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Divergent expression of laminin and fibronectin in non-tumorigenic and transformed liver epithelial cells.

The immunocytochemical expression of laminin and fibronectin by non-transformed liver epithelial cells and by transformed cells derived from the same cell line, TRL1215, was examined in ethionine-transformed cells (ETC), untreated control cells at the same high passage level (HPC), and untreated, low passage cells (LPC). At confluence, a divergent expression of laminin and fibronectin was observed in the three sublines. In flat areas of polygonal cells, LPC showed abundant laminin staining and sparse fibronectin staining; HPC had intermediate expression of both; and ETC had sparse laminin staining and abundant fibronectin. Specifically, the laminin network was often found at intercellular junctions, outlining individual LPC, outlining groups of HPC, and having a focal expression in ETC. A fine reticulum of laminin was seen in large areas of LPC, in relatively small areas of HPC, and in multilayered areas of ETC. Fibronectin was visible as thick, matted fibrils, which were sparse in LPC, loosely arranged in HPC and dense in ETC. Prior studies had shown that the increased fibronectin expression in the transformed cells was associated with increased expression of actin stress fibres, increased cell spreading and increased numbers of focal contacts between cell and substrate. The divergent expression of laminin and fibronectin shown here indicates that these two matrix proteins need not be expressed in a parallel manner during transformation, and that increased fibronectin, but not laminin, is associated with maximal cell spreading and adhesion.

Animals

Genome-Wide Characterization and Salt-Responsive Expression Divergence of Chromosome Group 2 and Group 6 TaBADH Genes in Wheat.

Betaine aldehyde dehydrogenase (BADH) catalyzes the final step in glycine betaine biosynthesis, but the evolutionary divergence and differential salt responsiveness of BADH homeologs in bread wheat remain unclear. We identified six TaBADH genes and analyzed their phylogenetic relationships, conserved motifs, gene structures, promoter cis-acting elements and synteny. RNA-seq and qRT-PCR were used to compare expression in salt-tolerant Jimai 60 and salt-sensitive Chinese Spring under 200 mM NaCl, and BADH activity, glycine betaine, H2O2 and malondialdehyde (MDA) were measured during treatment. The genes separated into chromosome group 2 and group 6 clades with distinct structural and transcriptional patterns. TaBADH-2B encoded a shorter protein and lacked several conserved motifs. Group 6 genes showed stronger salt-responsive expression in Jimai 60, with TaBADH-6D displaying the strongest and most sustained induction. Jimai 60 also showed higher BADH activity and glycine betaine accumulation and lower H2O2 and MDA contents at later time points. Expression of TaBADH-6D improved E. coli growth under 200 mM NaCl. These findings identify homeolog-specific divergence within the BADH wheat family and support TaBADH-6D as a candidate for plant-level functional validation.

TaBADH-6D

Karyotypic analysis of two related cervical carcinoma cell lines that contain human papillomavirus type 18 DNA and express divergent differentiation.

The cell lines C-4I and C-4II were established in culture from a nonkeratinizing squamous carcinoma of the uterine cervix. Both lines contain human papillomavirus (HPV) type 18 DNA (Brandt et al., Cold Spring Harbor Laboratories, 5:179, 1987) and both are hypodiploid with similar, but not identical, karyotypes. Each line expresses multiple characteristics of ectocervical epithelial differentiation, but the characteristics differ between the lines. In the present study, G banding of the lines showed that cells of both lines have two normal chromosomes 1-5, 8-10, 13, 16, and 17, one normal chromosome 12 and 14, and no normal chromosomes 15 and 18. The lines share three abnormal chromosomes, der(8)t(8q;12q), der(18)t(18q;?), and i(5p). There are specific differences between the lines. C-4I has two normal chromosomes 6, while C-4II has one; C-4II has two chromosomes 11 and der(18)t(18q;?), while C-4I lacks both chromosomes 11 and has one der(18)t(18q;?). Each line has unique markers that include del(11)(p11), del(22)(q12), and del(21)(q21) in C-4I and i(15q), der(X)t(Xq;9p), der(6)t(6p;14q), and del(4)(q21) in C-4II. The results show that these phenotypically distinct lines are derived from the same clone and that the 8q arm (the site of HPV 18 integration) is present in three copies in both lines. They also define several chromosome rearrangements that are compatible with the expression of specific differentiation markers.

Carcinoma

Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.

