adults to study the association between lifestyle behaviors and biological aging using mathematical models. They assessed signs of aging in individuals who engaged in some form of moderate to vigorous physical activity in their leisure time and followed a diet that resembled a mediterranean diet compared to individuals who followed a less-healthy lifestyle. A Mediterranean diet focuses on plant-based foods and healthy fats. It includes vegetables, fruits, whole grains, fish and extra virgin olive oil as a source of healthy fats. The researchers studied diet, exercise, and variations in healthy lifestyle behaviors across different age groups, genders, and body mass indices (BMI).

Dr. Thomas and colleagues combined data collected over a period of 20 years from 1999-2018 for their study. The study included 42,625 participants between the ages of 20-85 and assessed the adherence to the Mediterranean diet and an exercise regimen using a point based system. Inclusion of fruits and vegetables, legumes, cereals, fish and a ratio of mono-unsaturated to saturated fats were each awarded one point. A healthy Mediterranean diet also includes a mild-moderate amount of alcohol, which is 0-1 glass for women and 0-2 glasses for men. So, a point was given if a mild-moderate amount of alcohol was consumed. Dairy products and meat are not part of the Mediterranean diet. If participants had consumed these foods but had consumed it less than a specific amount, they were still awarded a point. The points were totaled and found to be between 0 and 9. Higher scores meant a higher adherence to the Mediterranean diet. Leisure time physical activity (LTPA) describes any physical activity performed during participants free disposable time. The researchers assessed LTPA based on the frequency, duration and intensity to calculate points / scores for each activity. They categorized the activity levels based on the scores per week into four groups ranging from – sedentary (0 points), low (<500 points), moderate (500-1000 points) and high (>1000 points). Biological age was calculated using an algorithm called PhenoAge. The algorithm calculates biological age based on chronological age and 8 biomarkers obtained from blood samples.

The study included individuals across different races, socio-economic backgrounds, marital statuses, income to poverty ratios, and with various lifestyle-related factors (e.g., smoking, BMI category, total energy intake), making it a representative population of US adults. The researchers found very interesting observations relating to diet and exercise. They discovered that adherence to a relatively healthy diet and engagement in  physical activity were independently associated with a lower biological age. Participants with a healthy diet and some level of activity were on average 1 biological year younger than the participants with the least healthy diet and sedentary lifestyle. Another very interesting finding was that individuals who had a less healthy diet but who were active even at a low level showed delayed biological aging. However, delayed biological aging was not found in participants with a healthy diet and a sedentary lifestyle, suggesting that moderate physical activity is a key component of healthy biological aging.

The findings of this study reiterates the need for better lifestyle choices across all strata of the population as the results were consistent regardless of age, sex and BMI category. A nutritious diet and moderately active lifestyle can have a positive impact on health, aging and quality of life. Getting older is inevitable, but you may be one year younger with a healthy diet and an exercise routine.

Reviewed by: Trang Nguyen, Giulia Mezzadri, Erin Cullen, Maaike Schilperoort 

 

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Unveiling the secrets of pain: decoding the structure of a human receptor for effective relief

Pain is an essential sensation for the survival of organisms. It acts as a protective mechanism, signaling potential harm and prompting animals to recognize noxious stimuli for avoiding future harm. For example, individuals unable to feel pain sensations (a rare congenital disease) seem advantaged at first glance; however they are actually at a high risk of unknowingly injuring themselves. While acute pain serves a crucial role in preserving well-being, chronic or persistent pain can severely impact the quality of life. Unfortunately, the mechanisms underlying the transition from acute to chronic pain remains poorly understood, making diagnosis and treatment challenging. Although opioids are commonly used to manage chronic pain, they carry the risk of addiction and interference with normal brain activity. As an alternative, targeting directly the receptors involved in pain pathways, such as the transient receptor potential (TRP) family, offers a promising avenue for developing analgesic therapies.

A recent study (https://www.nature.com/articles/s41467-023-38162-9) led by Dr. Arthur Neuberger, a postdoctoral research scientist in the department of Biochemistry and Molecular Biophysics within Dr. Alexander Sobolevsky’s lab, investigated the structure and inhibition mechanism of human TRPV1 and its interaction with a potential analgesic compound known as SB-366791.

TRPV1, a receptor found on nerve cells, plays a pivotal role in sensing pain and heat. It is a temperature-sensitive TRP ion channel, commonly referred to as the vanilloid receptor 1 or capsaicin receptor (pungent compound from chili pepper). TRPV1 functions as an ion channel involved in pain sensation, becoming activated in response to noxious signals. When activated, TRPV1 opens, leading to a decrease in the electrical resistance of the cell membrane and the subsequent flow of ions. If the strength of the noxious signal and the response of the ion channel are sufficient, a change in the membrane potential occurs, allowing the signal to be transmitted from the peripheral nervous system to the spinal cord and ultimately to the brain (Figure 1).

Figure 1. Overview of the pain-processing pathway. When exposed to noxious stimuli, such as the burning sensation of a flame on the skin or the heat sensation of capsaicin on the tongue, TRPV1 ion channels are activated in the peripheral nervous system. The resulting heat signal is transmitted through nerve fibers and follows spinal pathways until it reaches the brain, where it triggers the generation of a pain response. Figure created using Biorender.

The study, published in Nature Communications, significantly advanced our understanding of the three-dimensional structure of TRPV1, providing crucial insights into its functional properties. The researchers employed advanced techniques, such as cryo-electron microscopy (cryo-EM), to determine the precise arrangement of human TRPV1. Additionally, whole-cell patch clamp electrophysiology (technique that measures the electrical signals as flow of ions across the cell membrane providing information on how the cell responds to certain stimuli or drugs) was used to propose the inhibition of TRPV1 by SB-366791. These cutting-edge techniques provided valuable insights into the architecture and functional characteristics of TRPV1 (Figure 2). Through their investigations, the researchers successfully identified the specific binding site of SB-366791 on the vanilloid site of TRPV1, utilizing cryo-EM and mutagenesis techniques. This discovery suggests that the analgesic compound may exert its effects by selectively inhibiting TRPV1 activity. Furthermore, the study revealed the structural changes that occur within TRPV1 upon binding to SB-366791. These structural alterations affect the conformation of the protein, demonstrating that even in the closed state of TRPV1, SB-366791 can bind and stabilize the closed conformation. This mechanism has the potential to reduce pain signaling. Understanding these structural modifications is important for the development of novel analgesic drugs targeting TRPV1.

Traditionally, pharmacological and physiological investigations of TRPV1 have primarily focused on rodent and squirrel orthologues. However, since the TRPV1 channel plays a central role in almost every aspect of human physiology and disease, including pain and temperature perception, the recent study by Neuberger and colleagues is significant. By specifically examining the human TRPV1 structure and its interaction with SB-366791, this research opens up new possibilities for the development of effective analgesic therapies and sets the stage for future investigations in the field of pain management.

Figure 2. Overview of cryo-electron microscopy (cryo-EM) and the structure of human TRPV1 in complex with the inhibitor SB-366791. In cryo-EM, a beam of electrons is directed at a frozen solution containing the protein of interest. The resulting electrons pass through a lens system, creating a magnified image on a detector. From this image, a three-dimensional model of the protein’s structure is generated. The structure of hTRPV1 in complex with SB-366791 is visualized from two perspectives: parallel to the membrane and extracellularly. In the images, the TRPV1 subunits are color-coded as green, yellow, pink, and blue, while the lipids are represented as purple sticks. (Figure modified from Neuberger et al., 2023)

Reviewed by: Maaike Schilperoort, Giulia Mezzadri and Trang Nguyen

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