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Colorectal cancer (CRC) is a major cancer, and its precise diagnosis is especially important for the development of effective therapeutics. In a series of metabolome analyses, the levels of very long chain fatty acids (VLCFA) were shown to be elevated in CRC tissues, although the endogenous form of VLCFA has not been fully elucidated. In this study we analyzed the amount of nonesterified fatty acids, acyl-CoA species, phospholipids and neutral lipids such as cholesterylesters using liquid-chromatography–mass spectrometry. Here we showed that VLCFA were accumulated in triacylglycerol (TAG) and nonesterified forms in CRC tissues. The levels of TAG species harboring a VLCFA moiety (VLCFA-TAG) were significantly correlated with that of nonesterified VLCFA. We also showed that the expression level of elongation of very long-chain fatty acids protein 1 ( ELOVL1 ) is increased in CRC tissues, and the inhibition of ELOVL1 decreased the levels of VLCFA-TAG and nonesterified VLCFA in CRC cell lines. Our results suggest that the upregulation of ELOVL1 contributes to the accumulation of VLCFA-TAG and nonesterified VLCFA in CRC tissues.

Receptor activator of NFkB ligand (RANKL) is a TNF-family cytokine required for osteoclast formation, as well as immune cell and mammary gland development. It is produced as a membrane-bound protein that can be shed to form a soluble protein. We created mice harboring a sheddase-resistant form of RANKL, in which soluble RANKL is undetectable in the circulation. Lack of soluble RANKL does not affect bone mass or structure in growing mice but reduces osteoclast number and increases cancellous bone mass in adult mice. Nonetheless, the bone loss caused by estrogen deficiency is unaffected by the lack of soluble RANKL. Lymphocyte number, lymph node development, and mammary gland development are also unaffected by the absence of soluble RANKL. These results demonstrate that the membrane-bound form of RANKL is sufficient for most functions of this protein but that the soluble form does contribute to physiological bone remodeling in adult mice. RANKL is a cytokine produced as a membrane-bound and a secreted protein. Here, using mice lacking soluble RANKL, the authors show that the secreted protein is important for osteoclast function, but not for mammary gland and lymphocyte development.

Enhancers, critical determinants of cellular identity, are commonly recognized by correlative chromatin marks and gain-of-function potential, although only loss-of-function studies can demonstrate their requirement in the native genomic context. Previously, we identified an erythroid enhancer of human BCL11A , subject to common genetic variation associated with the fetal haemoglobin level, the mouse orthologue of which is necessary for erythroid BCL11A expression. Here we develop pooled clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 guide RNA libraries to perform in situ saturating mutagenesis of the human and mouse enhancers. This approach reveals critical minimal features and discrete vulnerabilities of these enhancers. Despite conserved function of the composite enhancers, their architecture diverges. The crucial human sequences appear to be primate-specific. Through editing of primary human progenitors and mouse transgenesis, we validate the BCL11A erythroid enhancer as a target for fetal haemoglobin reinduction. The detailed enhancer map will inform therapeutic genome editing, and the screening approach described here is generally applicable to functional interrogation of non-coding genomic elements. A CRISPR-Cas9 approach is used to perform saturating mutagenesis of the human and mouse BCL11A enhancers, producing a map that reveals critical regions and specific vulnerabilities; BCL11A enhancer disruption is validated by CRISPR-Cas9 as a therapeutic strategy for inducing fetal haemoglobin by applying it in both mice and primary human erythroblast cells. BCL11A enhancer disruption analysed BCL11A is a transcriptional repressor that inhibits expression of fetal globin genes in adults, and is a potential therapeutic target for the treatment of β-globinopathies such as β-thalassemia and sickle cell disease. The enhancer of BCL11A is subject to common genetic variation associated with fetal hemoglobin level. Here, Daniel Bauer and colleagues use a CRISPR–Cas9 approach to perform saturation mutagenesis of the human and mouse BCL11A enhancers, producing a map that reveals critical regions and specific vulnerabilities. They validate BCL11A enhancer disruption by CRISPR–Cas9 as a therapeutic strategy for inducing fetal haemoglobin by applying it in both mice and primary human erythroblast cells.

