Science with Angela

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Week 6 In the Books!


Abstract #35 Divergent outputs of the ventral lateral geniculate nucleus mediate visually evoked defensive behaviors from Dr. Andrew Huberman's lab. No preprint but open access. Andrew hosts a podcast 'The Huberman Lab' that many of you likely know about. Deep dives into neuroscience of behavior & well-being. I particularly liked this one on grief, which gave me tools & insight to help me cope with the transition of my son moving away for university. I know that likely elicits an eyeroll from many of you, because this is not a bad thing, but transitions are hard, loss is hard, even though it can be associated with growth and new beginnings. Emotions are complicated! Anyway, I thought I would take a look at some of his research so chose a recent Cell Reports paper from his lab.


Summary: Rapid alternations between exploration and defensive reactions require ongoing risk assessment. How visual cues and internal states flexibly modulate the selection of behaviors remains incompletely understood. Here, we show that the ventral lateral geniculate nucleus (vLGN)—a major retinorecipient structure—is a critical node in the network controlling defensive behaviors to visual threats. We find that vLGNGABA neuron activity scales with the intensity of environmental illumination and is modulated by behavioral state. Chemogenetic activation of vLGNGABA neurons reduces freezing, whereas inactivation dramatically extends the duration of freezing to visual threats. Perturbations of vLGN activity disrupt exploration in brightly illuminated environments. We describe both a vLGN→nucleus reuniens (Re) circuit and a vLGN→superior colliculus (SC) circuit, which exert opposite influences on defensive responses. These findings reveal roles for genetic- and projection-defined vLGN subpopulations in modulating the expression of behavioral threat responses according to internal state.

schematic of two opposing circuits in the thalamus that control the defense response to threats


The activities of these neurons affect the outcome of responding or not responding to a (perceived) threat. The data revealed two divergent vLGNGABA output pathways to the Re and SC, each of which exert opposite influences on freezing behaviors. The outputs to the SC dominate the response in conditions where both outputs (vLGN→SC and vLGN→Re) are simultaneously activated. Activation of vLGNGlut→SC neurons resulted in the generation of diverse, long-lasting defensive behaviors even in the absence of looming stimuli, and caused mice to completely avoid exploration of the upper, well-illuminated chamber.


I liked this interesting discussion point "Given the presence of the vLGN and its homologs across species, and its role in defensive and anxiety-related behaviors shown here, the vLGN is an interesting structure to consider in the context of depression, generalized anxiety, and phobias. In each of these disorders, sensory stimuli such as light, sound, and time of day have been shown to modulate the presence and scale of adverse behavioral and emotional responses.". 


This abstract reminded me a lot of a JEDI awardee that I worked with, Dr. Benjamin Suarez-Jimenez. It was one of the first times I thought deeply about competing approach-avoidance behaviors, where for instance something you enjoy is associated with some risk - how do you assess these situations, what happens when your ability to 'correctly' assess these situations goes awry, and what triggers maladaptive approach-avoidance behaviors. These are fascinating quesitons to me (and not unrelated to me both wanting and not wanting my son to progress to the next natural stage of his life!). 


Abstract #36 YAP inhibits HCMV replication by impairing STING-mediated nuclear transport of the viral genome from Dr. Keejung Yoon's lab. Open access, no preprint available. I chose this paper because I loved 'all the words' - YAP, viral replication, STING, nuclear transport etc. 


