Depleting myeloid-biased haematopoietic stem cells rejuvenates aged immunity.

Ageing of the immune system is characterized by decreased lymphopoiesis and adaptive immunity, and increased inflammation and myeloid pathologies1,2. Age-related changes in populations of self-renewing haematopoietic stem cells (HSCs) are thought to underlie these phenomena3. During youth, HSCs with balanced output of lymphoid and myeloid cells (bal-HSCs) predominate over HSCs with myeloid-biased output (my-HSCs), thereby promoting the lymphopoiesis required for initiating adaptive immune responses, while limiting the production of myeloid cells, which can be pro-inflammatory4. Ageing is associated with increased proportions of my-HSCs, resulting in decreased lymphopoiesis and increased myelopoiesis3,5,6. Transfer of bal-HSCs results in abundant lymphoid and myeloid cells, a stable phenotype that is retained after secondary transfer; my-HSCs also retain their patterns of production after secondary transfer5. The origin and potential interconversion of these two subsets is still unclear. If they are separate subsets postnatally, it might be possible to reverse the ageing phenotype by eliminating my-HSCs in aged mice. Here we demonstrate that antibody-mediated depletion of my-HSCs in aged mice restores characteristic features of a more youthful immune system, including increasing common lymphocyte progenitors, naive T cells and B cells, while decreasing age-related markers of immune decline. Depletion of my-HSCs in aged mice improves primary and secondary adaptive immune responses to viral infection. These findings may have relevance to the understanding and intervention of diseases exacerbated or caused by dominance of the haematopoietic system by my-HSCs.

Flow rate resonance of actively deforming particles.

Lymphoid organs are unusual multicellular tissues: they are densely packed, but the lymphocytes trafficking through them are actively moving. We hypothesize that the intriguing ability of lymphocytes to avoid jamming and clogging is in part attributable to the dynamic shape changes that cells undergo when they move. In this work, we test this hypothesis by investigating an idealized system, namely, the flow of self-propelled, oscillating particles passing through a narrow constriction in two dimensions (2D), using numerical simulations. We found that deformation allows particles with these properties to flow through a narrow constriction in conditions when non-deformable particles would not be able to do so. Such a flowing state requires the amplitude and frequency of oscillations to exceed threshold values. Moreover, a resonance leading to the maximum flow rate was found when the oscillation frequency matched the natural frequency of the particle related to its elastic stiffness. To our knowledge, this phenomenon has not been described previously. Our findings could have important implications for understanding and controlling flow in a variety of systems in addition to lymphoid organs, such as granular flows subjected to vibration.

Multiple waves of fetal-derived immune cells constitute adult immune system.

It has been over three decades since Drs. Herzenberg and Herzenberg proposed the layered immune system hypothesis, suggesting that different types of stem cells with distinct hematopoietic potential produce specific immune cells. This layering of immune system development is now supported by recent studies showing the presence of fetal-derived immune cells that function in adults. It has been shown that various immune cells arise at different embryonic ages via multiple waves of hematopoiesis from special endothelial cells (ECs), referred to as hemogenic ECs. However, it remains unknown whether these fetal-derived immune cells are produced by hematopoietic stem cells (HSCs) during the fetal to neonatal period. To address this question, many advanced tools have been used, including lineage-tracing mouse models, cellular barcoding techniques, clonal assays, and transplantation assays at the single-cell level. In this review, we will review the history of the search for the origins of HSCs, B-1a progenitors, and mast cells in the mouse embryo. HSCs can produce both B-1a and mast cells within a very limited time window, and this ability declines after embryonic day (E) 14.5. Furthermore, the latest data have revealed that HSC-independent adaptive immune cells exist in adult mice, which implies more complicated developmental pathways of immune cells. We propose revised road maps of immune cell development.

C-reactive protein, but not neutrophil-lymphocyte ratio, is inversely associated with muscle strength only in older men: NHANES 1999-2002.

