2022
2022 Writng Style
Week of Dec 13, 2022
ZC
Cystic fibrosis transmembrane conductance regulator (CFTR) has been extensively studied in the context of the disease, cystic fibrosis, which is caused by the mutation of the CFTR gene. CFTR may also involve in infectious diseases, such as pneumonia-caused acute respiratory distress syndrome (ARDS), evidenced by the rapid downregulation of CFTR after viral and bacterial infections. Indeed, Erfinanda et al. found that inhibition of CFTR will increase weight gain and the wet-to-dry ratio of perfused lungs as a measure of edema, which can be attenuated by WNK1 and TRPV4 inhibitors. CFTR potentiator, ivacaftor, increases the CFTR’s open probability and rescues the barrier function of the lungs. This research is a classical paradigm illustrating the role of CFTR in lung barrier function via the CFTR-WNK1-TRPV4 pathway and provides a new strategy to treat ARDS by targeting CFTR.
LQ
Microenvironmental factors can promote the proliferation of small pulmonary artery (PAs) cells to develop pulmonary artery hypertension (PAH). Tuberous sclerosis complex2 (TSC2) can inhibit cell growth. However, the role of TSC2 in PAH and related mechanisms have not been well studied. The study determined that TSC2 showed a decrease in PAH patients and mice. TSC2 deficiency can promote matrix stiffness to increase the proliferation of PA vascular smooth muscle cells (PAVSMC) through increasing YAP/TAZ and mTOR activity in vitro and in vivo. SIRT1 activator SRT2104 can restore the abundance of TSC2 to ameliorate PAH. For further study, the authors can interfere with the expression of YAP/TAZ to make sure TSC2 deficiency indeed affects PAH development through them. The disadvantage of this study is human sample size is too small.
AJM
Lung lymph nodes (LLNs) are vital to age-related susceptibility to severe respiratory infections; However, comprehensive studies of human LLNs have been limited. In this paper, the authors analyzed lung and mesenteric lymph nodes from 84 donors with no history of smoking across young, middle, and old age groups. Individuals >30 years of age had a significantly greater prevalence of black LLNs due to atmospheric particulate within resident macrophages. Regardless of particulate burden, resident macrophages from aged individuals had impaired turnover and greater pro-inflammatory cytokine expression; However, a cells' particulate burden was correlated with reduced inflammatory cytokine production. Impaired macrophage actions will impact adaptive immunity, as suggested by disrupted B cell follicle architecture in aged LLNs. Overall, this paper provides direct insight into LLNs and implicates both age-related dysfunction and prolonged exposure to environmental pollutants to age-related respiratory infections.
KK
Tuberculosis treatment failure associated with evolution of antibiotic resilience
Widespread antibiotic treatment regimens to treat Mycobacterium tuberculosis (Mtb) infections have exerted intense selective pressure, leading to a number of survival mechanisms that must be considered in designing new antibiotics. To characterize Mtb adaptation to antibiotics, Liu et al performed genomic analysis of more than 50,000 clinical Mtb isolates and analyzed the within-sample mutational burdens to identify alleles consistently undergoing positive selection. Mutations in the transcriptional regulator resR were common in drug-resistant strains, and the authors found that resR mutations did not alter antibiotic sensitivity or survival to treatment; instead, they dramatically increased growth following antibiotic treatment. Using fluorescently labeled amino acids, the authors showed that resR mutants rapidly synthesized cell walls compared to WT following antibiotic exposure, due in part to concomitant mutations in the resR target whiB. The authors called this previously undescribed phenotype antibiotic resilience, and it merits consideration in the design of novel antibiotics and treatment strategies.
Week of Nov 16, 2022
AJM
The memory B cell response to influenza vaccination is impaired in older persons
B cells in aged individuals mount an impaired antibody response to vaccination; However, the mechanism underpinning this age-related deficiency in B cell antibody production remains undetermined. This paper examines circulating vaccine-specific B cells in young and old individuals before and after influenza vaccination. Through scRNA-Seq and flow cytometry, the authors identify a reduction in a small, FcRL5+ B memory-subpopulation following vaccination in the elderly, however, characterization of this phenotype is limited to associations to various diseases. Further, the authors demonstrate that this population has differences in BCR-variable and heavy chain rearrangement in the elderly. Overall, this paper provided support to altered B cell dynamics in aged individuals and generated useful data (which I tested with B-RAY previously:: https://drive.google.com/drive/folders/1pz9IU5e-BYc_5pjCaBm3etSKIdMXhsks?usp=share_link).
ZC
CDKs can regulate nuclear localization of target proteins via multisite phosphorylation near nuclear localization signal (NLS) and/or nuclear export signal (NES). However, little is known about how each site contributes to the fine-tuning regulation of CDK and appropriate spatial-temporal distribution of protein in the cell. Faustova et al. used synthetic CDK-targeted proteins to show different sites and different motifs control the timing of their nuclear shuttling. They further designed proteins that have different patterns with different CDK inputs. Overall, this research well demonstrates the idea of synthetic biology (i.e. “build to understand”).
LQ
Atypical CXCL12 signaling enhances neutrophil migration by modulating nuclear deformability
It has not been well studied what biochemical factors and how they affect the transmigration of neutrophils. With the help of the customized microscope and micropillars, the authors discovered that CXC chemokine CXCL12 could enhance the motility of neutrophils by improving their nuclear pliability which shows a lower aspect ratio and higher circularity. Also, CXCL12 needed the engagement of ACKR3(CXCR7), activated PKA, and strengthened chromatin condensation to induce nuclear deformation to promote the migration of neutrophils. A trivial problem in this paper is the authors did not show consistency in the gene name of ACKR3. In future studies, the authors can focus on how nuclear deformity affects neutrophil transmigration under some diseases.
KK
RNA-activated protein cleavage with a CRISPR-associated endopeptidase
CRISPR-Cas systems are best known for their nuclease functions, but their proteolytic functions are comparatively poorly studied. To characterize CRISPR-associated proteases (CASP), Strecker et al used mutant proteins and cryo-EM to characterize the structure, substrate, and mechanism of the Desulfonema ishimotonii CASP Csx29 and its associated CRISPR effector, Cas7-11. The authors identified that this CASP system is activated by specific RNA interactions with CRISPR-bound RNA, which is independent of nuclease functions. Additional experiments found that Csx29-Cas7-11 activation disinhibited the transcription factor CASP-sigma via cleavage of its inhibitor, and the authors created a proof-of-concept reporter system with the GFP gene based on this interaction. This study represents an exciting discovery which could allow for experimental RNA sensing in future work.
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Week of Nov 2/2022
AJM
Anti-CD19 CAR T cell therapy for refractory systemic lupus erythematosus
Systemic Lupus Erythematosus (SLE) is characterized by autoantibody production, prompting several B cell-targeted therapeutics, such as anti-CD20 antibody-mediated depletion. However, current B cell-depletion methods fail to eliminate tissue-resident B cells, limiting the effectiveness of such interventions. Herein, the authors proposed anti-CD19 CAR-T cells would provide more complete B cell depletion for SLE, testing in a small cohort of severe-SLE participants (n=5). All participants had minor adverse events and significantly improved clinical symptoms of SLE at a 3 month follow-up, with multi-organ improvements, reduced dsDNA antibodies, and circulating inflammatory factors. Following CAR-T, a greater proportion of peripheral blood B cells were naïve in all patients, assessed by protein markers and B cell Receptor heavy chain sequencing. However, only peripheral blood B cells were assessed and the completeness of B cell depletion was not measured, despite it being a study goal. Further, while antibody titers against vaccines were reported, the authors did not comment if this implies bone-marrow plasma cells are protected from CAR-T therapy. Overall, further follow-up is needed on the durability of clinical improvements and long-term impacts of anti-CD19 CAR-T therapy for SLE, but this study presents a promising alternative for patients refractory to current methods.
LQ
Posttranscriptional Regulation of the Human LDL Receptor by the U2-Spliceosome
Hypercholesterolemia is always caused by the mutation of low-density lipoprotein receptor (LDLR). However, the mechanism of posttranscriptional regulation of the LDLR by the U2-spliceosome has not been well studied. Through RNAi screening, Q-PCR, and RNA sequencing, the authors discovered intron 3 retention transcript was increased to further decrease the surface abundance of LDLR in the patients with NAFLD or bariatric surgery. 3 variations of RBM25 showed correlation with hypercholesterolemia. Overexpression of RBM25 with 3 mutants decreased the uptake of LDL but had no effect on the intron 3 retention transcripts. For the future study, they probably can continue to find out the true causal of intron 3 retention.
Edit:
LDLR
ZC
Mitochondria are essential for keeping homeostasis of muscle satellite cells (SCs), which normally stay in quiescence and can proliferate to repair after injury. However, how mitochondrial dynamic change (i.e. fusion and fission) affects proliferation and repair is unknown. Hong et al. first compared the transcriptomes between quiescent and postinjury SCs and found mitochondrial fission protein Drp1 is upregulated in 3-day-post-injury (dpi) SCs. They further compared quiescent and postinjury SCs from wt and Drp1-knockout mice and proved mitochondrial fission can impair the OXPHOS and mitophagy causing defects in muscle regeneration. Their rescue experiments in both genetic and pharmacological ways enhance the reliability of the whole story and further investigations on the roles of the fusion protein (e.g. Mfn1, Mfn2) would be interesting.