Comparative genomic analyses provide insight into the mechanisms underlying gene-family evolution and crop adaptation. Here, we used the legume phenylalanine ammonia-lyase (PAL) gene family as a model and integrated pan-genomic, phylogenetic, molecular evolutionary, duplication-mode, and transcriptomic analyses, while developing GFtool for gene family identification. Across 45 genomes, we identified 302 PAL genes and classified them into five Groups. Groups 1-3 represented ancient lineages shared with outgroups, whereas Groups 4 and 5 were legume-specific. Molecular-clock analyses placed the divergence of Group 2 near the Paleocene-Eocene transition, while Groups 4 and 5 diversified from the middle Eocene to the early Oligocene. WGD/segmental duplication broadly contributed to PAL copy-number expansion, whereas tandem duplication was enriched in Group 5 of Papilionoideae. Group 2 genes showed drought-induced expression, whereas Group 5 genes were associated with early root nodule development. GFtool provides a scalable framework for gene-family studies.

Fabaceae

Divergent expression of HLA-DC/MB, -DR, and -SB region products on normal and pathological tissues as detected by monoclonal antibodies.

A group of eight monoclonal antibodies directed against different monomorphic determinants of HLA-class II molecules was used to investigate the distribution of HLA-DC/DS/MB, -DR and -SB-like antigens on normal and pathological lymphoid and nonlymphoid tissues of human adult and fetal donors. HLA-MB/DC/DS-like molecules, as defined by the antibody TU 22, showed the most limited distribution as they were detected on B-lymphocytes, monocyte/macrophage subpopulations and distinct interstitial cells of various organs. HLA-DR and -SB-like antigens characterized by the other anti-HLA-class II reagents (TU34, TU35, TU37, TU39, TU43, TU58) were also present on these cell types. However, selective expression of HLA-DR and/or -SB like molecules was demonstrated with these antibodies on certain vascular endothelia, as well as different B-cell lymphomas and distinct epithelial cells in adults. Exclusive reactivity of the antibody TU39 shown on endothelial cells of fetal liver and kidney suggested specific functions of HLA-SB antigens during ontogeny. Furthermore, HLA-DR and/or -SB like molecules but not TU22+ HLA-DC/MB antigens were found to be inducible on normally Ia-like antigen negative epithelial cells of various diseased organs. Implications of this differential tissue distribution of HLA-DC/MB/DS, -DR and -SB like products in relation to organ transplantation, regulation of immune responses and cell differentiation are discussed.

Adult

Divergent expression of cytotoxic and microbicidal functions of rabbit alveolar and peritoneal macrophages: effects of non-specific activation and a natural microbicidal peptide, MCP-1.

Alveolar macrophages from NZW rabbits were intrinsically toxic to 6 xenogeneic cell lines and to Candida albicans in vitro. Macrophage-mediated candidacidal activity, but not cytostasis (inhibition of [3H] thymidine incorporation by target cells) or cytotoxicity (reduction in target cell number), was enhanced by prior injection of rabbits with Freund's complete adjuvant (FCA). Compared with alveolar macrophages, peritoneal macrophages were less candidacidal (median C. albicans killed, 24% versus 16%, p less than 0.01). In contrast to alveolar macrophages, peritoneal macrophages were not consistently cytostatic or cytotoxic. Only candidacidal activity was enhanced in FCA-elicited peritoneal macrophages (median C. albicans killed 28% versus 16% for resident peritoneal macrophages, p less than 0.01). Microbicidal concentrations of a cationic peptide produced by rabbit alveolar macrophages (MCP-1, 25-100 micrograms/ml) did not inhibit growth of 4 murine cell lines in vitro. Macrophage-mediated cytostasis and cytotoxicity were not enhanced by culture with exogenous MCP-1. Macrophage-mediated cytostasis was also unchanged in cultures containing 10(-5) 2' deoxycytidine. We conclude that rabbit macrophage populations are restricted in their expression of cytostatic and cytotoxic functions, that microbicidal activation can occur independently of cytotoxic activation and that in this system mechanisms of macrophage-mediated cytotoxicity to xenogeneic target cells are independent of MCP-1 and thymidine.

Animals

Normal and transformed human prokeratinocytes express divergent effects of a tumor promoter on cell cycle-mediated control of proliferation and differentiation.

The tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA), is shown to be a potent inhibitor of growth of normal human prokeratinocytes (HPK) cultured in serum-free medium. More specifically TPA inhibits the clonal growth of low density HPK cultures in a dose-dependent manner and the anti-proliferative effect of TPA is selective in that the inactive phorbol diester, 4-alpha-12,13-phorbol didecanoate, does not exert a similar effect. One-hour pulse exposure of HPK to TPA also has an effect comparable with continuous exposure to TPA; both treatments induce rapid growth arrest. Flow cytofluorometric analysis of DNA content shows that in TPA-treated HPK growth arrest is associated with accumulation of cells in both the G1 and G2/M phases of the cell cycle. Most interestingly, the data establish that the growth arrest of HPK induced by TPA is irreversible in that treated cells lose their colony-forming potential and that such cells are committed to differentiate without further cell cycle progression when placed in differentiation-promoting medium. In contrast, a human squamous carcinoma cell line, designated SCC-25, is insensitive to the anti-proliferative effect of TPA regardless of whether these cells are cultured in either serum-containing or serum-free medium. These data are interpreted to suggest that transformed human epithelial cells SCC-25 are defective in their ability to regulate their proliferation and differentiation by TPA-sensitive cell cycle-dependent mechanisms.

Adult

Tissue-specific expression of divergent actins in soybean root.

It has been proposed that the evolution of distinct classes of genes encoding the kappa-, lambda-, and mu-actins in soybean is the result of an ancient divergence in patterns of actin gene expression. In this study, antisera against a family of synthetic actin peptides from a divergent region within the predicted actin polypeptide sequences have been used to explore the differential expression of plant actins. Antiserum elicited against a 16-residue synthetic lambda-actin peptide SAc4:257 reacted with a 46-kilodalton protein in soybean extracts, showed specificity for the lambda-peptide over the divergent kappa- and mu-actin peptides in enzyme-linked immunosorbent assays, and reacted strongly and preferentially with root protoderm in apical roots and in lateral root primordia. Antiserum elicited against the synthetic kappa-actin peptide SAc1:257 reacted with 46-kilodalton protein on protein gel blots, showed partial specificity toward the immunogenic kappa-peptide over the divergent lambda- and mu-peptides, and reacted strongly with all root tissues with the exception of root cap. These data support the hypothesis that ancient classes of plant actin genes may have been preserved because of their role in developmentally controlled differences in tissue-specific actin expression and/or function. The possibility that other diverse actin classes have unique patterns of regulation is discussed.

Actins

Control of cAMP-induced gene expression by divergent signal transduction pathways.

A compilation of literature data and recent experiments led to the following conclusions regarding cyclic adenosine 3':5' monophosphate (cAMP) regulation of gene expression. Several classes of cAMP-induced gene expression can be discriminated by sensitivity to stimulation kinetics. The aggregation-related genes respond only to nanomolar cAMP pulses. The prestalk-related genes respond both to nanomolar pulses and persistent micromolar stimulation. The prespore specific genes respond only to persistent micromolar stimulation. The induction of the aggregation- and prestalk-related genes by nanomolar cAMP pulses may share a common transduction pathway, which does not involve cAMP, while involvement of the inositol 1,4,5-trisphosphate (IP3)/Ca2+ pathway is unlikely. Induction of the expression of prespore and prestalk-related genes by micromolar cAMP stimuli utilizes divergent signal processing mechanisms. cAMP-induced prespore gene expression does not involve cAMP and probably also not cyclic guanosine 3'.5' monophosphate (cGMP) as intracellular intermediate. Involvement of cAMP-induced phospholipase C (PLC) activation in this pathway is suggested by the observation that IP3 and 1,2-diacylglycerol (DAG) can induce prespore gene expression, albeit in a somewhat indirect manner and by the observation that Li+ and Ca2+ antagonists inhibit prespore gene expression. Cyclic AMP induction of prestalk-related gene expression is inhibited by IP3 and DAG and promoted by Li+, and is relatively insensitive to Ca2+ antagonists, which indicates that PLC activation does not mediate prestalk-related gene expression. Neither prespore nor prestalk-related gene expression utilizes the sustained cAMP-induced pHi increase as intracellular intermediate.

Cyclic AMP

Tissue, developmental, and tumor-specific expression of divergent transcripts in Wilms tumor.

The Wilms tumor locus on chromosome 11p13 has been mapped to a region defined by overlapping, tumor-specific deletions. Complementary DNA clones representing transcripts of 2.5 (WIT-1) and 3.5 kb (WIT-2) mapping to this region were isolated from a kidney complementary DNA library. Expression of WIT-1 and WIT-2 was restricted to kidney and spleen. RNase protection revealed divergent transcription of WIT-1 and WIT-2, originating from a DNA region of less than 600 bp. Both transcripts were present at high concentrations in fetal kidney and at much reduced amounts in 5-year-old and adult kidneys. Eleven of 12 Wilms tumors classified as histopathologically heterogeneous exhibited absent or reduced expression of WIT-2, whereas only 4 of 14 histopathologically homogeneous tumors showed reduced expression. These data demonstrate a molecular basis for the pathogenetic heterogeneity in Wilms tumorigenesis.

