Sc Gene Research Articles

ScMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis

IntroductionSingle-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data.ResultsscMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics.ConclusionsThe analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.

Efficient gene targeting in Aspergillus chevalieri used to produce katsuobushi.

In this study, we developed an efficient gene targeting system for the osmophilic fungus Aspergillus chevalieri, which is commonly used in the production of a dried bonito, katsuobushi. Specifically, we utilized the clustered regularly interspaced short palindromic repeats/Cas9 system to disrupt the ATP sulfurylase encoding sC gene. This results in methionine auxotroph and selenate-resistance. Additionally, we disrupted the DNA ligase IV encoding ligD gene, which is required for nonhomologous end joining. Using the sC marker and selenate-resistance as a selection pressure, we were able to rescue the sC marker and generate a ΔligD ΔsC strain. We determined that the gene targeting efficiency of the ΔligD ΔsC strain was significantly higher than that of the parental ΔsC strain, which indicates that this strain provides efficient genetic recombination for the genetic analysis of A. chevalieri.

Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility in GJ Rice (Oryza sativa L.) Subspecies.

Hybrids between different subspecies of rice Oryza sativa L. commonly show hybrid sterility. Here we show that a widely planted commercial japonica/GJ variety, DHX2, exhibited hybrid sterility when crossing with other GJ varieties. Using the high-quality genome assembly, we identified three copies of the Sc gene in DHX2, whereas Nipponbare (Nip) had only one copy of Sc. Knocking out the extra copies of Sc in DHX2 significantly improved the pollen fertility of the F1 plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of Sc. Moreover, the introgression of GS3 and BADH2/fgr from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding.

Newly identified breast luminal progenitor and gestational stem cell populations likely give rise to HER2-overexpressing and basal-like breast cancers

Breast Cancer (BrC) is a common malignancy with genetically diverse subtypes. There is evidence that specific BrC subtypes originate from particular normal mammary cell populations. However, the cell populations that give rise to most BrC subtypes are unidentified. Several human breast scRNAseq datasets are available. In this research, we utilized a robust human scRNAseq dataset to identify population-specific marker genes and then identified the expression of these marker genes in specific BrC subtypes. In humans, several BrC subtypes, HER2-enriched, basal-like, and triple-negative (TN), are more common in women who have had children. This observation suggests that cell populations that originate during pregnancy give rise to these BrCs. The current human datasets have few normal parous samples, so we supplemented this research with mouse datasets, which contain mammary cells from various developmental stages. This research identified two novel normal breast cell populations that may be the origin of the basal-like and HER2-overexpressing subtypes, respectively. A stem cell-like population, SC, that expresses gestation-specific genes has similar gene expression patterns to basal-like BrCs. A novel luminal progenitor cell population and HER2-overexpressing BrCs are marked by S100A7, S100A8, and S100A9 expression. We bolstered our findings by examining SC gene expression in TN BrC scRNAseq datasets and S100A7-A9 gene expression in BrC cell lines. We discovered that several potential cancer stem cell populations highly express most of the SC genes in TN BrCs and confirmed S100A8 and A9 overexpression in a HER2-overexpressing BrC cell line. In summary, normal SC and the novel luminal progenitor cell population likely give rise to basal-like and HER2-overexpressing BrCs, respectively. Characterizing these normal cell populations may facilitate a better understanding of specific BrCs subtypes.

The Spatial Heterogeneity in Newly Diagnosed Multiple Myeloma Patients - from Sub-Clonal Architecture to the Immune Microenvironment

The Spatial Heterogeneity in Newly Diagnosed Multiple Myeloma Patients - from Sub-Clonal Architecture to the Immune Microenvironment

Abstract 2360: Identifying differentially expressed miRNAs in CRC stem cell subpopulations

Abstract Our research goal is to discover the molecular mechanisms behind tumor heterogeneity in CRC. We previously showed that CRCs contain multiple subpopulations of cancer stem cells (CSCs) which may explain the occurrence tumor heterogeneity and resistance to treatment. To determine how CSC sub-populations might arise, we are studying miRNA expression in CRC SCs. MicroRNAs are known to regulate SC phenotype and are found to be dysregulated in many cancers. Hypothesis: Tumor heterogeneity results from existence of multiple CSC subpopulations that are regulated by distinct miRNAs. Accordingly, we are using bioinformatics and miRNA profiling to identify miRNAs that target SC genes in CRCs. Indeed, our miRNA expression profiling of normal and malignant ALDH+ human colonic SCs showed that miRNA92a targets the SC gene LRIG1 and upregulation of miRNA92a leads to decreased LRIG1 expression. We also discovered that miRNA23b targets the SC gene LGR5 and miRNA23b is upregulated in ALDH+ CSCs. We have identified several other candidate miRNAs that are predicted to target CD166, ALDH1A1, BMI1, LRG5, and LRIG1 SC genes. We are currently in the process of validating whether these miRNAs contribute to emergence of specific CSC sub-populations in CRCs. Thus, identifying miRNAs that regulate CSC subpopulations should provide new strategies to modulate CSC composition in order to sensitize tumors to treatments. Citation Format: Victoria A. Stark, Vignesh Viswanathan, Caroline O. Facey, Lynn M. Opdenaker, Bruce M. Boman. Identifying differentially expressed miRNAs in CRC stem cell subpopulations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2360.