Abstract: YES-associated protein (YAP), a critical actor of the mammalian Hippo signaling pathway involved in diverse biological events, has gained increased recognition as a cellular factor regulated by viral infections, but very few studies have investigated their relationship vice versa. In this study, the authors show that YAP impairs HCMV replication as assessed by viral gene expression analysis and progeny assays, and that this inhibition occurs at the immediate-early stages of the viral life cycle, at the latest. Using YAP mutants lacking key functional domains and shRNA against TEAD, the authors show that the inhibitory effects of YAP on HCMV replication are nuclear localization- and TEAD cofactor-dependent. Quantitative real-time PCR (qPCR) and subcellular fractionation analyses reveal that YAP does not interfere with the viral entry process but inhibits transport of the HCMV genome into the nucleus. Most importantly, we show that the expression of stimulator of interferon genes (STING), recently identified as an important component for nuclear delivery of the herpesvirus genome, is severely downregulated by YAP at the level of gene transcription. The functional importance of STING is further confirmed by the observation that STING expression restores YAP-attenuated nuclear transport of the HCMV genome, viral gene expression, and progeny virus production. We also show that HCMV-upregulated YAP reduces expression of STING (that seems counterproductive from the virus point of view... but then again STING is typically anti-viral). Taken together, these findings indicate that YAP possesses both direct and indirect regulatory roles in HCMV replication at different infection stages.


Author Summary: Human cytomegalovirus (HCMV) infections in immunocompromised patients cause morbidity and mortality, and congenital infections can lead to severe neurodevelopmental deficits such as microcephaly. This study shows that YAP, a transcription factor renowned for its roles in diverse cellular events, potently inhibits HCMV viral gene expression and subsequent infectious progeny production. Furthermore, the authors find that these inhibitory effects of YAP on HCMV replication are due to inefficient delivery of the HCMV genome into the nuclei of the host cells, thus hindering a key early step of the viral life cycle. Importantly, they pinpoint that YAP reduces STING protein levels, contributing to the impaired nuclear transport of the HCMV genome. Taken together, their findings provide insight into the molecular features of YAP regulation of viral replication, and novel antiviral approaches against HCMV and other herpesvirus infections.


Basically - Yap and it's cofactor Tead inhibit the expresion of "STING" which is required for HCMV genome delivery to the nucleus. (Hong et al., PNAS 2021: herpesvirus exploits STING to facilitate nuclear import of the viral genome. Following the entry of the viral capsid into the cell, STING binds the viral capsid, mediates capsid docking to the nuclear pore complex via physical interaction, and subsequently enables accumulation of the viral genome in the nucleus. Silencing STING in human cytomegalovirus (HCMV)-susceptible cells inhibited nuclear import of the viral genome and reduced the ensuing viral gene expression.) Typically, STING induces type I interferon production when cells are infected with intracellular pathogens. STING has been shown to activate downstream transcription factors STAT6 and IRF3 which are responsible for the antiviral response and innate immune response against intracellular pathogen.


Just in case you wanted some background:

Schematic of HCMV life cycle


Abstract #37 A plant-derived natural photosynthetic system for improving cell anabolism from Dr. Xianfeng Lin's Lab. No preprint, open access. THIS PAPER IS AMAZING. Photosynthesis in mammalian cells. Full stop. I skimmed the whole beautiful paper and it (I think) did a good job addressing some of the low-hanging criticism (What about ROS? Immune surveillance?) raised by the highly critical Twittersphere. COME ON THIS IS AN INCREDIBLE ACHIEVEMENT AND CAN WE PLEASE APPLAUD THIS GROUP AND THE ADVANCE. Sorry, I'm in an all caps mood today. 


Abstract: Insufficient intracellular anabolism is a crucial factor involved in many pathological processes in the body. The anabolism of intracellular substances requires the consumption of sufficient intracellular energy and the production of reducing equivalents. ATP acts as an ‘energy currency’ for biological processes in cells, and the reduced form of NADPH is a key electron donor that provides reducing power for anabolism. Under pathological conditions, it is difficult to correct impaired anabolism and to increase insufficient levels of ATP and NADPH to optimum concentrations. Here the authors develop an independent and controllable nanosized plant-derived photosynthetic system based on nanothylakoid units (NTUs). To enable cross-species applications, we use a specific mature cell membrane (the chondrocyte membrane (CM)) for camouflage encapsulation. As proof of concept, we demonstrate that these CM-NTUs enter chondrocytes through membrane fusion, avoid lysosome degradation and achieve rapid penetration. Moreover, the CM-NTUs increase intracellular ATP and NADPH levels in situ following exposure to light and improve anabolism in degenerated chondrocytes. They can also systemically correct energy imbalance and restore cellular metabolism to improve cartilage homeostasis and protect against pathological progression of osteoarthritis. Our therapeutic strategy for degenerative diseases is based on a natural photosynthetic system that can controllably enhance cell anabolism by independently providing key energy and metabolic carriers. This study also provides an enhanced understanding of the preparation and application of bioorganisms and composite biomaterials for the treatment of disease.