KK
Correct assembly of the nuclear pore complex (NPC) is critical to mitosis, but the mechanisms ensuring appropriate interactions between phenylalanine-glycine-rich nucleoporins (FG-Nups) during this process are poorly understood. In this study, Kuiper et al demonstrate that the molecular chaperone DNAJB6 surveils FG-Nups during NPC biogenesis and is necessary for appropriate NPC assembly. RNAi depletion of DNAJB6 halted NPC formation during interphase, and arresting HEK293T cells in interphase led to nuclear envelope herniations enriched with DNAJB6 and FG-Nups. Using proximity ligation assays, the authors found that DNAJB6 interacts directly with FG-Nups, and they also found that ectopically restoring DNAJB6 to depleted cells disrupted liquid-liquid phase separation and aggregation of FG-Nups. This study identifies a novel mechanism for molecular chaperone proteins in protein homeostasis during NPC biogenesis.
Week of 10/19/2022
LQ
The discrepancy between effector (Tef), memory (Tmem) or exhausted (Tex) T cells and related mechanisms regulating Naïve CD8 T cells differentiation to be these three subsets have not been well studied. The authors adopted lymphocytic choriomeningitis virus model of acute-resolving (infected by Armstrong) or chronic infection (infected by clone 13), which would promote CD8T cells differentiate to be Tef, Tmem, and Tex respectively. Through analyzing the data from scRNA-seq and scATATC-seq, the authors confirmed shared clusters TCF-1+ stem/progenitor-like subsets under both infections, and a subset of Tex cells sharing partial signatures of Nature killer cells. Also, the study revealed PD-1 blockade and Btg-1 gene could promote the differentiation of Tex to be Exh-Progenitor, Exh-Intermediate, Exh-KLR and Exh-Term. Exh-KLR shared partial signatures of Tmem cells and Tef.The same research pattern can be used for CD4T cells.
KK
Spatiotemporal dynamics of membrane surface charge regulates cell polarity and migration
Cell polarity and migration are highly coordinated processes involving large signaling and cytoskeletal networks, and the inner membrane surface charge (zeta potential) has been proposed as a master organizer of these networks. To characterize the regulatory role of zeta potential in cell migration and polarity, Banerjee et al used in vitro models with genetically encoded sensors for charged lipids and optogenetic actuators which could acutely modulate membrane surface potential. The authors found that relatively small changes in zeta potential triggered formation of membrane protrusions and changes in cell migration and polarity. They then used knockouts and pharmacological inhibition of signaling and cytoskeletal networks to demonstrate that the phenotypic changes they observed were mediated by the Ras/PI3K/Akt/TORC2/F-actin network. Though this study failed to identify the specific molecular mediators directing changes in zeta potential, it represents an exciting discovery suggesting a novel regulatory mechanism for polarity and migration.
ZC
MYB orchestrates T cell exhaustion and response to checkpoint inhibition
The precursor of exhausted T cell (TPEX) is defined as PD-1 positive with co-expression of transcription factors TCF1 and ID3 and surface markers CXCR5 and Ly108, which are essential in giving rise to exhausted T cell (TEX) and responding to the chronic infection and checkpoint inhibition. However, the heterogeneity and functionality of subgroups among the traditionally defined TPEX are largely unknown. Using single-cell RNAseq, Tsui et al. first identified the CD62L+ subpopulation in TPEX, which is also enriched with transcription factor MYB, then they found that this subpopulation has the stem-like repopulation capability and is indispensable to control chronic infection but not acute. Beyond, the MYB-dependent CD62+ TPEX is the only group among all three groups (i.e. CD62+ TPEX, CD62L− TPEX, and TEX cells) showing proliferative response in the context of therapeutic PD-1 inhibition, suggesting its potential role in future antitumor therapeutics. Linking the transcriptome with the phenotype in preset populations as a creature of habit may impede the discoveries and cause confusion.
AJM
tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis
Methyltranferases TRMT61A and TRMT6 epigenetically modify tRNAs to impact their activity; However, the biological function of TRMT61A/TRMT6-mediated tRNA modification has not been explored. To address this gap, the authors conditionally knock-outed TRMT61A in CD4 T cells, demonstrating TRMT61A-KO yielded normal TCR signaling and early activation markers but impaired subsequent proliferation and differentiation in vitro and in vivo. tRNA m1A-Seq and RiboTag-Seq revealed TRMT61A-KO T cells had hypo-modification of a subset of tRNAs that led to deficient translation of key metabolic and cycling genes following activation. Overall, this paper reveals the biological implications of TRMT61A/TRMT6-mediated tRNA modification in regulating rapid CD4 T cell responses, demonstrating an important epigenetic regulatory mechanism of immunity.
Week of 10/5/2022
AJM
Live-seq enables temporal transcriptomic recording of single cells
Current methods to study cellular heterogeneity either a) are limited in the number of molecules studied or b) destroy cells to capture a snapshot in time. In this paper, the authors detail Live-seq, a transcriptome profiling technique that allows repeated cytoplasm sampling of the same cell over time. The authors give an honest review of Live-seq's operational difficulties, sequencing limitations, and minor biological impacts of cytoplasm sampling. Nevertheless, the authors demonstrate Live-seq aligns with single-cell RNA-seq transcriptome analyses, aids cell trajectory models, and has a unique power to identify gene expression at basal state leading to heterogeneous cellular responses. Lastly, the authors use Live-seq to demonstrate heterogeneous Nfkbia expression in monocytes impacts their inflammatory response to LPS stimulation. Overall, Live-seq is a promising addition to RNA-seq as a way to strengthen basic understanding of heterogeneous cellular responses.
KK
Inferring and perturbing cell fate regulomes in human brain organoids
While mice and other model organisms have provided valuable insight into the transcriptional regulation of neural development, the transcriptional programs controlling human brain development are not as clearly understood. In order to identify transcriptional networks that control cell fate in human brains, Fleck et al applied single-cell RNA-seq and ATAC-seq to human stem cell-derived organoids at different stages of development. To identify the gene regulatory networks (GRNs) controlling cell development and fate, the authors developed an algorithm called Pando, which identifies candidate regulatory regions, assigns genes and transcription factor (TF) binding sites to the regions, and then models the relationship between gene expression, TF expression, and binding site accessibility. Using this algorithm, the authors identified networks of genes associated with regions or developmental pseudotime, and then they performed CRISPR perturbation of 20 TFs in mosaic organoids to characterize their effects on neural development. This paper provides a powerful tool to combine single-cell technologies with organoids for identification of GRNs in development.
LQ
The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death
The death and granule loss of intestine epithelial cells named Paneth cell can cause the dysfunction of the epithelial barrier, which will further lead to Crohn's disease. The role of Intraepithelial lymphocytes(IELs) in the death or dysfunction of Paneth cells has not been well studied. This study identified γδ IEL favored the survival of Paneth cells with or without the risk gene ATG16L1. Through measuring the supernatant from the coculture of Paneth cells and γδ IELs, the authors discovered γδ IELs protected Paneth cells through secretion of apoptosis inhibitor 5(API5). This discovery was confirmed through the injection of AIP15 into Crohn's disease mice model without ATG16L1 gene and human organoids with ATG16L1. However, the authors did not check the protective effect of API5 in Crohn's disease mice model with ATG16L1 gene.
ZC
Antibiotic combinations reduce Staphylococcus aureus clearance
Antibiotics are the most effective treatment for bacterial infection, whereas resistance to antibiotics could impair the treatment and become a global public health issue. Researchers want to investigate whether combination antibiotic use may overcome the resistance, especially the long-term clearance with multiple antibiotics. They used miniaturized plating and automated image analysis to measure the survival of S.aureus at different time points after antibiotics administration and found that combination may have various interactions in early killing, but reciprocal suppression is widespread in long-term clearance. Moreover, the use of β-Lactamase inhibitors worsens the efficacy of clearance-suppressive drug combinations. This paper tests the combination in different phases and reveals counterintuitive (to me) results, which can be significant guidelines for the clinical use of antibiotics.
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Week of 10/5/2022
AJM
Independent origins of fetal liver haematopoietic stem and progenitor cells
Hematopoietic stem cells and early progenitors appear together during fetal development in a small window of time, suggesting a delicate balance exists to ensure both HSC and progenitor populations are produced. Using fate mapping, the authors propose, in the fetal liver, HSCs and progenitors derive from the same HLF+ precursor, unique from conventional HSC-derived progenitor generation. The authors revealed varying levels of transcription factor EVI1 expression determine HSC or progenitor development. The authors conclusions are a departure from current scientific understanding of the hematopoietic system and must be more rigorously explored; However, a unique developmental trajectory of fetal liver progenitors could explain their distinct phenotypes and deserve further investigation.
LQ
Fibroblast GSK-3α Promotes Fibrosis via RAF-MEK-ERK Pathway in the Injured Heart
It has not been well studied how cardiac fibroblast (CF) -GSK3α (glycogen synthase kinase-3) affects the development of myocardial fibrosis. In this study, the authors determined CF- GSK3α deletion could alleviate fibrosis by preventing myofibroblast transformation without sabotaging the normal function of the heart. Through the kinome analysis, and in vivo/vitro tests, this research confirmed CF-GSK3α knockout could ameliorate fibrosis by inhibiting the Raf-Mek-Erk signaling pathway. However, the authors did not mention if GSK3α was elevated in patients with myocardial fibrosis. Furthermore, the study did not directly check the effect of GSK3a overexpression in vivo. Also, fig 5 could not support the conclusion that Gsk3a could promote fibroblast to myoblast transformation.