To evaluate the association of inflammation (C-reactive protein (CRP) and neutrophil-lymphocyte ratio (NLR) levels) with muscle strength in older adults. We also aimed to evaluate whether these associations are sex-specific. A cross-sectional study was performed with data from the National Health and Nutrition Examination Survey (NHANES) 1999-2000 and 2001-2002. A total of 2387 individuals over 50 years of both sexes were evaluated, according to the eligibility criteria for the strength test. Muscle strength was measured by Kinetic Communicator isokinetic dynamometer; while the NLR was obtained by the ratio of the total neutrophil for lymphocyte count and CRP was quantified by latex nephelometry. Linear regression analyses, crude and adjusted for confounders, were used to estimate the coefficients and 95 % confidence intervals for peak strength (muscle strength) by tertiles of NLR and CRP. There was no association between NLR and peak strength for both sexes. CRP levels were inversely associated with peak force in men [2nd tertile ß = -3.33 (-15.92; 9.25); 3rd tertile ß = -24.69 (-41.18; -8.20), p for trend = 0.005], but not in women [2nd tertile ß = -3.22 (-15.00; 8.56); 3rd tertile ß = -9.23 (-28.40; -9.94), p for trend = 0.332]. In conclusion, NLR levels were not associated with muscle strength in both sexes. CRP levels were inversely associated with muscle strength in older men, but not in women, suggesting that the association between inflammation and muscle strength in older adults can be sex-specific.

Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation.

Dietary fibres can exert beneficial anti-inflammatory effects through microbially fermented short-chain fatty acid metabolites^1,2, although the immunoregulatory roles of most fibre diets and their microbiota-derived metabolites remain poorly defined. Here, using microbial sequencing and untargeted metabolomics, we show that a diet of inulin fibre alters the composition of the mouse microbiota and the levels of microbiota-derived metabolites, notably bile acids. This metabolomic shift is associated with type 2 inflammation in the intestine and lungs, characterized by IL-33 production, activation of group 2 innate lymphoid cells and eosinophilia. Delivery of cholic acid mimics inulin-induced type 2 inflammation, whereas deletion of the bile acid receptor farnesoid X receptor diminishes the effects of inulin. The effects of inulin are microbiota dependent and were reproduced in mice colonized with human-derived microbiota. Furthermore, genetic deletion of a bile-acid-metabolizing enzyme in one bacterial species abolishes the ability of inulin to trigger type 2 inflammation. Finally, we demonstrate that inulin enhances allergen- and helminth-induced type 2 inflammation. Taken together, these data reveal that dietary inulin fibre triggers microbiota-derived cholic acid and type 2 inflammation at barrier surfaces with implications for understanding the pathophysiology of allergic inflammation, tissue protection and host defence.

Diverse mutational landscapes in human lymphocytes.

The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

ZBTB46 defines and regulates ILC3s that protect the intestine.

RORγt is a lineage-specifying transcription factor that is expressed by immune cells that are enriched in the gastrointestinal tract and promote immunity, inflammation and tissue homeostasis1-15. However, fundamental questions remain with regard to the cellular heterogeneity among these cell types, the mechanisms that control protective versus inflammatory properties and their functional redundancy. Here we define all RORγt+ immune cells in the intestine at single-cell resolution and identify a subset of group 3 innate lymphoid cells (ILC3s) that expresses ZBTB46, a transcription factor specifying conventional dendritic cells16-20. ZBTB46 is robustly expressed by CCR6+ lymphoid-tissue-inducer-like ILC3s that are developmentally and phenotypically distinct from conventional dendritic cells, and its expression is imprinted by RORγt, fine-tuned by microbiota-derived signals and increased by pro-inflammatory cytokines. ZBTB46 restrains the inflammatory properties of ILC3s, including the OX40L-dependent expansion of T helper 17 cells and the exacerbated intestinal inflammation that occurs after enteric infection. Finally, ZBTB46+ ILC3s are a major source of IL-22, and selective depletion of this population renders mice susceptible to enteric infection and associated intestinal inflammation. These results show that ZBTB46 is a transcription factor that is shared between conventional dendritic cells and ILC3s, and identify a cell-intrinsic function for ZBTB46 in restraining the pro-inflammatory properties of ILC3s and a non-redundant role for ZBTB46+ ILC3s in orchestrating intestinal health.