Here, we describe that lysine-specific demethylase 1 (Lsd1/KDM1a), which demethylates histone H3 on Lys4 or Lys9 (H3K4/K9), is an indispensible epigenetic governor of hematopoietic differentiation. Integrative genomic analysis, combining global occupancy of Lsd1, genome-wide analysis of its substrates H3K4 monomethylation and dimethylation, and gene expression profiling, reveals that Lsd1 represses hematopoietic stem and progenitor cell (HSPC) gene expression programs during hematopoietic differentiation. We found that Lsd1 acts at transcription start sites, as well as enhancer regions. Loss of Lsd1 was associated with increased H3K4me1 and H3K4me2 methylation on HSPC genes and gene derepression. Failure to fully silence HSPC genes compromised differentiation of hematopoietic stem cells as well as mature blood cell lineages. Collectively, our data indicate that Lsd1-mediated concurrent repression of enhancer and promoter activity of stem and progenitor cell genes is a pivotal epigenetic mechanism required for proper hematopoietic maturation. Our blood contains many different types of cells. Red blood cells carry oxygen around the body, whereas white blood cells are a key part of our immune system. All these different types of blood cells are derived from special cells in our bone marrow called hematopoietic stem cells. The type of blood cell that the stem cell becomes depends on the genes that are expressed as proteins in that stem cell. Gene expression can be controlled in a number of ways, including epigenetic process that influence the expression of genes without altering the underlying sequence of bases in the DNA. For example, DNA is wrapped around histone proteins and the addition of a methyl group to these proteins, a process known as histone methylation, can increase the expression of a gene, whereas the removal of a methyl group (demethylation) can repress gene expression. Lysine-specific demethylase 1 (Lsd1) is an enzyme that is known to mediate the demethylation of lysine amino acids on histone proteins. The role of Lsd1 in embryonic stem cells has been widely studied, and deletion of the gene that codes for Lsd1 is known to result in the death of mice embryos. However, very little is known about its roles in the later stages of mammalian development. Here, Kerenyi et al. use new genetic tools to knock out the gene for Lsd1 at different stages of development in order to examine its impact on the formation of new blood cells. They find that Lsd1 is required for the successful differentiation of hematopoietic stem cells into different types of blood cells, and that knocking out Lsd1 results in a severe loss of white and red blood cells. Moreover, they show that the lack of Lsd1 causes problems during both the early and later stages of development. Kerenyi et al. go on to demonstrate that Lsd1 regulates the activity of promoters and enhancers of various genes associated with hematopoietic stem cells. They also show that knocking out the Lsd1 gene results in impaired silencing of these genes, and that the incomplete expression of these genes is not compatible with the maturation of blood cells. Lsd1 has recently been proposed as the potential target for the treatment of leukemia and other blood disorders. However, the fact that a loss of Lsd1 function has adverse effects during both the early and later stages of blood cell development suggests that research into drugs that target Lsd1 should not begin until a suitable time window for the administration of such drugs can be identified.

Developmental silencing of fetal globins serves as both a paradigm of spatiotemporal gene regulation and an opportunity for therapeutic intervention of β-hemoglobinopathy. The nucleosome remodeling and deacetylase (NuRD) chromatin complex participates in γ-globin repression. We used pooled CRISPR screening to disrupt NuRD protein coding sequences comprehensively in human adult erythroid precursors. Essential for fetal hemoglobin (HbF) control is a non-redundant subcomplex of NuRD protein family paralogs, whose composition we corroborated by affinity chromatography and proximity labeling mass spectrometry proteomics. Mapping top functional guide RNAs identified key protein interfaces where in-frame alleles resulted in loss-of-function due to destabilization or altered function of subunits. We ascertained mutations of CHD4 that dissociate its requirement for cell fitness from HbF repression in both primary human erythroid precursors and transgenic mice. Finally we demonstrated that sequestering CHD4 from NuRD phenocopied these mutations. These results indicate a generalizable approach to discover protein complex features amenable to rational biochemical targeting. Comprehensive CRISPR mutagenesis targeting all members of the NuRD complex identifies a specific subcomplex required for fetal globin silencing and informs a rational targeting strategy for elevating globin levels while avoiding cytotoxicity.

PDGFRA-expressing mesenchyme supports intestinal stem cells. Stomach epithelia have related niche dependencies, but their enabling mesenchymal cell populations are unknown, in part because previous studies pooled the gastric antrum and corpus. Our high-resolution imaging, transcriptional profiling, and organoid assays identify regional subpopulations and supportive capacities of purified mouse corpus and antral PDGFRA + cells. Sub-epithelial PDGFRA Hi myofibroblasts are principal sources of BMP ligands and two molecularly distinct pools distribute asymmetrically along antral glands but together fail to support epithelial growth in vitro. In contrast, PDGFRA Lo CD55 + cells strategically positioned beneath gastric glands promote epithelial expansion in the absence of other cells or factors. This population encompasses a small fraction expressing the BMP antagonist Grem1 . Although Grem1 + cell ablation in vivo impairs intestinal stem cells, gastric stem cells are spared, implying that CD55 + cell activity in epithelial self-renewal derives from other subpopulations. Our findings shed light on spatial, molecular, and functional organization of gastric mesenchyme and the spectrum of signaling sources for epithelial support. Digestive epithelia self-renew or differentiate in response to mesenchymal cues. Manieri et al. characterize gastric corpus and antral mesenchyme separately and identify PDGFRA Lo CD55 + cells as those selectively supporting epithelial growth in vitro.