ZC
A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids
Duplication and mutation during evolution lead to four RAG paralogues, i.e., RagA-D, in mammals, which are essential for the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway in sensing amino acid availability. It is unknown that the minor differences in sequences and structures of RAGs will cause functional divergence of them. Gollwitzer et al. constructed HEK293FT cell lines that only express comparable levels of different Rag in different cells, and found stronger phosphorylation of downstream TFEB and TFE3 in RagD-containing cells compared with RagC-containing cells. Further mechanistic study revealed that increased binding between RagD and p18 enhances mTORC1 recruitment and phosphorylation of TFEB and TFE3 due to the structural variation of the C- and N- terminus of RagD compared with RagC. This study illustrated the structural and functional differences among RagA-D in mammalian cells in vitro, suggesting a possible metabolic regulation by interchanging paralogue protein, though in vivo validation is needed in the future.
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Week of 9/18/2022
LQ
Embryonic and neonatal waves generate distinct populations of hepatic ILC1s
Group1 innate lymphoid cells(ILCs) including circulating nature killer cells(cNK) and tissue-resident ILC1 are imperative in innate immune responses against pathogens and tumors. However, their ontogeny has not been well studied. This research used fate mapping and scRNA seq to demonstrate that cNK cells appeared one week after birth and displayed a constant replenish rate across all organs(liver, spleen, salivary glands, uterus ) and stages of life, while ILC1 showed different turnover rates with tissue-dependent. The first emergence of ILC1 in all tissues happened at the embryonic stage and the following surge appeared after birth to replace the ILC1 cells in all tissues except the liver. Hepatic ILC1s from embryonic and neonatal stages differentiated to be cytotoxic and helper-like, respectively, which was controlled by Hobit gene. However, the authors didn't check the ontogeny of the intestine, skin, or kidney.
KK
Phosphorylation of muramyl peptides by NAGK is required for NOD2 activation
Muramyl dipeptide (MDP) is a component of bacterial cell walls recognized uniquely by the cytosolic sensor NOD2; however, the molecular determinants of MDP recognition by NOD2 are unknown. To identify positive regulators of MDP sensing, Stafford et al performed gene-trap mutagenesis and treated cells with modified MDP. They identified the sugar kinase NAGK as a factor for MDP recognition, and they used phosphoproteomics and pull-down assays to identify that NAGK function is specific to NOD2 and upstream of NOD2. Using in vitro kinase assays, they demonstrated that NAGK is required for MDP phosphorylation and subsequent recognition of p-MDP by NOD2. Though this study lacked direct evidence of MDP binding to NAGK, it highlights a novel link between metabolism and innate immunity.
AJM
Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins
Cancer cells overcome nutrient depravation through lysosomal catabolism of extracellular proteins. To reveal novel targets in this process, the authors implicated TMEM251, herein termed LYSET, in extracellular protein utilization. LYSET was previously considered a non-essential gene; However, using LYSET KO cells and comprehensive mRNA, proteomic, and quantitative imaging, the authors demonstrated LYSET is critical for lysosomal enzyme trafficking by stabilizing the phosphotransferase required for their modification. Interestingly, the authors showed a disease-associated variant of LYSET can recapitulate lysosomal storage disease phenotypes in vitro. Overall, the authors rigorously establish LYSET in lysosomal maturation with implications in cancer and lysosomal storage disease.
ZC
The role of somatosensory innervation of adipose tissues
Conventional surgical or chemical denervation methods to investigate the physiological role of innervation between certain neurons and tissues are limited due to their low selectivity. Wang et al. focused on sensory innervation with inguinal white adipose tissue (iWAT) and found robust projection from thoracolumbar dorsal root ganglia (DRGs) to iWAT based on the evidence of different imaging strategies. The authors injected Cre-dependent diphtheria toxin subunit and randomized mutated AAV9, which can retrograde from fat to DRGs with low toxicity and off-target effects, to selectively ablate the sensory fibers. And they found enhanced lipogenesis and thermogenesis programs in the sensory-ablated mouse. Taken all, the authors developed a new denervation method with high selectivity not only to find the importance of sensory innervation of iWAT here but also can apply this tool to investigate other innervation in the future.
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Week of 9/7/2022
AJM
RASA2 ablation in T cells boosts antigen sensitivity and long-term function
CAR T cells have limited efficacy against solid cancers due to the immunosuppressive microenvironment within the tumor mass. To identify genes involved in T cell resistance, the authors performed a CRISPR-Cas9 screen under multiple immunosuppressive stimuli, revealing RASA2 as an inhibitor to TCR-mediated activation. Further analyses using RNA-Seq and cancer cell-killing assays demonstrated RASA2 is upregulated under chronic stimuli and ablation confers enhanced activating signaling to specific antigens. Overall, utilizing RASA2-KO CAR T cells yields greater efficacy against liquid and solid tumors by removing an intrinsic negative feedback mechanism in TCR signaling. Future experiments can utilize RASA2-KO CAR T cell therapy against spontaneous solid tumors as nude mice with adoptively transferred cancer cells were the only model used herein.
LQ
Post-translational control of beige fat biogenesis by PRDM16 stabilization
PR domain-containing 16 (PRDM16) can promote the biogenesis of beige adipocytes, which is protective against metabolic diseases. However, the regulation of the PRDM16 protein expression has not been well-studied. In this study, the authors identified CUL2-APPBP2 could reduce the stability of PRDM16 protein by catalyzing its polyubiquitination. CUL2–APPBP2 loss sufficiently prolonged the half-life of PRDM16 and activated beige adipocyte biogenesis. In aged adipose tissue, CUL2–APPBP2 expression was increased and adipocyte thermogenesis was repressed by degrading PRDM16 protein. More importantly, strengthened PRDM16 protein stability induced by CUL2–APPBP2 loss counteracted diet-induced metabolic disorders, such as obesity, glucose tolerance, and insulin resistance. In the future, they can focus on how the CUL2–APPBP2–PRDM16 interaction is regulated under other pathological situations.
ZC
A monocyte–leptin–angiogenesis pathway critical for repair post-infection
Monocytes among other immune cells are recruited to the infection sites. However, monocytes-unlike neutrophils-are not required for bacterial clearance, instead contributing to wound repair. Deficiency of the monocyte leads to delayed healing, disordered angiogenesis, and adipocyte expansion. Elevated leptin level in monocyte-deficient mice and other experiments suggest that monocyte participates in wound healing by producing ghrelin to regulate adipocyte and leptin level. Of note, incomplete rescue by administrating exogenous ghrelin and indirect evidence of monocyte-sourced ghrelin opposing leptin may indicate an alternative pathway of monocyte in wound healing.
KK
RNA editing underlies genetic risk of common inflammatory diseases
RNA editing by proteins including ADAR1 prevents interferon response mediated by the dsRNA sensor MDA5, and a lack of RNA editing can lead to inappropriate inflammation. In this paper, the authors examine RNA editing in humans at the whole-transcriptome levels, proposing RNA editing QTLs (edQTLs) as a class of trait associated with disease. The authors demonstrated that edQTLs are enriched in GWAS for autoimmune diseases, and from GTEx analysis they showed that edQTLs in immune cells explained the largest portion of autoimmune disease heritability. The authors also found that immunogenic dsRNAs identified from edQTLs were frequently antisense transcripts which stimulated interferon response when transfected into cells lacking RNA editing capacity. This study represents the first analysis of RNA editing associated with human disease at the systems level and identifies edQTLs as a novel contributor to common autoimmune diseases.
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Weeks of 7/10/2022
AR
Because of the experimental constraints associated with the Nipah and Hendra paramyxoviruses that require biosafety-level-4 (BSL4) containment, it is difficult to study these viruses' target cells and cellular effects. The authors used human pluripotent stem-cell-derived cell types as a model to prove these viruses preferentially select for arterial epithelial cells (ECs). To test for selective targeting, the authors developed a protocol for effective differentiation of hPSCs into arterial and veinous ECs and used live imaging to evaluate the differences, noticing more multinucleated syncytia in artery cells. Furthermore, the authors used CRISPR/Cas9 to delete EFNB2, which arterial ECs express higher levels of, and found that viral replication decreased while there was no pseudovirus entry. This supports the role of EFNB2 as an entry receptor for the virus, offering an explanation for the preferential selection for arterial ECs over venous ECs. It is important to acknowledge that this study does not account for capillaries, lymphatic vessels, or organ ECs.
AJM
Memory B cells (MBCs) reside in sites of past infection to provide rapid protection upon re-exposure; however, a lack of high-resolution investigations has impeded understanding of tissue resident MBCs’ heterogeneous functions. In this paper, the authors revealed distinct subsets of MBCs in the lung and lymph node following infections. High-affinity MBCs were demarcated by CCR6+CXCR3+ expression and responsible for both initial and re-exposure protection. Alternatively, CCR6+CXCR3- MBCs arose from separate clones undergoing alternative selection processes and contributed non-specific immune complexes. High-resolution approached such as scRNA-Seq and scBCR-Seq revealed the heterogeneity of MBCs in sites of infection in both markers, origin, and function, demonstrating the need for such powered investigations across immune cell populations to improve therapeutic interventions.
LQ
Core control principles of the eukaryotic cell cycle
The current understandings of the roles of S-CDK and M-CDK in the cell cycle events regulation are opposite. The authors reconciled different views and adopted phosphoproteomic assays in fission yeast to discover the mystery of cell cycle control. They found S-CDK and M-CDK substrate specificities were similar and they were not specialized for the S phase and mitosis alone. Also, S-CDK could not drive mitosis because protein phosphatase decreased its activity. Increasing S-CDK activity in vivo was sufficient to overcome substrate specificity differences between S-CDK and M-CDK, and allowed S-CDK to carry out M-CDK function. In future studies, they can check how this is related to other biological processes.