Ablation of cDC2 development by triple mutations within the Zeb2 enhancer.

The divergence of the common dendritic cell progenitor1-3 (CDP) into the conventional type 1 and type 2 dendritic cell (cDC1 and cDC2, respectively) lineages4,5 is poorly understood. Some transcription factors act in the commitment of already specified progenitors-such as BATF3, which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer4,6-but the mechanisms controlling the initial divergence of CDPs remain unknown. Here we report the transcriptional basis of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis7 suggested that Nfil3 acts upstream of Id2, Batf3 and Zeb2 in cDC1 development but did not reveal its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and chromatin immunoprecipitation followed by sequencing identified endogenous NFIL3 binding in the -165 kb Zeb2 enhancer8 at three sites that also bind the CCAAT-enhancer-binding proteins C/EBPα and C/EBPß. In vivo mutational analysis using CRISPR-Cas9 targeting showed that these NFIL3-C/EBP sites are functionally redundant, with C/EBPs supporting and NFIL3 repressing Zeb2 expression at these sites. A triple mutation of all three NFIL3-C/EBP sites ablated Zeb2 expression in myeloid, but not lymphoid progenitors, causing the complete loss of pre-cDC2 specification and mature cDC2 development in vivo. These mice did not generate T helper 2 (TH2) cell responses against Heligmosomoides polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths9-11. Thus, CDP divergence into cDC1 or cDC2 is controlled by competition between NFIL3 and C/EBPs at the -165 kb Zeb2 enhancer.

High neutrophil-to-lymphocyte ratio is a significant predictor of depressive symptoms in maintenance hemodialysis patients: a cross-sectional study.

BACKGROUND: Depression is one of the most important psychiatric disorders in chronic kidney disease patients who undergo maintenance hemodialysis (MHD). Previous studies have shown that low-grade inflammation is involved in the progression of depressive symptoms. The neutrophil-to-lymphocyte ratio (NLR) is an inflammatory marker that is inexpensive and easy to measure. However, the association between NLR and depression symptoms in MHD patients has not been examined. METHODS: In this single-center, cross-sectional study, we included 160 patients undergoing MHD. The Patient Health Questionnaire-9 (PHQ-9) was used to assess depressive symptoms. NLR was calculated as the ratio of neutrophils to lymphocytes. Multinomial logistic regression and multivariate linear regression analyses were used to examine the association between NLR and depressive symptoms in MHD patients. RESULTS: Depressive symptoms were detected in 36.7% of the 160 MHD patients. Multinomial logistic regression showed that NLR was a significant predictor of mild (odds ratio [OR]: 1.383, 95% confidence interval [CI]: 1.015-1.884, p = 0.04) and moderate/moderately severe depressive symptoms (OR: 1.441, 95% CI: 1.017-2.042, p = 0.04) in MHD patients, adjusted for age, sex, Kt/V, dialysis duration, history of kidney transplantation, history of hypertension, and Charlson comorbidity index score. In addition, multivariate linear regression analysis showed that NLR was an independent influencing factor for PHQ-9 score in MHD patients, after adjusting for confounding factors. CONCLUSIONS: These findings suggest that NLR can be used as a biomarker for predicting depressive symptoms in MHD patients.

Brain motor and fear circuits regulate leukocytes during acute stress.

The nervous and immune systems are intricately linked1. Although psychological stress is known to modulate immune function, mechanistic pathways linking stress networks in the brain to peripheral leukocytes remain poorly understood2. Here we show that distinct brain regions shape leukocyte distribution and function throughout the body during acute stress in mice. Using optogenetics and chemogenetics, we demonstrate that motor circuits induce rapid neutrophil mobilization from the bone marrow to peripheral tissues through skeletal-muscle-derived neutrophil-attracting chemokines. Conversely, the paraventricular hypothalamus controls monocyte and lymphocyte egress from secondary lymphoid organs and blood to the bone marrow through direct, cell-intrinsic glucocorticoid signalling. These stress-induced, counter-directional, population-wide leukocyte shifts are associated with altered disease susceptibility. On the one hand, acute stress changes innate immunity by reprogramming neutrophils and directing their recruitment to sites of injury. On the other hand, corticotropin-releasing hormone neuron-mediated leukocyte shifts protect against the acquisition of autoimmunity, but impair immunity to SARS-CoV-2 and influenza infection. Collectively, these data show that distinct brain regions differentially and rapidly tailor the leukocyte landscape during psychological stress, therefore calibrating the ability of the immune system to respond to physical threats.