Rapid and marker-free gene replacement in citric acid-producing Aspergillus tubingensis (A. niger) WU-2223L by the CRISPR/Cas9 system-based genome editing technique using DNA fragments encoding sgRNAs

Strains belonging to Aspergillus section Nigri, including Aspergillus niger, are used for industrial production of citric acid from carbohydrates such as molasses and starch. The objective of this study was to construct the genome editing system that could enable rapid and efficient gene replacement in citric acid-producing fungi for genetic breeding. Using the citric acid-hyperproducer A.tubingensis (formerly A.niger) WU-2223L as a model strain, we developed a CRISPR/Cas9 system-based genome editing technique involving co-transformation of Cas9 and the DNA fragment encoding single guide RNA (sgRNA). Using this system, ATP-sulfurylase gene (sC) knock-out strain derived from WU-2223L was generated; the knock-out efficiency was 29 transformants when 5μg Cas9 was added to 5× 105 protoplasts. In the gene replacement method based on this system, a DNA fragment encoding sgRNAs that target both the gene of interest and marker gene was used, and replacement of nitrate reductase gene (niaD) using sC gene as a marker gene was attempted. More than 90% of the sC-knock-out transformants exhibited replaced niaD, indicating efficient gene replacement. Moreover, one-step marker rescue of the sC marker gene was accomplished by excising the knock-in donor via intramolecular homologous recombination, enabling marker-free genome editing and drastically shortening the gene replacement period by circumventing the transformation procedure to recover the sC gene. Thus, we succeeded in constructing a CRISPR/Cas9 system-based rapid and marker-free gene replacement system for the citric acid-hyperproducer strain WU-2223L.

Abnormalities in Brainstem Auditory Evoked Potentials in Sheep with Transmissible Spongiform Encephalopathies and Lack of a Clear Pathological Relationship.

Scrapie is transmissible spongiform encephalopathy (TSE), which causes neurological signs in sheep, but confirmatory diagnosis is usually made postmortem on examination of the brain for TSE-associated markers like vacuolar changes and disease-associated prion protein (PrPSc). The objective of this study was to evaluate whether testing of brainstem auditory evoked potentials (BAEPs) at two different sound levels could aid in the clinical diagnosis of TSEs in sheep naturally or experimentally infected with different TSE strains [classical and atypical scrapie and bovine spongiform encephalopathy (BSE)] and whether any BAEP abnormalities were associated with TSE-associated markers in the auditory pathways. BAEPs were recorded from 141 clinically healthy sheep of different breeds and ages that tested negative for TSEs on postmortem tests to establish a reference range and to allow comparison with 30 sheep clinically affected or exposed to classical scrapie (CS) without disease confirmation (test group 1) and 182 clinically affected sheep with disease confirmation (test group 2). Abnormal BAEPs were found in 7 sheep (23%) of group 1 and 42 sheep (23%) of group 2. The proportion of sheep with abnormalities did not appear to be influenced by TSE strain or PrPSc gene polymorphisms. When the magnitude of TSE-associated markers in the auditory pathways was compared between a subset of 12 sheep with and 12 sheep without BAEP abnormalities in group 2, no significant differences in the total PrPSc or vacuolation scores in the auditory pathways could be found. However, the data suggested that there was a difference in the PrPSc scores depending on the TSE strain because PrPSc scores were significantly higher in sheep with BAEP abnormalities infected with classical and L-type BSE, but not with CS. The results indicated that BAEPs may be abnormal in sheep infected with TSEs but the test is not specific for TSEs and that neither vacuolation nor PrPSc accumulation appears to be responsible for the clinical abnormalities.