KK
cGAS–STING drives the IL-6-dependent survival of chromosomally instable cancers
Though the innate immune signaling molecules cGAS and STING are critical for inflammatory stress caused by chromosomal instability (CIN) in tumor cells, they are rarely inactivated in metastatic cancer. To understand the role of cGAS and STING in CIN-related inflammation, the authors employed CRISPR-Cas9 knockouts of cGAS-STING signaling components in tumor cells with or without CIN. They found that cGAS-STING-dependent IL6-STAT3 signaling promoted survival tumor survival in response to CIN, and they demonstrated that IL6R blockade inhibited growth of tumors with CIN. This paper highlights a new treatment strategy that could be used with existing drugs that induce CIN, though the findings are currently limited to cancers with highly active IL6-IL6R signaling.
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Week of June 30
AR
When using cerebral organoids as models, they lack cortical cellular diversity, suggesting ineffective patterning of early neural stem cells (NSCs). In order for the organoid to develop correctly, it is imperative that NSCs maintain self-renewal and differentiation capacity. Therefore, the authors tested various derivation methods, comparing them to Allen Human Brain Atlas samples using bulk and single-cell RNA-seq data by employing pairwise differential gene expression comparisons and transcriptomic analysis. Through these comparisons, immunostaining, and FACS sorting, the authors found that short and early Dual SMAD and WNT inhibition is both effective and required to adequately maintain cortical organoid NSC identity while suppressing non-cortical NSC fates, specifically noting preferential selection for outer radial glia. This derivation method can be used to more accurately model cortical disease phenotypes.
AJM
A lipase-independent pathway of lipid release and immune modulation by adipocytes
Adipose tissue homeostasis is supported by lysosomal catabolism of excess lipids by adipose tissue macrophages (ATMs). However, contrary to the prevailing theories, the authors previously revealed ATM lipid catabolism is distinct from that of macrophage-derived foam cells and ATM lipid accumulation is not dependent on adipocyte release of free fatty acids. In this paper, they confirm adipocytes release a unique lipid-droplet-filled exosome that is taken up by ATMs and can induce ATM-features from monocytes. These findings are the first to characterize the atypical adipocyte-derived exosomes (AdExos) both in structure, rate of release, and targets as well as uncover an important stimulus in the distinctive ATM activation profile. Further work into AdExo content changes that occur in obesity may be important for immune regulation.
LQ
Microglia-mediated degradation of perineuronal nets promotes pain
Activated microglia can enhance the activity of spinal nociceptive circuits in nerve injury, however, the mechanism has not been well studied. The authors discovered that perineuronal nets(PNN) could selectively enwrap spinoparabrachial projection neurons, which integrated nociceptive information in the spinal cord and conveyed it to supraspinal brain regions to induce pain sensation. The study also found that activated microglia could degrade PNNs to induce pain-related behaviors. For future studies, they can check if other immune cells have a role in this process.
KK
Brown adipose tissue monocytes support tissue expansion
While monocytes and macrophages are known to reside in and infiltrate every organ, their role in brown adipose tissue (BAT) homeostasis and the mechanism of their renewal in BAT remain unclear. Using scRNA-seq on CD45+ cells combined with pulse-chase experiments, they identified that monocytes contributed significantly to BAT macrophage renewal, though resident macrophage proliferation was able to partially compensate for loss of monocyte renewal in CCR2 -/- mice. The authors also used a model of adipose tissue expansion to show that monocytes were specifically recruited during BAT expansion, and antibody depletion of CCR2 in this model prevented BAT expansion. Through histology, they also identified that CCR2-depleted mice in this model maintained BAT "brownness". This study provides important insights into the influence of monocytes on BAT dynamics and provides targets for further investigation into the role of immune cells in metabolic disease.
Recommended research focus--considering this in atherosclerosis and obesity(AT) in your study
Generation and Release of Mitochondrial-Derived Vesicles in Health, Aging and Disease
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Week of June 15
KK
Deciphering the immunopeptidome in vivo reveals new tumour antigens
Current understanding of the repertoire of tumor MHC-I-associated peptides (immunopeptidome) is limited, hampering development of novel therapies. To address this issue, Jaeger et al developed a model to measure the tumor immunopeptidome in vivo by adding a Cre-inducible affinity tag to mouse MHC-I in a Cre-inducible lung adenocarcinoma model, allowing for specific profiling of tumor MHC-I. Using scRNA-seq in this model, the authors showed the shifts in the tumor immunopeptidome throughout cancer progression, and they found that mRNA expression and translation efficiency did not predict immunopeptidome composition. The latter finding is important because it challenges current strategies for identification of neoantigens for therapeutic targeting. While some of the findings from this study are limited to a specific type of cancer, the model developed here provides a novel framework which will be valuable for future immunopeptidomics research.
LQ
Caspase-7 activates ASM to repair gasdermin and perforin pores
The authors believed Caspase7 had a unique function in the regulated cell death, which was different from the previous discoveries Caspase 7 was a backup in Caspase3-regulated apoptosis. This study showed that caspase7-deficient intestine epithelial cells didn't exhibit normal extrusion, which was necessary for removing dead cells and keeping intact epithelial barrier. Caspase 7 could also cleave and activate acid sphingomyelinase(ASM) to generate ceramide to counteract gasdermin D pores, which may promote the completion of epithelial cell extrusion. Meanwhile, in hepatocytes infected by Chromobacterium violaceum and Listeria monocytogenes, cleaved caspase7 and ASM are produced to clear the bacterias. In future studies, they can focus on which aspect of apoptosis leads to bacterial clearance.
AJM
Lifelong multilineage contribution by embryonic-born blood progenitors
Hematopoietic stem cells (HSCs) have long been considered the main source of blood cells, however, the contribution of other progenitor populations has not been established. In this paper, the authors use several tracing methods to reveal clonal embryonic multipotent progenitor cells (eMPPs) are a significant source of both myeloid and lymphoid blood cells, particularly in early adulthood. These eMPPs are heterogeneous clones derived from early embryonic long-term HSCs and persist throughout a lifetime. This is an important discovery, demonstrating differences in origin between immune cells throughout a lifetime that could contribute to age-associated disease.
AR
An exercise-inducible metabolite that suppresses feeding and obesity
It is well-established that physical exercise has metabolic benefits, yet the molecular and cellular mechanisms by which these benefits are obtained is unclear. Using mass spectometry and untargeted metabolomics of blood plasma (that was collected from mice after they ran on a treadmill), the authors uncovered an exercise-induced metabolite, N-lactoyl-phenylalanine (Lac-Phe). To further investigate this molecule's role, they increased Lac-Phe in diet-induced obese (DIO) mice and found that this led to decreased food consumption, yet did not impact energy or movement. Furthermore, the chronic administration of the molecule reduced fat and led to weight loss while bettering glucose homeostasis. The authors were thus able to conclude that physical activity increases the production of Lac-Phe from lactate and this metabolite suppresses appetite and adiposity.
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Week of June 6
AJM
Hematopoietic stem cells (HSCs) are shielded from age-associated inflammation by an unknown mechanism. Given the anti-inflammatory power of adiponectin, the authors investigated its role in HSC quiescence via HSC/blood cell-specific adiponectin receptor knock-out mice. Specific deletion of adiponectin receptors led to increased proliferation and reduced HSC self-renewal potential of HSCs. The authors demonstrate the loss of adiponectin-signaling primarily effects HSCs through increased IFNγ and TNFα production in immune cells, leading to accelerated loss of HSC self-renewal in ageing and infection. These results reinforce the importance of adipokines in systemic immune fitness during ageing and infection. Future work should establish the relationship of adipokine levels to HSC self-renewal in more models and in humans.
LQ
The longitudinal dynamics and natural history of clonal haematopoiesis
To understand what factors and how they control clonal haematopoiesis develops, this study tracked 697 clonal haematopoiesis clons from 385 individuals(55-93yr).The authors found 92.4% of clones expanded with a stale exponential rate, except some genes(DNMT3A, TET2, U2AF1, SF3B1, and SRSF2) mutant caused different growth rates. Through analysis of 1731 sequences of haematopoiesis colonies from 7 older individuals, they revealed that DMNT3A-mutant clones expanded early in life and showed a slower growth rate in old age. And splicing gene(SRSF2, U2AF1, and SF3B1) mutations drove expansion only in later life(>60yr),whereasTET2-mutant clones emerged across all ages. Finally, they showed that SRSF2, U2AF1-mutant could induce faster clonal growth driving a higher risk of malignant progression.But they didn't talk about the difference between males and females.KK
BRD2 compartmentalizes the accessible genome
The spatial organization of heterochromatin and euchromatin regions is key to regulation of gene expression and cell function, but the molecular mechanism through which accessible chromatin domains (ACDs) are compartmentalized is unknown. To address this question, Xie et al used super-resolution 3D ATAC-PALM microscopy in cells lacking cohesin, the master regulator of chromatin loops, and found that cohesin loss caused mixing of distant ACDs in addition to its predicted effects on local domains. The authors performed a screening and identified that these unexpected findings were mediated by BRD2. Using super-resolution microscopy and Hi-C sequencing, they found that BRD2 promotes spatial mixing and maintains active chromatin compaction upon cohesin loss. Following modeling and simulation, they proposed a model where cohesin and BRD4 antagonize BRD2 binding to chromatin, thereby suppressing chromatin compartmentalization. This paper provides uncovers a novel mechanism for chromosomal spatial organization.
AR
your recently published article haha
It is widely accepted that macrophages are involved in atherosclerotic cardiovascular disease risk, but little is known about the extent of their role. The authors created AtheroSpectrum--a new tool for analyzing monocyte transcriptomes to visualize the evolution of macrophages to foam cells and inflammatory profile--and used single cell transcriptomic profiles to identify genes correlated with pathogenic foaming. The AtheroSpectrum yielded both homeostatic foaming and inflammatory pathogenic foaming, from which the authors identified a subset of 30 genes that they showed contribute to cardiovascular events. Ultimately, the authors created a CR-30 risk score model for this pathogenic foaming gene set which, when combined with common risk factors, can be used to better calculate the risk for atherosclerotic cardiovascular disease.