Base Sequence

A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia.

As the largest group of vertebrates, fish exhibit frequent turnover of sex-determining (SD) genes. Here, we assemble a chromosome-level YY red tilapia genome and identify figla-like (figlal) as the SD gene on tilapia linkage group (LG) 1. Integrative phylogenetic and genomic evidence suggests that figlal originated from a tilapia-specific duplication and transposition of the ancestral bHLH family gene figla from LG12 to LG1. Fluorescence in situ hybridization reveals expression divergence between figla and figlal, with figla expressed in female oocytes and figlal expressed in male gonadal somatic cells during early gonadal differentiation. The shift in expression after duplication might be driven by the insertion of cis-regulatory elements mediated by transposable elements. Knockout of figlal in XY fish results in male-to-female sex reversal as indicated by ovarian morphology, down-regulation of the male pathway gene dmrt1, and up-regulation of the female pathway gene cyp19a1a in the gonads. In contrast, overexpression of figlal in XX fish induces female-to-male sex reversal. These findings implicate figlal as an SD gene on tilapia LG1 and reveal the history of a unique evolutionary innovation in which a female oocyte gene evolved into a male SD gene via duplication, transposition, and cis-regulatory rewiring.

Animals

Evolutionary Genomics Unravels the Responses and Adaptation to Climate Change in a Key Alpine Forest Tree Species.

Despite widespread biodiversity loss, our understanding of how species and populations will respond to accelerated climate change remains limited. In this study, we integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa, a key alpine forest tree species primarily distributed in the mountainous regions of a global biodiversity hotspot. Over historical timescales, our findings demonstrate that demographic dynamics, divergent selection, and long-term balancing selection have shaped and maintained genetic variation within and between populations. In examining genomic signatures of contemporary climate adaptation, we found that haplotype blocks, potentially caused by inversion polymorphisms that suppress recombination, are linked to enriched combinations of locally adaptive environmental variations. We further assessed the relative contributions of environmentally induced plastic responses, constitutive expression divergence between genetic clusters, and their interactions in driving gene expression variation and divergence. Notably, we observed a strong correlation between sequence divergence and constitutive differential expression among genetic clusters. Finally, by incorporating genetic adaptation, migration, and genetic load into our predictions of population-level climate change risks, we identified western populations-primarily distributed in the Hengduan Mountains, a region known for its environmental heterogeneity and significant biodiversity-as the most vulnerable to climate change. These populations should be prioritized for conservation and management. Overall, our study advances the understanding of the relative roles of long-term natural selection, local environmental adaptation, and immediate plastic expression changes in shaping the responses of natural populations of keystone species to climate change.

Climate Change

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs

Inducible cephalosporinase production in clinical isolates of Enterobacter cloacae is controlled by a regulatory gene that has been deleted from Escherichia coli.

Cephalosporin hyper-resistant Enterobacter cloacae strains are isolated with increasing frequency from hospital infections. Resistance is principally due to the chromosomal ampC gene encoding a cephalosporinase. In contrast to Escherichia coli which expresses ampC constitutively from a promoter located in the upstream frdD gene, E. cloacae displays inducible ampC expression. By cloning the ampC gene it was shown that a linked genetic locus, ampR, mediated the induction by beta-lactams. In the absence of the antibiotic the 30,500 dalton AmpR protein represses ampC expression. The ampR gene shows a highly compact arrangement and is situated between the divergently expressed ampC gene and the frd operon from which it is separated by a bifunctional transcription terminator. The promoters for ampR and ampC substantially overlap and mRNA analyses showed that on induction transcription from the ampC promoter increased greatly whereas that from ampR did not. Two regions of sequence homology flank the ampR gene and it is proposed that a homologous recombination event between these in an ancestral enteric bacterium may have led to the deletion of ampR from the E. coli genome.

Base Sequence

Genome-guided stage- and tissue-resolved transcriptome analysis of Serrodes campana identifies sex-biased antennal expression and candidate chemosensory-related genes.