KIT as a master regulator of the mast cell lineage.

The discovery in 1987/1988 and 1990 of the cell surface receptor KIT and its ligand, stem cell factor (SCF), was a critical achievement in efforts to understand the development and function of multiple distinct cell lineages. These include hematopoietic progenitors, melanocytes, germ cells, and mast cells, which all are significantly affected by loss-of-function mutations of KIT or SCF. Such mutations also influence the development and/or function of additional cells, including those in parts of the central nervous system and the interstitial cells of Cajal (which control gut motility). Many other cells can express KIT constitutively or during immune responses, including dendritic cells, eosinophils, type 2 innate lymphoid cells, and taste cells. Yet the biological importance of KIT in many of these cell types largely remains to be determined. We here review the history of work investigating mice with mutations affecting the white spotting locus (which encodes KIT) or the steel locus (which encodes SCF), focusing especially on the influence of such mutations on mast cells. We also briefly review efforts to target the KIT/SCF pathway with anti-SCF or anti-Kit antibodies in mouse models of allergic disorders, parasite immunity, or fibrosis in which mast cells are thought to play significant roles.

Neutrophil-to-lymphocyte ratio and lactate dehydrogenase for early diagnosis of AIDS patients with Talaromyces marneffei infection.

BACKGROUND: This study aimed to explore the value of neutrophil-to-lymphocyte ratio (NLR) in combination with routine blood tests, lactate dehydrogenase (LDH), and T-lymphocyte subsets for the early diagnosis of acquired immunodeficiency syndrome (AIDS) combined with Talaromyces marneffei (TM) infection. METHODS: A total of 166 confirmed AIDS patients were enrolled in this study. The observation group included 80 AIDS patients with TM infection, and the control group consisted of 86 AIDS patients with other complications. Regression analysis was performed to evaluate the predictive value of each index and the combination of these indexes for AIDS combined with TM infection using receiver operating characteristic (ROC) curve analysis. RESULTS: NLR and LDH were significantly higher in patients in the observation group compared with those in the control group, and the differences were statistically significant (P<0.05). There was no statistical difference in platelets, infantile granulocytes (IGM), and nucleated red blood cells (NRBC) between the 2 groups (P>0.05). The area under the operating characteristic curve (AUC) of the observed indicators were: NLR, 0.628; hemoglobin (HGB), 0.704; LDH, 0.607; lymphocyte (LYM) count, 0.744; CD4+ T lymphocyte count, 0.789; and CD8+ T lymphocyte count, 0.701. The combined AUC of multiple indicators was 0.815, with a sensitivity and specificity of 76.2% and 76.1%, respectively. CONCLUSIONS: NLR, HGB, LYM, LDH, and T lymphocyte subsets were diagnostic for early AIDS combined with TM infection , and CD4+ T lymphocytes had the best diagnostic efficacy alone.

Neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) are more prominent in retinal artery occlusion (RAO) compared to retinal vein occlusion (RVO).

AIM: To evaluate the association between the value of neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), monocyte to high-density lipoprotein ratio (MHR) and the development of retinal artery occlusion (RAO) and retinal vein occlusion (RVO). METHODS: This retrospective study assessed 41 RAO, 50 RVO and 50 control (age and gender matched senile cataract) participants. The NLR, PLR and MHR parameters of patients' peripheral blood were analyzed. A receiver operating characteristics (ROC) curve analysis and the best cutoff value were used to specify the predictive value of NLR, PLR and MHR in RAO and RVO. RESULTS: The NLR, PLR and MHR were significantly higher in RAO group compared to the control group (p<0.001, p<0.001 and p = 0.008; respectively). The NLR, PLR and MHR were also significantly higher in the RVO group compared to the control group (p<0.001, p = 0.001 and p = 0.012, respectively). The NLR and PLR were significantly higher in the RAO group compared to the RVO group (p<0.001 and p = 0.022, respectively). The optimal cut-off value of NLR to predict RAO was >2.99, with 90.2% sensitivity and 100% specificity. The PLR to predict RAO was > 145.52, with 75.6% sensitivity and 80.0% specificity. CONCLUSION: Higher NLR, PLR and MHR are related to the occurrence of RAO and RVO. NLR and PLR are more prominent in RAO compared to RVO.