From the paper "Owing to the closed environment of the knee joint cavity, we first measured the efficiency of red light to penetrate skin and muscle. Values of 58.1% and 49.8%, respectively, were achieved (Extended Data Fig. 8a), which demonstrates that red light can effectively penetrate the knee joint cavity in our model. Next, we investigated whether intra-articular injection of the CM-NTUs and subsequent exposure to light irradiation can inhibit the progression of osteoarthritis induced by anterior cruciate ligament transection (ACLT) surgery in mice (Fig. 5a)." "Gait analysis showed that the maximum contact and maximum intensity of the right hind limb of mice in the ACLT control group were significantly reduced compared with that in the sham group, and this effect was rescued in ACLT mice treated with CM-NTUs and light (Fig. 5m,n)."


schematic of experimentresults showing rescue of gait with CM-NTU+light

(n) Gait assessment scores for maximum contact maximum intensity (right hind limb) in mice 8 and 12 weeks after operation (n = 12, mean ± s.d.). grey=sham (no ACLT surgery), orange=vehicle dark, yellow=vehicle light, dark blue=CM-NTU dark, turquoise=CM-NTU light (!!!)


It's incredible - this is, to me, the kind of science that makes your jaw drop. I wouldn't care if it only marginally rescued but it almost fully resuced. Maybe not forever but ... amazing. Great research briefing to go with it: Plant-cell machinery for making metabolites transferred to mammalian cells


Abstract #38 Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer from Dr. Agata Smogorzewska's lab. Open Access, posted on biorxiv 15 months before publication (that's one of the longest I've seen - kudos to this group for having the courage and conviction to do that!


Abstract: Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage. The FA repair pathway protects against endogenous and exogenous carcinogenic aldehydes. Individuals with FA are hundreds to thousands fold more likely to develop head and neck (HNSCC), oesophageal and anogenital squamous cell carcinomas (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or infection with human papillomavirus (HPV). Here, by sequencing genomes and exomes of FA SCCs, we demonstrate that the primary genomic signature of FA repair deficiency is the presence of high numbers of structural variants. Structural variants are enriched for small deletions, unbalanced translocations and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not in the context of HPV infection, and lead to somatic copy-number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte-intrinsic inflammatory signalling, which would contribute to the aggressive nature of FA SCCs. We propose that the genomic instability in sporadic HPV-negative HNSCC may arise as a result of the FA repair pathway being overwhelmed by DNA interstrand crosslink damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA-crosslinking damage.


(The biorxiv summary is pretty much the same - if anything has a bit more info)


The authors obtained genomic data on sporadic HNSCCs from the Cancer Genome Atlas and showed that these tumors had  structural-variant numbers in their genomes. Smoking history correlated with the number of structural variants: The more the patients smoked, the more variants were detected in their tumors. The tumors with the highest numbers also had signs of elevated alcohol exposure—a correlation that means drinking and smoking, which both subject the body to aldehydes, may fuel cancer by similar mechanisms as those at play in Fanconi anemia.


This sheds light on how HNSCC arises in people without FA and without HPV - but rather due to smoke & alcohol - aldehydes derived from these substances likely overhwelm the FA repair pathway, and on top of that the DNA damage results in copy-number alterations of HNSCC drivers (PIK3CA, MYC, CSMD1, PTPRD, YAP1, MXD4, and EGFR.)