Reviews to share (not for writing):
Substoichiometric action of long noncoding RNAs
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Week of 5/24/2022
LQ
PHGDH heterogeneity potentiates cancer cell dissemination and metastasis
The study focused on the role of PHGDH in breast cancer metastasis and related mechanisms. The authors discovered heterogeneous or low PHGDH expression increased the displacement of the breast tumor. Through gene-set enrichment analysis, they defined the increasing sialylation of integrin αβ was the underlying mechanism of the metastasis caused by low PHGDH protein expression. The research also defined hexosamine-sialic acid pathway couples low PHDGH expression to promote the silylation of integrin αβ. They found the PHDGH mRNA showed opposite expression compared with protein, so for future studies, they can focus on the factors regulating the translation step of PHGDH, which may be another key point in promoting tumor metastasis.
KK
Compatibility rules of human enhancer and promoter sequences
The quantitative effect of distal enhancers on activation of specific promoters is critical to understanding human gene regulation. In order to characterize this relationship, Bergman et al designed a assay called STARR-seq. The authors cloned a set of 1000 enhancer and 1000 promoter sequences in pairwise comparisons into reporter plasmids and added a molecular barcode for each pair, allowing for quantitation of expression for each enhancer-promoter pair. Using this assay, the authors discovered that nearly all enhancer sequences activated promoter sequences by similar amounts, irrespective of sequence specificity. However, they successfully identified separate classes of enhancer and promoter sequences with relatively subtle differences in activation. Although this study did not account for all potential mechanisms regulating enhancer-promoter interactions, it provided valuable insight into the nature of their relationship.
AJM
Gibbin mesodermal regulation patterns epithelial development
Chromatin remodeling is crucial in embryogenesis for mesoderm and ectoderm specification; however, crucial regulators are shared between the layers and thus the mechanism to transmit lineage-specific morphogenesis is unclear. In this paper, the authors, using human embryonic stem cells, identified and characterized the AHDC1 locus as a regulator of mesoderm-specific gene expression and named its protein Gibbin. The authors used BASU proximal proteomics to reveal Gibbin interacts with methyl-CpG-binding proteins. Indeed, loss of Gibbin resulted in hypermethylation in critical mesoderm regulators; Gibbin-KO prevented mesoderm maturation and subsequent interactions with the ectoderm, resulting in deleterious abnormalities in dermis and epidermis development. In conclusion, the authors progress from discovery to molecular characterization to phenotypic relevance to establish a role for Gibbin in mesoderm-specific function and ectoderm development, introducing an important mechanism by which Gibbin-regulated methylation enforces lineage commitment.
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Week of 5/4/2022
AJM
Cerebrospinal fluid regulates skull bone marrow niches via direct access through dural channels
Mounting evidence suggests the central nervous system (CNS) has a specialized immunological environment arising from the skull bone marrow (BM) niche; however, further data is needed to demonstrate a regulatory connection between the CNS and this niche. In this paper, the authors investigated the impact of cerebral spinal fluid (CSF) factors on the skull BM niche, revealing regulation of myeloid cells' egress into the dura and myelopoiesis. First, the authors showed skull BM immune cells respond to chemoattractant injected into the CSF, and ligands important to monocyte and neutrophil trafficking are present in the CSF during homeostasis. Using spinal cord injury and CSF transfer, they revealed CSF factors are responsible for increased monocytes numbers within the CNS and matched reduction within the skull BM niche despite a higher proportion of myeloid-progenitor populations. The authors demonstrated a regulatory link between CSF and the skull BM, strengthening the unique importance of this niche for the CNS. Upon this foundational knowledge, further research can expand into the role of this specialized immune surveillance in neurological diseases and disorders.
LQ
Neuroimmune cardiovascular interfaces control atherosclerosis
It's well known that the nervous and vascular systems interact at multiple levels, however, it's not clear about the effects of neuronal control on atherosclerosis. The authors discovered human atherosclerosis-diseased adventitia segments showed expanded axon networks. Mouse Neuron immune interfaces (NICIs) existing in adventia formed by leukocytes and nervous established a structural artery–brain circuit (ABC).ABC peripheral nervous system components were activated followed by atherosclerosis progression, whereas coeliac ganglionectomy led to the disintegration of adventitial NICIs, reduced disease progression, and enhanced plaque stability.
KK
Intron-mediated induction of phenotypic heterogeneity
Ribosomes require significant cellular resources for their synthesis and maintenance, and regulating their expression levels is thus critical to optimal cellular function. In this study, the authors examined intron retention as a mechanism for regulating ribosomal protein expression in yeast using a model of LiCl-induced osmotic stress and a technique called isogrowth profiling, where changes in growth and transcriptomes can be distinguished from general stress and growth inhibition responses. Expression of the RPS22B transcript showed a bimodal distribution under stress and high glucose conditions which the authors found was determined by retention of an intron in the 5' UTR of RPS22B. Through this mechanism, yeast cells induced phenotypic heterogeneity which enhanced the population's fitness under varying cellular conditions.
A large-scale binding and functional map of human RNA-binding proteins
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Week of 4/22/2022
LQ
Somatic mutation rates scale with lifespan across mammals
To understand the role of somatic mutation in cancer and aging, this study performed whole-genome sequencing across 15 mammalian species.The authors did comparative analysis between previously reported human data and the seq data of these 15 species.3 shared mutation signatures caused by 5--methylcytosine deamination, endogenous damage, and oxidative DNA damage were confirmed in all mammals, which supported the theory that somatic mutagenesis was caused by endogenous mutational processes.The analysis didn't find association between somatic mutation and cancer, which is different from previous larger research . This research also reported the somatic mutation rate showed strong anticorrelation with lifespan but weak correlation with body mass. The disadvantage of this research is the sample size is small, which may cause the failure of association confirmation between somatic mutation and cancer.
KK
Nonlinear control of transcription through enhancer–promoter interactions
Chromosome structure can regulate transcription through three-dimensional enhancer-promoter interactions, but the relationship between enhancer-promoter proximity and transcriptional output is unknown. In this study, Zuin et al set out to model the effects of physical and genomic distance between promoters and enhancers in regulating transcription in mouse embryonic stem cell lines. The authors generated hundreds of cell lines expressing eGFP under an ectopic Sox2 promoter with an enhancer inserted at random genomic distances. The authors measured RNA expression and used FISH to determine promoter-enhancer contact probability, allowing them to model the relationship between promoter-enhancer distances and transcriptional kinetics. They determined transcription levels determined by an enhancer depend on its genomic distance from the promoter and are described by a nonlinear relationship with their contact probabilities. This work does not account for the effects of other regulatory interactions in this setting, which would be a valuable direction to study in the future.
AJM
Mapping human haematopoietic stem cells from haemogenic endothelium to birth
In order to map the origin of hematopoietic stem cells (HSCs), the authors used CD34+/CD31+ haemato-vascular cells from human embryos of different developmental stages. The authors employed single cell RNA-Seq to identify reliable markers of HSCs and spatial transcriptomics to follow the temporal distribution and emergence of pre-HSCs and HSCs. To fill in missing transcripts to empower HSC clustering and marker identification, Markov affinity-based graph imputation of cells (MAGIC) is used, a method that shares information across similar cells, “via data diffusion”. From this, they generated gene "scoreboards" which can track HSC development, which they validate for in vitro HSC differentiation from progenitors. Further, they determine extraembryonic HSCs share many HSC markers but are distinct and are poised to traffic to the liver. In total, the authors determined crucial markers for HSCs necessary for isolating transplantable HSCs and described differences between HSCs and innate-like progenitors residing in the embryonic liver.
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Week of 3/28/2022
LQ
Neutrophils direct preexisting matrix to initiate repair in damaged tissues
New connective tissues can be produced during internal organ healing injuries, the mechanism of which is not very clear. This study confirmed the tissue of origin for the matrix that was transferred to wounds dominated the scaring or regeneration of the healing tissue through proteomics, genetic lineage-tracing method(NHS-FITC). SCRNA seq data indicated neutrophils could transfer the preexisting matrix dependent on the HSF–integrin AM/B2-kindlin3 cascade. The authors could inhibit matrix transfer and the formation of peritoneal adhesions by interfering with the cascade without impeding the process of wound healing. Further studies are needed to refine which subsets of neutrophils enable matrix transport.
Edit:
Impaired healing and excessive scarring are a tremendous burden for the global healthcare system, so it's critical to understand the repair process to restore and preserve the normal function of injured organs. But the mechanism related to this is not clear. The authors used the methods of proteomics, the genetic lineage-tracing method(NHS-FITC) to confirm that pre-existing matrix was transferred to wounds and the tissues that were the source of the matrix dictated the scaring and regeneration of the healing tissue.The data from Immunohistochemistry staining and single-cell seq confirmed neutrophils transferred the matrix dependent on the HSF-integrin AM/B2-kinlin3 cascade. The authors could inhibit matrix transfer and the formation of peritoneal adhesions by interfering with the cascade without impeding the process of wound healing. Further studies are needed to refine which subsets of neutrophils enable matrix transport.
KK
Rixosomal RNA degradation contributes to silencing of Polycomb target genes
The Polycomb protein complex (PRC1/2) is a key component of epigenetic silencing essential for cell fate which is known to promote chromatin compaction, but additional mechanisms through which PRC1 maintains silencing are unknown. To identify additional mechanisms for epigenetic silencing, Zhou et al studied the rixosome, a highly conserved multienzyme complex also involved in heterochromatin regulation. Via mass spectrometry and ChIP, the authors discovered that the rixosome interacts with PRC1/2 complexes. Using ChIP- and PRO- sequencing and RNAi, they found that the rixosome is recruited to transcription start sites by PRC1/2 and that the rixosome degrades nascent RNAs. This study uncovers a novel mechanism through which eukaryotes can control cell fate and growth.