Ligand-independent activation of AhR by hydroquinone mediates benzene-induced hematopoietic toxicity.

Although it has been well recognized that benzene exposure can cause hematopoietic disorders such as aplastic anemia and leukemia, the underlying molecular mechanism remains to be fully understood. Emerging evidence indicated that aryl hydrocarbon receptor (AhR) plays important roles in hematopoietic and immune systems. This study investigated the activation of aryl hydrocarbon receptor (AhR) by hydroquinone (HQ) and its role in HQ-induced DNA damage and apoptosis in cultured human lymphocytes (JHP cells). We also investigated the effect of ROS on AhR activation and functions in JHP cells exposed to HQ with and without regulator including N-acetyl-l-cysteine (NAC), a potent antioxidant, and tert-butylhydroquinone (TBHQ), a Nrf2 activator. Results showed that HQ can cause oxidative stress, DNA damage and apoptosis. Pretreatment of an AhR antagonist (CH223191) can significantly increase the cell survival and mitigate HQ-induced toxicities such as DNA damage and apoptosis. We found that HQ can obviously increase expressions of total protein of AhR and prompt nuclear translocation compared to the control group. Interestingly, NAC can block HQ-induced AhR activation and DNA damage and apoptosis. Conclusively, our results indicated that HQ toxicity is mediated by AhR which is in turn regulated by ROS generated by HQ. The interaction between AhR and ROS drive and amplify the hematopoietic toxicity of HQ. This study provided new insights of mechanism and potential targets for the prevention and treatment to benzene-induced hematopoietic toxicity.

Altered Frequencies and Functions of Innate Lymphoid Cells in Melanoma Patients Are Modulated by Immune Checkpoints Inhibitors.

Monoclonal antibodies targeting immune checkpoints improved clinical outcome of patients with malignant melanoma. However, the mechanisms are not fully elucidated. Since immune check-point receptors are also expressed by helper innate lymphoid cells (ILCs), we investigated the capability of immune checkpoints inhibitors to modulate ILCs in metastatic melanoma patients as well as melanoma cells effects on ILC functions. Here, we demonstrated that, compared to healthy donors, patients showed a higher frequency of total peripheral ILCs, lower percentages of CD117+ ILC2s and CD117+ ILCs as well as higher frequencies of CD117- ILCs. Functionally, melanoma patients also displayed an impaired TNFα secretion by CD117- ILCs and CD117+ ILCs. Nivolumab therapy reduced the frequency of total peripheral ILCs but increased the percentage of CD117- ILC2s and enhanced the capability of ILC2s and CD117+ ILCs to secrete IL-13 and TNFα, respectively. Before Nivolumab therapy, high CCL2 serum levels were associated with longer Overall Survival and Progression Free Survival. After two months of treatment, CD117- ILC2s frequency as well as serum concentrations of IL-6, CXCL8 and VEGF negatively correlated with both the parameters. Moreover, melanoma cells boosted TNFα production in all ILC subsets and increased the number of IL-13 producing ILC2s in vitro. Our work shows for the first time that PD-1 blockade is able to affect ILCs proportions and functions in melanoma patients and that a specific subpopulation is associated with the therapy response.

Variable roles of interleukin-17F in different cancers.