The polymorphism nt 76 in exon 2 of SC is more frequent in Whites than in Blacks

Abstract The Scianna blood group system comprises seven antigens encoded by alternative forms of SC. The SC gene also has two polymorphisms in the leader sequence, at nucleotides 54 (C/T, silent) and 76 (C/T, 26His/Tyr) in exon 2, which are not involved in expression of blood group antigens. The nucleotide change at position 76 has an Nla III restriction enzyme site; thus, DNA samples from 100 Caucasians and 100 African Americans were analyzed for the SC nucleotide 76 change. DNA from Caucasian and African American donors was tested by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) using the restriction enzyme Nla III. In selected samples, sequencing of exon 2 was performed. PCR-RFLP results for samples from 100 donors (mostly Caucasian) and 100 African American donors (400 alleles) showed the nucleotide 76T variant had a prevalence of 25 percent in Whites and 5 percent in African Americans. In 11 samples (2 C/C, 3 C/T, and 6 T/T) sequencing of exon 2 confirmed the presence of the expected nucleotides at position 76. The allele frequency in Caucasians was 0.75 for nt76C and 0.25 for nt76T. In African Americans, the frequencies were, respectively, 0.95 and 0.05. Immunohematology 2009;25:18–19.

Negative-feedback regulation of proneural proteins controls the timing of neural precursor division

Neurogenesis requires precise control of cell specification and division. In Drosophila, the timing of cell division of the sensory organ precursor (SOP) is under strict temporal control. But how the timing of mitotic entry is determined remains poorly understood. Here, we present evidence that the timing of the G2-M transition is determined by when proneural proteins are degraded from SOPs. This process requires the E3 ubiquitin ligase complex, including the RING protein Sina and the adaptor Phyl. In phyl mutants, proneural proteins accumulate, causing delay or arrest in the G2-M transition. The G2-M defect in phyl mutants is rescued by reducing the ac and sc gene doses. Misexpression of phyl downregulates proneural protein levels in a sina-dependent manner. Phyl directly associates with proneural proteins to act as a bridge between proneural proteins and Sina. As phyl is a direct transcriptional target of Ac and Sc, our data suggest that, in addition to mediating cell cycle arrest, proneural protein initiates a negative-feedback regulation to time the mitotic entry of neural precursors.

A defect of LigD (human Lig4 homolog) for nonhomologous end joining significantly improves efficiency of gene-targeting in Aspergillus oryzae

Gene-targeting by homologous recombination occurs rarely during transformation since nonhomologous recombination is predominant in Aspergillus oryzae. To develop a highly efficient gene-targeting system for A. oryzae, we constructed disrupted strains harboring a gene ( ligD) encoding human DNA ligase IV homolog that is involved in the final step of DNA nonhomologous end joining. The A. oryzae ligD disruptants showed no apparent defect in vegetative growth and/or conidiation, and exhibited increased sensitivity to high concentration of methyl methansulfonate causing double-stranded DNA breaks compared with that of wild-type strain, but not to ethyl methanesulfonate and phleomycin. Gene replacement of the prtR, a gene encoding a transcription factor which regulates extracellular proteolytic genes, using the Aspergillus nidulans sC gene as the selectable marker resulted in 100% of gene-targeting efficiency in the ligD disruptant, compared to less than 30% for a wild-type, when the length of the homologous flanking sequences used was longer than 0.5 kb. Similarly, gene-targeting efficiency was as high as 100% for aspartic protease-encoding gene ( pepA). Furthermore, using this ligD disruptant system of A. oryzae, we readily succeeded in disrupting five mitogen-activated protein kinase (MAPK) genes, namely mpkA, mpkB, hogA, mpkC and A. oryzae unique MAPK ( mpkD). Such results show that the ligD disruptant system is an extremely convenient genetic background for gene-targeting in A. oryzae.

A conserved trans-regulatory landscape for scute expression on the notum of cyclorraphous Diptera

Bristles on the notum of many cyclorraphous flies are arranged into species-specific stereotyped patterns. The positions of bristles correlate with differences in the spatial expression of the scute (sc) gene in those species examined so far. However, a major upstream activator of scute, Pannier (Pnr), is expressed in a conserved domain over the entire medial notum. Here we examine the expression patterns in Calliphora vicina of stripe (sr), u-shaped (ush), caupolican (caup) and wingless (wg), genes known to modify the activity of Pnr or to act downstream of Pnr in Drosophila. We find that, with minor differences, their expression patterns are conserved. This suggests that the function of a trans-regulatory network of genes is relatively unchanged in derived Diptera and that many differences are likely to be due to changes in cis-regulatory sequences of scute.