Ceramide, the central molecule in sphingolipid synthesis, is a bioactive lipid that serves as a regulatory molecule in the anti-inflammatory responses, apoptosis, programmed necrosis, autophagy, and cell motility of cancer cells. In particular, the authors have reported differences in sphingolipid content in colorectal cancer tissues. The associations among genetic mutations, clinicopathological factors, and sphingolipid metabolism in colorectal cancer (CRC) have not been investigated. The objective of this study is to investigate the association between genes associated with sphingolipid metabolism, genetic variations in colorectal cancer (CRC), and clinicopathological factors in CRC patients. We enrolled 82 consecutive patients with stage I–IV CRC who underwent tumor resection at a single institution in 2019–2021. We measured the expression levels of genes related to sphingolipid metabolism and examined the relationships between CRC gene mutations and the clinicopathological data of each individual patient. The relationship between CRC gene mutations and expression levels of ceramide synthase ( CERS ), N -acylsphingosine amidohydrolase ( ASAH) , and alkaline ceramidase ( ACER ) genes involved in sphingolipid metabolism was examined CRES4 expression was significantly lower in the CRC KRAS gene mutation group (p = 0.004); vascular invasion was more common in colorectal cancer patients with high CERS4 expression (p = 0.0057). By examining the correlation between sphingolipid gene expression and clinical factors, we were able to identify cancer types in which sphingolipid metabolism is particularly relevant. CERS4 expression was significantly reduced in KRAS mutant CRC. Moreover, CRC with decreased CERS4 showed significantly more frequent venous invasion.

Noonan syndrome is characterized by short stature, facial dysmorphia and a wide spectrum of congenital heart defects 1 , 2 . Mutations of PTPN11 , KRAS and SOS1 in the RAS-MAPK pathway cause ∼60% of cases of Noonan syndrome 3 , 4 , 5 , 6 , 7 , 8 , 9 . However, the gene(s) responsible for the remainder are unknown. We have identified five different mutations in RAF1 in ten individuals with Noonan syndrome; those with any of four mutations causing changes in the CR2 domain of RAF1 had hypertrophic cardiomyopathy (HCM), whereas affected individuals with mutations leading to changes in the CR3 domain did not. Cells transfected with constructs containing Noonan syndrome–associated RAF1 mutations showed increased in vitro kinase and ERK activation, and zebrafish embryos with morpholino knockdown of raf1 demonstrated the need for raf1 for the development of normal myocardial structure and function. Thus, our findings implicate RAF1 gain-of-function mutations as a causative agent of a human developmental disorder, representing a new genetic mechanism for the activation of the MAPK pathway.

In aging mice, osteoclast number increases in cortical bone but declines in trabecular bone, suggesting that different mechanisms underlie age-associated bone loss in these 2 compartments. Osteocytes produce the osteoclastogenic cytokine RANKL, encoded by Tnfsf11. Tnfsf11 mRNA increases in cortical bone of aged mice, suggesting a mechanism underlying the bone loss. To address this possibility, we aged mice lacking RANKL in osteocytes. Whereas control mice lost cortical bone between 8 and 24 months of age, mice lacking RANKL in osteocytes gained cortical bone during this period. Mice of both genotypes lost trabecular bone with age. Osteoclasts increased with age in cortical bone of control mice but not in RANKL conditional knockout mice. Induction of cellular senescence increased RANKL production in murine and human cell culture models, suggesting an explanation for elevated RANKL levels with age. Overexpression of the senescence-associated transcription factor Gata4 stimulated Tnfsf11 expression in cultured murine osteoblastic cells. Finally, elimination of senescent cells from aged mice using senolytic compounds reduced Tnfsf11 mRNA in cortical bone. Our results demonstrate the requirement of osteocyte-derived RANKL for age-associated cortical bone loss and suggest that increased Tnfsf11 expression with age results from accumulation of senescent cells in cortical bone.

The strain associated with orthogonal cutting with and against the grain of hinoki ( Chamaecyparis obtusa ) was measured. Digital image correlation method was used to measure strain distributed in the area within 0.5 mm of the cutting edge. The relationship between strain and the use of different grain angles (− 15° ≤  φ  ≤ + 15°) was investigated. The compressive strain parallel to the cutting direction was detected in the area above the path of the cutting edge regardless of φ . The tensile strain normal to the cutting direction which generated cleavage ahead of the tool decreased with increasing φ , when the cutting angle was 30°. While cutting with the grain, shear strain above the path of the cutting edge was positive when the cutting angle was 30°, although it changed to negative with larger cutting angles. The maximum principal strain given by a cutting angle of 50° was less affected by φ than those given by the other cutting angles. The maximum principal strain ahead of the tool was minimized when the cutting angle was 50° and + 5° ≤  φ  ≤ + 10°.