The very first line of the Acknowledgements: We thank the participants and their families who donated their tissues to IFAR


Abstract #39 Domestic dog lineages reveal genetic drivers of behavioral diversification from Dr. Elaine Ostrander's lab. Open Access, preprint posted on biorxiv one month earlier. This paper had me at "dog". 


Abstract: Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.


My superficial summary/interpretation is that the behavioral differences come down to differences in regulatory regions that control neurodevelopmental genes. (e.g. axon guidance in sheepdog). 


I kind of loved to read "One of the most significant behavioral correlations identified herein was with the herder lineage and non-social fear, anxiety-related behavior in response to phenomena that trigger fear responses, potentially related to a hyper-awareness of surroundings. This factor was also significantly correlated with the terrier and scent hound lineages, and all three lineages are those for which acute sensitivity to specific environmental stimuli is advantageous: herding dogs are keenly aware of subtle changes in the body language of livestock, terriers of stimuli signaling hidden prey, and scent hounds track the movements of game using non-visual cues"  because I have the most beautiful good boy in the world Ozzie who is a Black Mouth Cur (I think - he's a rescue) and he is totally skittish no matter how much you reassure him. 


Here's a picture of Ozzie for you (and others on this website):

picture of ozzie, black mouth cur, in a house


Abstract #40 Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease from Dr. Emma Rawlins' lab. Open access and preprint on biorxiv about 17 months earlier - different title: Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells and a few new authors on the published paper. 


AbstractVariation in lung alveolar development is strongly linked to disease susceptibility. However, underlying cellular and molecular mechanisms are difficult to study in humans. We have identified an alveolar-fated epithelial progenitor in human fetal lungs, which we grow as self-organizing organoids that model key aspects of cell lineage commitment. Using this system, we have functionally validated cell-cell interactions in the developing human alveolar niche, showing that Wnt signaling from differentiating fibroblasts promotes alveolar-type-2 cell identity, whereas myofibroblasts secrete the Wnt inhibitor, NOTUM, providing spatial patterning. We identify a Wnt-NKX2.1 axis controlling alveolar differentiation. Moreover, we show that differential binding of NKX2.1 coordinates alveolar maturation, allowing us to model the effects of human genetic variation in NKX2.1 on alveolar differentiation. Our organoid system recapitulates key aspects of human fetal lung stem cell biology allowing mechanistic experiments to determine the cellular and molecular regulation of human development and disease.


Abstract #41 Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription from Dr. Mitch Guttman's lab. Open Access, no preprint.  I chose this one because I love RNA and nuclear organization, Mitch's work is great and my dear friend and former LSE editor Dr. Shawna Hiley is now part of his group. 


Abstract: Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments—with multiple active genes simultaneously colocalizing within the same B compartment—and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.


I think this is interesting - but also I feel like we've heard a lot about transcription within heterochromatin - for instance "A heterochromatin-dependent transcription machinery drives piRNA expression" (which, I assume, are the genes that are being transcribed in the B compartment - that they are within what otherwise looks like heterochromatin? I would love to know more about features that discern genes that are transcribed in the B compartment (all 3 of them) vs those transcribed in the A compartment - as someone not having to actually do the work ;) )


So, what does drive compartmentalization into A/B - beyond transcription? - This came up in the discussion.


  • One possibility is that these compartments reflect differential gene density: DNA regions contained within A compartments are generally gene dense, whereas those in B compartments are generally gene poor. This would explain why A/B compartments are correlated with transcriptional activity but may not regulate transcription state, because gene-dense regions are more likely to be transcriptionally active.
  • A/T sequence content of the genome,
  • the prevalence of SINE and LINE elements, 
  • and the replication timing of DNA. In fact, multiple studies have found that early and late replicating domains correspond to A and B compartments, respectively. 
  • Yet another possibility is that these compartments reflect patterns of histone modifications.




"The woods are lovely, dark and deep"

Robert Frost