Serrodes campana is an erebid moth of ecological and forestry relevance; its larvae are mainly associated with the soapberry tree, Sapindus mukorossi, whereas adults exhibit fruit-piercing behavior. However, stage- and tissue-resolved transcriptomic resources for this species remain limited. Here, using a chromosome-level reference genome, we performed a genome-guided transcriptome analysis of S. campana based on 12 RNA-seq libraries representing major developmental stages and key adult tissues. Global transcriptomic analyses revealed pronounced transcriptional differentiation across developmental stages and tissue types. Tissue-enriched gene sets and functional enrichment analyses identified distinct molecular signatures associated with developmental, sensory, and pheromone-associated tissues. Comparative analysis of female and male antennae further revealed sex-biased expression of several candidate chemosensory-related genes. Among 153 curated chemosensory-related candidate genes, most odorant receptor genes showed strong antennal enrichment, whereas other major chemosensory gene families displayed broader but still tissue-preferential expression patterns. In addition, an exploratory comparison of female terminal abdominal gland tissue and male terminal abdominal coremata revealed divergent expression profiles and highlighted candidate genes potentially associated with pheromone-related physiology, reproduction, and tissue-specific signaling. Together, this study provides the first genome-guided stage- and tissue-resolved transcriptomic resource for S. campana and offers a useful foundation for future studies of chemosensory detection, sex-biased gene expression, and pheromone-associated biology in this species.

Animals

Regulatory elements involved in Drosophila Adh gene expression are conserved in divergent species and separate elements mediate expression in different tissues.

Alcohol dehydrogenase (ADH) is expressed in a complex temporal and spatial pattern from tandem promoters (proximal and distal) in Drosophila melanogaster, and from two closely linked genes (Adh-1 and Adh-2) in D. mulleri. The expression patterns of Adh-1 and the proximal promoter, and Adh-2 and the distal promoter are similar, but not identical. We show that the mulleri Adh genes are appropriately expressed when introduced into the melanogaster genome, indicating that the cis- and trans-acting elements which regulate the corresponding promoters are functionally equivalent in the two species. By analyzing the expression of in vitro generated mutants of the mulleri Adh locus, we define at least three regulatory regions of the mulleri Adh genes and show that different control elements mediate the expression of Adh in different tissues.

Alcohol Dehydrogenase

Loss of Methylthioadenosine Phosphorylase (MTAP) Expression: A Potentially Useful Tool for Distinguishing Sarcomatoid Urothelial Carcinoma From Inflammatory Myofibroblastic Tumor.

Inflammatory myofibroblastic tumor (IMT) and sarcomatoid urothelial carcinoma (SarUC) can have striking histologic overlap but have significantly different prognoses and clinical management paradigms. Loss of methylthioadenosine phosphorylase (MTAP) protein expression by immunohistochemistry (IHC) serves as a useful surrogate for homozygous 9p21 deletion, a recurrent genomic alteration in urothelial carcinoma (UC). We analyzed MTAP expression by IHC in 65 SarUCs and 27 urinary tract IMTs to evaluate its utility in navigating this challenging differential diagnosis. Overall, MTAP loss was significantly more frequent in SarUC (55%) compared with IMT (4%) (P < .0001). Among 46 biphasic SarUCs with independently evaluable epithelial and mesenchymal components, divergent expression patterns were frequent. The most common pattern was retention of MTAP staining in both epithelial and mesenchymal components (19/46; 41% of cases), followed by selective retention of MTAP in the epithelial component and loss in the mesenchymal component (16/46; 35% of cases). MTAP loss was observed in both the epithelial and mesenchymal components in 11 out of 46 (24%) SarUC cases. None of the 46 biphasic SarUC cases showed selective MTAP loss in the epithelial component but retention in the mesenchymal component. MTAP IHC was also particularly valuable in assessing clonal relationships in 2 challenging biphasic cases in which the differential diagnosis included a collision between a noninvasive low-grade papillary UC and an IMT versus a subtle IMT-like SarUC arising in association with an overlying noninvasive low-grade papillary UC. Next-generation sequencing on a subset of cases (n = 11) was useful for confirming 9p deletion in cases with MTAP loss by IHC, and for demonstrating molecular hallmarks of urothelial neoplasia thereby providing additional diagnostic support for morphologically challenging SarUC cases with IMT-like morphology. Therefore, MTAP IHC can be useful in evaluating spindle cell lesions of the urinary tract, as loss is significantly more common in SarUC than in IMT, and enriched in the mesenchymal component of biphasic SarUC. However, MTAP loss can be seen in both entities, and the diagnosis of IMT-like spindle cell tumors in the urinary tract requires careful integration of morphologic, immunohistochemical, and molecular data.

Humans