AJM
Genetic instability from a single S phase after whole-genome duplication
In animals, whole genome duplication (WGDs) leads to chromosome instability and is associated to cancer, however, the immediate molecular changes following WGD are not well studied. To assess immediate changes, Gemble et al. analyzed the first round of replication in three models of WGD, revealing increased DNA damage during S phase. The authors determined WGD cells had similar levels of S phase proteins compared to diploid controls and increasing S phase proteins reduced WGD-induced DNA damage. Further, they confirmed unscheduled WGD in Drosophila neuroblasts induced more DNA damage compared to programmed polyploidy in the same organism, an effect abrogated by overexpression of S phase proteins. Overall, the authors refined a mechanism of WGD-induced DNA damage. However, despite the array of quantitative methods employed, the authors use non-quantitative terms to detail important background and findings, including the frequency of WGD in cancers and its role in cancer pathogenesis. In line, the authors do not deliver a clear goal for their research as they reference WGD’s importance to cancer, but limit contextualizing their findings to a poorly described single gene enrichment analysis on tetraploid cancer cells. The authors could further investigate the consequences of WGD-induced DNA damage in cancer pathogenesis.
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Week of 3/14/2022
AJM
Tryptophan depletion results in tryptophan-to-phenylalanine substitutants
Interferon-gamma stimulation induces frameshifted protein accumulation through an understudied mechanism, thus, the authors investigated the role of interferon-gamma-induced tryptophan depletion. For the first time, the authors revealed codon-reassignment occurs in humans by using an out-of-frame reporter constructs and mass spectrometry to reveal tryptophan-to-phenylalanine reassignment was enhanced following interferon-gamma treatment due to tRNA mismatch. To assess the implication of this mechanism, they utilized proteomic data from a wide range of tumors and found the occurrence of tryptophan-to-phenylalanine reassignments was significantly enriched in tumors compared to adjacent tissue, and could aid in immune evasion. This presents a unique regulatory mechanism that warrants future investigation into its importance in other chronic disease states where interferon-gamma is increased.
LQ
Inhibition of IL11 Signaling Reduces Aortic Pathology in Murine Marfan Syndrome
Marfan syndrome(MFS) is a genetic disorder caused by fibrillin mutation. The researchers confirmed IL11 was upregulated in aortic VSMCs to cause ERK-related thoracic aortic dilation, inflammation, and fibrosis in MFS through separately crossing MFS mice with IL11-tagged EGFP mice or IL11ra1-/- mice. This study also reported an antibody against IL11RA(X209) can ameliorate the symptoms caused by MFS by reducing COL1A1, IL11, MMP2/9 and phosphor-ERK expression.
But the authors didn’t check if X209 would affect the normal physiology function considering IL11’s role in the development of B cells, hematopoietic stem cell and megakaryocyte progenitor cells.
Edit:
Marfan syndrome(MFS) is a genetic disorder caused by fibrillin mutation, which is associated with TGFb-stimulated ERK activity in via the elevation of IL11 in VSMCs. The researchers confirmed IL11 was upregulated in aortic VSMCs to cause ERK-related thoracic aortic dilation, inflammation, and fibrosis in MFS through separately crossing MFS mice with IL11-tagged EGFP mice or IL11ra1-/- mice. This study also reported an antibody against IL11RA(X209) can ameliorate the symptoms caused by MFS by reducing COL1A1, IL11, MMP2/9, and phosphor-ERK expression. The limitation of the research is the mouse model has a big difference from human patients.The mice model has a gender bias.
KK
Insular cortex neurons encode and retrieve specific immune responses
It has long been understood that the brain can sense the immune system and even affect immune function. In this study, Koren et al sought to determine if the brain stores immune-related information and what impact this would have on immune function. To identify the specific neurons reacting to immune stimulus, the authors used TRAP reporter mice which expressed custom DREADD receptors on activated neurons in a DSS colitis model. When the DREADD receptors on DSS-activated neurons were specifically reactivated 4 weeks later, the authors observed a recurrence of colitis-like pathology even in the absence of further DSS treatment, and they recapitulated these findings in a model of zymosan-induced peritonitis. Although the authors never addressed the mechanism through which peripheral nerves induced an inflammatory response, this study is the first to show a peripheral immune response associated with specific neuronal activation.
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Week of 2/24/2022
AJM
Establishment of fetomaternal tolerance through glycan-mediated B cell suppression
During pregnancy, placental trophoblasts present immunogenic non-self antigens, however, it is unclear why robust CD4 and CD8 T cell responses do not occur. In this paper, the authors investigated the interactions between CD4 T cells and antigen presenting cells that confer tolerance. Contrary to their hypothesis, regulatory T cells were not necessary to repress CD4 activation. Using OT-II OVA-specific CD4 T cells and fetus expressing OVA, they discovered B cells capacity to present antigens was crucial to CD4 tolerance to their cognate antigen. Trophoblast presentation induced B cell tolerance by adding a glycan to non-self antigens that was observed to signal through a CD22-Lyn pathway that is known to cause immunosuppression. The authors do not investigate the B cell actions that confer CD4 Tolerance such as cytokine production or decreased antigen presentation, which would be important to understanding how B cells can induce tolerance elsewhere.
LQ
Twin study reveals non-heritable immune perturbations in multiple sclerosis
To dissect the influence of genetic predisposition and environmental factors on the development of Multiple sclerosis(MS), this research adopted CITE-seq, cytoF, mass cytometry to uveal the genetic variance of immune cells from monozygotic twin pairs discordant for MS and their siblings, which included monocytes' shifting from being non-classical to inflammatory classical, higher expression of CD25 and dysregulation of CD25-IL2 axis in Th cells. This study also confirmed the Th cells' proliferation promoted the progression of MS. Furthermore, this research reported the elevated CD25 in Th cells was driven by genetic and early environmental factors through comparing non-twins MS patients with healthy donors. The disadvantage of this paper is the sample size is too small.
KK
In this study, Jomaa et al set out to understand the mechanisms controlling competition between the nascent polypeptide-associated complex (NAC) and the signal recognition particle (SRP) in determining cotranslational protein localization. To identify how SRP overcomes NAC antagonism to the same ribosomal binding site, the authors mutated peptides with signals for different subcellular locations and found that ER-targeting signal sequences in nascent polypeptides weakened NAC-ribosome binding, allowing SRP to bind to ER-targeted peptides. However, through TIRF and FRET the authors also identified direct binding between NAC and SRP, and after mutating both proteins they discovered that SRP first binds to ribosome-bound NAC, after which the globular domain of NAC dissociates and SRP directs the protein to the ER. Although the paper could have used more examples of this model in an in vivo setting to confirm their findings, the authors provided convincing evidence supporting the model for NAC acting as a "sorter" for nascent polypeptides that subsequently recruits SRP for ER protein targeting.
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Week of 2/10/2022
LQ
Single-cell transcriptomic analysis of human colonic macrophages reveals niche-specific subsets
This research adopted Sc-seq and immunofluorescence staining to compare two major constituents of monocyte-like cells in the human gut: lamina propria macrophages (LpMs) and muscularis macrophages (MMs). LpMs preferentially showed pro-inflammatory, high antigen-presenting, and phagocytic capacity. While MMs are skewed towards to be associated with immune activation, angiogenesis, and neuronal homeostasis. They also showed spatial differences:LpMs are close to surface epithelium, while MMs are adjacent to neurons and vessels. Besides the differences, they also share some similarities they are controlled by the interaction with tissue-resident cells and some key transcription factors. It would be more persuasive and direct if they used spatial transcriptomes instead of immunofluorescence staining for the spatial and cell-cell interaction parts in this research.
Edit;
This research mainly compared two major constituents of monocyte-like cells in the human gut: lamina propria macrophages (LpMs) and muscularis macrophages (MMs). Based on the sc-seq results, LpMs preferentially showed pro-inflammatory, high antigen-presenting, and phagocytic capacity, while MMs showed upregulation in genes associated with immune activation, angiogenesis, and neuronal homeostasis. They also show localization differences: LpMs are close to the surface epithelium, while MMs are adjacent to neurons and vessels. Both of them are controlled by the interaction with tissue-resident cells and some key transcription factors. It would be more persuasive and direct if they used spatial transcriptomics instead of immunofluorescence staining for the spatial and cell-cell interaction parts in this research.
AJM
TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
The authors investigated the pathogenic mechanism by which mislocation of nuclear RNA-binding/splicing protein TDP-43 leads to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). They knocked-down TDP-43 by CRISPR inhibition and intersected differential spliced genes with ALS/FTD risk loci, identifying inclusion of two novel non-conserved introns in UNC13A. UNC13A is key to synapse function and harbors two ALS/FTD risk SNPs. Decreased TDP-43 expression and ALS/FTD risk SNPs can synergistically induce UNC13A non-conserved intron expression in a dose-dependent manner, as implicated by correlation in ALS/FTD patient datasets, iCLIP of endogenous TDP-43 binding, and UNC13A RT-qPCR following TDP-43 knock-down, SNP-expressing minigenes, and TDP-43 binding motif mutations. Ribosome footprinting suggested these UNC13A non-conserved introns result in mRNA instability, and quantitative proteomics confirms subsequent protein loss. These results explain UNC13A SNPs risk in TDP-43-dependent ALS/FTD and suggest a mode for loss of TDP-43 function to decreased synaptic function. One other study demonstrated UNC13A knockout blocks synaptic transmission in vivo; the authors could have confirmed this finding in their paper to strengthen UNC13A non-conserved intron in disease pathogenesis.