BACKGROUND: Interleukin (IL)-17 family is a group of six cytokines that plays a central role in inflammatory processes and participates in cancer progression. Interleukin-17A has been shown to have mainly a protumorigenic role, but the other members of the IL-17 family, including IL-17F, have received less attention. METHODS: We applied systematic review guidelines to study the role of IL-17F, protein and mRNA expression, polymorphisms, and functions, in cancer. We carried out a systematic search in PubMed, Ovid Medline, Scopus, and Cochrane libraries, yielding 79 articles that met the inclusion criteria. RESULTS: The findings indicated that IL-17F has both anti- and protumorigenic roles, which depend on cancer type and the molecular form and location of IL-17F. As an example, the presence of IL-17F protein in tumor tissue and patient serum has a protective role in oral and pancreatic cancers, whereas it is protumorigenic in prostate and bladder cancers. These effects are proposed to be based on multiple mechanisms, such as inhibition of angiogenesis, vasculogenic mimicry and cancer cell proliferation, migration and invasion, and aggravating the inflammatory process. No solid evidence emerged for the correlation between IL-17F polymorphisms and cancer incidence or patients' prognosis. CONCLUSION: IL-17F is a multifaceted cytokine. There is a clear demand for more well-designed studies of IL-17F to elucidate its molecular mechanisms in different types of cancer. The studies presented in this article examined a variety of different designs, study populations and primary/secondary outcomes, which unfortunately reduces the value of direct interstudy comparisons.

A non-canonical role for pyruvate kinase M2 as a functional modulator of Ca2+ signalling through IP3 receptors.

Pyruvate kinase isoform M2 (PKM2) is a rate-limiting glycolytic enzyme that is widely expressed in embryonic tissues. The expression of PKM2 declines in some tissues following embryogenesis, while other pyruvate kinase isozymes are upregulated. However, PKM2 is highly expressed in cancer cells and is believed to play a role in supporting anabolic processes during tumour formation. In this study, PKM2 was identified as an inositol 1,4,5-trisphosphate receptor (IP3R)-interacting protein by mass spectrometry. The PKM2:IP3R interaction was further characterized by pull-down and co-immunoprecipitation assays, which showed that PKM2 interacted with all three IP3R isoforms. Moreover, fluorescence microscopy indicated that both IP3R and PKM2 localized at the endoplasmic reticulum. PKM2 binds to IP3R at a highly conserved 21-amino acid site (corresponding to amino acids 2078-2098 in mouse type 1 IP3R isoform). Synthetic peptides (denoted 'TAT-D5SD' and 'D5SD'), based on the amino acid sequence at this site, disrupted the PKM2:IP3R interaction and potentiated IP3R-mediated Ca2+ release both in intact cells (TAT-D5SD peptide) and in a unidirectional 45Ca2+ flux assay on permeabilized cells (D5SD peptide). The TAT-D5SD peptide did not affect the enzymatic activity of PKM2. Reducing PKM2 protein expression using siRNA increased IP3R-mediated Ca2+ signalling in intact cells without altering the ER Ca2+ content. These data identify PKM2 as an IP3R-interacting protein that inhibits intracellular Ca2+ signalling. The elevated expression of PKM2 in cancer cells is therefore not solely connected to its canonical role in glycolytic metabolism, rather PKM2 also has a novel non-canonical role in regulating intracellular signalling.

A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues.

Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells.

Different cell imaging methods did not significantly improve immune cell image classification performance.

Developments in high-throughput microscopy have made it possible to collect huge amounts of cell image data that are difficult to analyse manually. Machine learning (e.g., deep learning) is often employed to automate the extraction of information from these data, such as cell counting, cell type classification and image segmentation. However, the effects of different imaging methods on the accuracy of image processing have not been examined systematically. We studied the effects of different imaging methods on the performance of machine learning-based cell type classifiers. We observed lymphoid-primed multipotential progenitor (LMPP) and pro-B cells using three imaging methods: differential interference contrast (DIC), phase contrast (Ph) and bright-field (BF). We examined the classification performance of convolutional neural networks (CNNs) with each of them and their combinations. CNNs achieved an area under the receiver operating characteristic (ROC) curve (AUC) of ~0.9, which was significantly better than when the classifier used only cell size or cell contour shape as input. However, no significant differences were found between imaging methods and focal positions.