KK
https://rupress.org/jem/article/219/3/e20211846/212998/Single-cell-transcriptomic-analysis-of-human
T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma
While immune checkpoint inhibitors (ICI) represent a major advance in cancer treatment, they carry a significant risk of causing severe immune-related adverse events (irAEs), and identifying the patients most likely to develop irAEs remains a significant challenge. Using single-cell RNA and V(D)J sequencing, as well as CyTOF, on PBMCs from pre- and early- ICI-treated patients with metastatic melanoma, the authors found that two pre-ICI features were associated with irAEs: CD4+ TM levels and activated CD4+ TM TCR diversity. They validated these findings by using deconvolution algorithms applied to bulk RNA and TCR sequencing data, and they built a model combining CD4+ TM levels and TCR diversity to predict irAEs. Importantly, severe irAEs were independent of both clinical variables and treatment response. The authors hypothesized that patients with irAEs may have had subclinical autoimmune disorders that were activated by ICI therapy, and while they found associations between activated CD4+ TM cells and autoimmune disease in two bulk-seq data sets, the evidence they presented toward that point was relatively weak. However, this paper provides a valuable platform starting point for further investigations into prediction and mechanistic understanding of ICI-associated irAEs.
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Week of 1/31/2022
AJM
Bone marrow endothelial dysfunction promotes myeloid cell expansion in cardiovascular disease
The authors investigated the cardiovascular disease (CVD)-induced hematopoietic skew towards the myeloid lineage, revealing the process is dependent on bone-marrow angiogenesis. de novo vessel outgrowth was captured temporally and systemically by immunofluorescence and magnetic resonance imaging tracking of endothelial activation markers. Angiogenesis during hypertension and following myocardial infarction (MI) occurred in all but was limited to sites of hematopoiesis. Angiogenic and IL-6 producing endothelial cells permitted increased hematopoiesis and myeloid skew in competitive bone marrow transfers. While this paper admirably included mouse models of hypertension, atherosclerosis, and acute MI, the authors observed but do not investigate conflicting results across models. They then choose to focus on acute MI, however, CVD is a chronic condition. Further investigation could include models of chronic conditions that experience acute MI insult which would better model CVD pathogenesis.
LQ
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
How liver cells are spatially organized in their distinct microenvironment niches and how cell-cell interaction determine the identity of individual cells, which were not fully understood. Based on the information from single-cell CITE-seq and single-nuclei seq, the authors were able to confirm the tentative cell clusters. With the adoption of spatial transcriptomes and spatial proteomics, they could further localize the cells and finally draw a cellular zonation pattern, which is the distribution of cells at portal, periportal, mid, central (four parts of a liver section).They compared the transcriptomes of the cells from 7 species and finally found a heavy overlap across them, especially the ALK1-BMP9/10 axis that is important for the development of Kupfer cells. And they also demonstrated LAM was induced by local lipid exposure by comparing normal and steatotic liver. The limitation of this research is human samples are limited. In the future, they can check the disparity of the cells related to age, sex, ethnicity, or pathological parameters.
Edit:
It's not well studied how liver cells are spatially organized in their distinct microenvironment niches and affect each other. The authors could confirm the tentative cell clusters with single-cell or nuclei transcriptomes. The authors could further localize the cells and confirm the zonation of the cells in the livers. By comparing the transcriptomes from 7 species, this study could verify there was heavy overlap across them, especially the ALK-BMP9/10 axis that is vital for the development of Kupfer cells. The authors also demonstrated LAM was induced by local lipid exposure by comparing normal and steatotic liver. The limitation of this research is the human sample size is small. In the future, they can check the disparity of the cells related to age, sex, ethnicity, or pathological parameters.
KK
Sequence specificity in DNA binding is mainly governed by association
Traditionally, interactions between DNA-binding proteins and their target sequences have been thought to depend primarily on the rate of dissociation, with the rate of association being independent of sequence specificity. However, it is unknown whether binding retention to a sequence is caused by differences in recognition or in dissociation. Markland et al. set out to understand the mechanisms controlling association and dissociation rates in the Lac repressor using a combination of mathematical models, protein-binding microarrays, and single-molecule kinetics experiments. By varying the Lac repressor protein, the authors found that the efficiency of target recognition was the main determinant of sequence specificity, meaning that the probability of binding determined the nature of protein-DNA interactions more than the probability of dissociation. These findings lead to the important conclusion that changing the rate of binding rather than the rate of dissociation reduces the risk of a protein lagging on off-target sequences, though it would be beneficial to see these results replicated in other models.
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Week of 1/20/2022
AJM
https://www.nature.com/articles/s41587-021-01139-4
KK
https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(20)30378-7#%20
Mesenchymal stem cell (MSC) transplantation has shown promise as therapy for reducing inflammation during acute respiratory distress syndrome (ARDS), which is a key pathology in SARS-CoV-2 infection. However, the potential utility of MSCs in treating SARS-CoV-2 ARDS is uncertain because of the risk they could be infected and killed following transplantation. Here, Schafer et al showed that while human MSCs do express low levels of SARS-CoV-2 entry receptors, they are resistant to SARS-CoV-2 infection and maintain some anti-inflammatory properties when co-cultured with infected human cell lines. This study lacked some depth as it used only IDO-1 expression as a proxy for anti-inflammatory behavior, failed to examine MSC viral loads, and could have attempted to use experimental models more relevant to SARS-CoV-2 infection. However, these findings also underline the potential of MSC therapy to improve outcomes for human patients, and they have served as part of the evidence to justify multiple ongoing MSC clinical trials in critically ill patients infected with SARS-CoV-2.
LQ
https://www.nature.com/articles/s41593-020-00780-7
To understand how gray matter inflammation affects the spine structure to promote the development of MS, the authors injected interferon-γ and tumor necrosis factor α (TNF-α) into the somatosensory cortex of myelin–oligodendrocyte glycoprotein-immunized mice and performed a craniotomy and implanted a cranial window to monitor their neuronal activity.
Compared with previous research that focused on white matter, they confirmed the spine's loss of gray matter along with calcium accumulation during MS development, which can be further removed by local microglia and infiltrating monocyte-derived macrophages. This process can be reversed by the inhibitor of colony-stimulating factor 1 receptor (CSF1-R) that can inhibit the phagocytosis of macrophages.
The major problem of this research is we don’t know if CSF1-R as a microglia removal at a high dosage would affect other macrophages’ normal activity even at low dosage.
Edit:
To understand how gray matter inflammation affects the spine structure to promote the development of multiple sclerosis(MS), the authors injected interferon-γ and tumor necrosis factor α (TNF-α) into the somatosensory cortex of myelin–oligodendrocyte glycoprotein-immunized mice and performed a craniotomy and implanted a cranial window to monitor their neuronal activity, which is different from commonly used EAE and TMEV-IDD models. Compared with previous research that focused on white matter, they confirmed the spine's loss of gray matter along with calcium accumulation during MS development, which can be further removed by local microglia and infiltrating monocyte-derived macrophages. This process can be reversed by the inhibitor of colony-stimulating factor 1 receptor (CSF1-R) that can inhibit the phagocytosis of macrophages. However, it's unclear yet whether using a high dosage of CSF1-R for microglia removal will interfere with macrophages' other normal activity or not.
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Week of 12/17/2021
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To investigate the cascade of immunological events and the identity of critical players of the innate and adaptive immune response in multisystem inflammatory syndrome in children (MIS-C),this research used sc-seq, flow cytometry and Bioplex assay to analyze the blood and PBMC from 14 MIS-c patients and compared the analysis results with adult severe covid19 patients.The research observed MIS-c specific humoral immune response ,disassociation with vascular diseases, and immune cells changes, such as T cells ,B cells and NK cells and IFNr as a key regulator in the communication of theses immune cells, but they didn't see the immune characters change after treatment of IVIG or systemic corticosteroids, which make the traditional treatment used for MIS-c questionable.The sample size is too small and they used adult severe covid19 patients as control, which make this research less representative and some specificity of MIS-c buried.(edited version)
AJM
In order to elucidate genetic drivers of intracranial aneurysm (IA), Barak et al. employed whole-exome sequencing, associating loss-of-function mutations in PPIL4 with familial IA. In order to substantiate PPIL4 in IA pathogenesis, the authors utilized two model systems; heterozygous PPIL4-depletion resulted in impaired cranial vasculature development, characterized by reduced cerebral vessel abundance and diameter and subsequent reduced blood flow. Interesting next steps include following models of heterozygous PPIL4 mutations to adulthood to better understand the impact of the significant cerebrovascular impairments on subsequent development.
EDIT(1/26/2022): In order to elucidate genetic drivers of intracranial aneurysm (IA) (((this isn’t a clear significance))), Barak et al. employed whole-exome sequencing, associating loss-of-function mutations in PPIL4 with familial IA. In order to substantiate PPIL4 in IA pathogenesis, the authors utilized two model systems; heterozygous PPIL4-depletion resulted in impaired cranial vasculature development, characterized by reduced cerebral vessel abundance and diameter and subsequent reduced blood flow. (((Need a concluding sentence that accurately explains the selling point and significance, your opinion on how much you agree this selling point))). Interesting next steps include following models of heterozygous PPIL4 mutations to adulthood to better understand the impact of the significant cerebrovascular impairments on subsequent development.
KK
Epigenetic Age and the Risk of Incident Atrial Fibrillation
In this paper, Roberts et al used epigenetic markers and epidemiological techniques to attempt to identify mechanisms that make chronological age one of the most important risk factors for atrial fibrillation (AF). The authors used 5 epigenetic "clock" measures as estimates of "biological age" to find statistically significant correlations between epigenetic age markers (which are modifiable, unlike chronological age) and the risk of AF in 5600 patients across 3 studies. This association persisted for 2 of the clocks even after multivariable adjustment for chronological age and other known AF risk factors, but chronological age showed a significant independent correlation as well--indicating that epigenetic age does not account for all of the risk associated with chronological age. The authors used Mendelian randomization analysis to attempt to identify causality in the relationship between epigenetic age and AF, but there were no differences observed, likely due in part to a lack of statistical power. In the future, other patient cohorts could be incorporated to increase statistical power, and experimental studies modifying epigenetic age could attempt to identify potential for reversal of AF risk.
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Week of 09/27/2021
KK- https://www.nature.com/articles/nmeth.3337
Because current methods for separating cell types from tissue samples for RNA sequencing analysis fail to fully capture all cell subsets and have risk of cell type bias, Newman et al set out to create a tool that could robustly identify proportions of pre-selected cell types within bulk RNA samples. Using support vector regression, the authors created CIBERSORT, which uses an input matrix of reference gene expression signatures to estimate cell type proportions from heterogeneous samples. Following testing on multiple data sets, CIBERSORT was more robust and consistent than any previously published tool for identifying relative cell type proportions from bulk RNA seq or microarray samples. While powerful, this tool lacks discriminating power between some cellular subtypes and is limited by the quality of the input reference matrix--which can also fail to robustly identify cellular transitions. Future directions for this work include addressing the above issues, incorporating the ability to use single-cell RNA sequencing data for input, and eliminating systematic bias toward certain cell types.
LQ-https://www.science.org/doi/10.1126/sciadv.abb8471
This paper is about molecular mechanism of how microenvironment (mechanical cues) affect macrophages’ phenotype through YAP/TAZ. It used 3 dimensional culture method to approve this. However, the role of YAP/TAZ in mechanotransduction was already known in 2011.The whole design of this paper is very traditional, which includes idea and test methods. And this research doesn’t involve too much of practical use. I think it will be more meaningful if it can carry out the whole research under the situation of some diseases.
AJM-https://pubmed.ncbi.nlm.nih.gov/33406440/
Recent studies demonstrated B cell metabolic dynamics are distinct to power their unique antibody production, upregulating fatty-acid (FA) beta oxidation over glycolysis during germinal center reactions. However, FAs are diverse and can be dysregulated during immune challenge, thus, the authors of this paper sought to investigate the importance of monounsaturated FAs (MUFAs) and endogenous FAs to B cell actions with the goal of establishing a targetable regulatory system for B cell responses. In vitro, activated B cells shuttled glucose to endogenous production of palmitoleic acid (PO) and oleic acid (OA), which are subsequently used in FA-beta oxidation. Lack of endogenous production confers halted proliferation and inhibits class-switch recombination in an mTORC1-dependent manner, however, these actions can be rescued with exogenous OA. In vivo, during immune challenge, OA is increased in serum and OA deficiency prevented productive B cell responses. These results demonstrate a relationship between MUFAs and humoral immune fitness, however, MUFA modulation impacts many processes and their roles in B cell responses is beyond this paper.
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Week of 11/01/2021
KK-https://www.science.org/doi/10.1126/scitranslmed.abj1008
Although red blood cells (RBC) have long been thought to have little function other than to transport oxygen, Lam et al here demonstrate that RBC express TLR9, an innate immune sensor, and propose a mechanism through which it can sense circulating DNA in sepsis as part of the inflammatory response. The authors used a combination of imaging, in vitro and in vivo mouse experiments, ex vivo human cell culture experiments, and clinical trial data to show that RBCs bind CpG-containing DNA, which in turn elicits a conformational change and spurs splenic erythrophagocytosis, contributing to severe anemia seen in septic patients. The concept that the authors propose is relatively novel, and they demonstrate the overall point well through use of multiple models--of the various pathogens used to demonstrate their point, Plasmodium falciparum seems an excellent choice. In some experiments their sample and effect sizes were relatively small, and the study lacks any real mechanistic insight into the observed phenomenon. Future studies will certainly attempt to elucidate the mechanism, and the authors' use of TLR9 KO RBCs in several experiments points to further translational work that can be done to attempt to modulate this phenomenon in an attempt to prevent anemia secondary to sepsis.
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Week of 11/08/2021
LQ: https://www.science.org/doi/10.1126/science.aba6500
This study mainly used single cell sequencing to dig out how cell states and gene program of fetal skin contribute to the pathological development of dermatitis and psoriasis through comparing the difference of macrophage, keratinocyte stromal cell, and their interaction with endothelial cells.
Compared with previous research that centering on adult stage, this study focuses on the dynamic cellular state evolving during fetal development, adulthood and disease.
The disadvantage of this paper is the fetal, adult normal and diseased skin are from different individuals, they may already have differences because of human heterogeneity.
For the future, they can use fetal skin stem cells to differentiate to be adult skin cell and adult diseased skin cells, which would be more objective if they are from the same individual.
They can also build a prediction model based on the dynamic gene change to evaluate if a person will get the disease.
AJM: https://www.science.org/doi/10.1126/science.abf9277
Despite being an immune privileged area, the central nervous system still requires immune surveillance, provided by distinct compartments of innate and adaptive immune cells. Within the dura mater, ~30% of CD45+ cells are B cells, with IgA+ plasma cells deriving from the gut, however, the populations and its origins were not thoroughly investigated until this paper. The authors first compared non-plasma dura B cells to bone marrow (BM) and blood B cells through flow cytometry, in situ fluorescent imaging, scRNA-seq, BCR-seq, and CyTOF, revealing dura B encompass both immature and mature naïve B, more similar to BM. They show these dura B cells likely originate primarily from flat cranial bones, develop in the unique niche provided in the dura, and drain to the lymphatics system. They next shift to age-related changes and claim there is an increase in antigen experienced, peripherally-derived B cells in the dura mater, however, their support for this does not fully negate the possibility that these are dura-derived and instead of leaking of peripheral B into the brain, it is the natural progression of dura B out. In fact, analysis of dura plasma cells suggests age-related increases in IgM+ B cells are dura-derived, which can occur extra-germinally. This investigation has provided new meaning to how the CNS maintains separation while still protecting and potentiates further understanding of the dura immune population’s impact on neurological and autoimmune disease.
KK: https://www.science.org/doi/10.1126/science.aaz4544
Actin remodeling is known to play a critical role in homeostasis and activation of the immune system, and while some regulators of this process have been implicated in both immune deficiency and autoimmune disease, the precise mechanism behind the clinical findings remains unknown. In this paper, Liu et al use mice with a T cell-specific knockout of WAVE2, one of the key regulators of actin dynamics, to demonstrate that the WAVE2 regulatory complex inhibits T cell activation via inhibition of mTOR signaling. WAVE2 cKO mice developed an autoimmune inflammatory disease phenotype secondary to T cell hyperactivation and proliferation, and this phenotype was reversed with in vitro and in vivo use of mTOR inhibitors. mTOR inhibitors are broadly immunosuppressive, so the use of other immunosuppressive agents (or more specific mTOR modulation) to demonstrate that the inhibition of the autoimmune phenotype was mTOR-specific would have been beneficial. Additionally, although the authors convincingly demonstrated the WAVE2-mTOR axis, further elaboration on WAVE2-mTOR kinetics during normal T cell function would have strengthened their conclusions and could serve as a launching point for further investigation.
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Week of 12/15/2021
AJM: https://genome.cshlp.org/content/early/2021/05/25/gr.271874.120
To address the issue of batch effects in scRNA-Seq analysis, the authors present CarDEC, a tool which utilizes an autoencoder to first learn the optimal dimension reduction in gene expression then reconstruct gene expression with loss of batch-related noise. Importantly, their method handles dimension reduction for highly variable genes (HVGs) first and applies this trained model to lowly variable genes (LVGs) reconstruction to improve batch effect correction in LSGs - a problem present in other methods which model batch effect using batch indicators. They compare CarDEC to commonly applied methods such as MNN, scVI, and Combat+DCA in datasets exhibiting strong batch effect due to different single-cell library generation protocols, different human subjects, and experimental timepoints. Each method’s batch effect correction is measured by variability between the mean gene expressions within a cell type based on the assumption that cell types should exhibit limited biological heterogeneity across batches. This assumption is problematic given the lack of experimental control in datasets used; thus, CarDEC’s improved variability metric could actually represent loss of important signals. Ideally, a dataset which tests the same exact sample across single-cell library generation protocols would provide better insight into CarDEC’s usefulness towards appropriate batch effect corrections.
KK: https://www.nature.com/articles/s41590-021-01023-y
In this paper, Yao et al uncover a role in metabolic inflammation for IRX3, which mediates the effects of FTO, the gene most associated with polygenic obesity. Previous studies had identified conflicting roles for IRX3 in various tissues, but here the authors used macrophage-specific IRX3 knockout mice in an obesity model to show that macrophage IRX3 deficiency increases thermogenesis, improves glucose homeostasis, increases insulin sensitivity, and decreases body weight and body fat composition. They also found that IRX3 inhibits adipocyte adrenergic signaling and acts as a transcription factor (stabilized by LPS) that promotes inflammatory cytokine production, showing a mechanistic role for IRX3 in obesity and related inflammation. While this paper provides valuable mechanistic insight and answers a major question regarding IRX3's role, all of the experiments were performed in vitro using cell lines or in mice. Additionally, this study fails to identify the initial insult that promotes inflammation and IRX3 activity.