Collection of blood stem cells from patients with sickle cell anemia

Prior to initiating gene therapy trials for sickle cell disease (SCD), methods to collect sufficient numbers of hematopoietic stem and progenitor cells will need to be developed. Bone marrow harvest entails significant morbidity that could be severe in patients with SCD. In addition, an ability to perform repeated stem cell collections so that several transfers of genetically modified cells could be attempted would be advantageous. In other settings, apheresis collection of mobilized blood stem cells has become the preferred source of stem cells for transplantation. Unfortunately, patients with SCD do not tolerate granulocyte-colony stimulating factor and therefore cannot be mobilized using these conventional methods. In this pilot study, we investigated whether withdrawal of hydroxyurea therapy results in an increase in circulating numbers of CD34+ cells and hematopoietic progenitors. In addition, we performed leukapheresis in one patient with severe SCD in an attempt to determine whether blood stem cell collection can be performed safely in patients who would be candidates for SC gene therapy trials. Our results highlight some of the potential difficulties in initiating gene therapy clinical trials for sickle cell disease.

The identification and expression of achaete-scute genes in the branchiopod crustacean Triops longicaudatus

The achaete-scute ( ac/ sc) genes are a highly conserved family of transcription factors that play important roles in the development of neural cells in both vertebrates and invertebrates. As such, the study of arthropod ac/ sc gene expression during neurogenesis has become a model system for investigating the evolution of neural patterning. To date, ac/ sc gene expression has been investigated in insects, chelicerates, and myriapods. Here we present the identification of two ac/ sc genes from the branchiopod crustacean Triops longicaudatus. Triops longicaudatus achaete-scute homologs 1 and 2 ( Tl-ASH1 and Tl-ASH2) exhibit dynamic and distinct expression profiles during Triops neurogenesis. Tl-ASH1 expression initiates in nearly all cells of the neurogenic region and subsequently in clusters of cells evenly spaced along the length of the developing limbs. In contrast, Tl-ASH2 initiates expression after Tl-ASH1. In the CNS, only a subset of Tl-ASH1 cells appears to express Tl-ASH2. Similarly, in the PNS individual Tl-ASH2 positive cells appear to arise from the clusters of Tl-ASH1 expressing cells. Shortly after activating Tl-ASH2 expression, these cells enlarge and divide. The expression dynamics of ac/ sc genes in Triops parallel those observed in insects and contrasts with those found in chelicerates and myriapods.

STAR: a novel high‐prevalence antigen in the Scianna blood group system

More than 20 years ago, a proband was described whose red blood cells (RBCs) typed Sc:1,-2,3. His serum sample contained an immunoglobulin G alloantibody that reacted with all RBCs tested except his own, his brother's, and those with the Sc:-1,-2 phenotype. Cloning of the SC gene allowed determination of the molecular basis associated with this novel high-prevalence antigen. Samples from frozen storage were obtained from the proband, his serologically matched brother, and 15 serologically mismatched family members. DNA was extracted, and amplified products from all 11 SC (ERMAP) exons and their flanking regions of the proband were sequenced. A single-nucleotide mutation was detected (139G>A) in Exon 3 that is predicted to encode a change of Amino Acid 47 from glutamic acid to lysine. The sequence analyses on samples from family members were as expected. The absence of the high-prevalence antigen STAR detected by the proband's antibody is likely associated with lysine at Position 47 of the Sc glycoprotein. This amino acid change is located on the extracellular portion of HERMAP, 10 residues upstream from the polymorphism associated with Sc1 and Sc2 (Gly57Arg). STAR expands the Sc blood group system to five antigens and has been assigned the ISBT Number 013005 (SC5).

Cloning and use of sC as homologous marker for Aspergillus niger transformation

The sC sequence from Aspergillus niger was cloned and developed into a homologous marker system for genetic transformation. The coding region of the sC gene amplified by PCR from the A. niger genome was provided with Aspergillus nidulans expression signals ( gpdA promoter and trpC terminator). This chimeric construct was used to successfully transform a spontaneous sC − isolate of A. niger to prototrophy. The transformants analyzed by Southern analysis showed integration of multiple copies of the transforming DNA. They also exhibited much higher ATP sulfurylase activity than the wild-type A. niger strain reinforcing the molecular data. This demonstrates the usefulness of the sC niger construct, driven by PgpdA, as a marker for A. niger transformation.

Tissue-specific androgen responses in primary cultures of lacrimal epithelial cells studied by adenoviral gene transfer

The lacrimal gland secretes most of the water and many proteins present in tear fluid. The composition of the tear fluid is affected dramatically by androgens, an observation which has been linked to the fact that more than 90% of the patients with Sjögren syndrome are female. Although the presence of androgen receptors in the lacrimal gland has been established, the molecular biology of the protective effects of androgens remains largely unknown. Here, we report the use of primary cultures of the lacrimal gland which express endogenous proteins under androgen control, as a more homologous test system for tissue-specific transcription studies. Infection with recombinant adenoviral vectors was the most efficient method to introduce foreign gene constructs in these cultures. A thus introduced mouse mammary tumor virus promoter was inducible with androgens and this effect was independent of the sexual genotype of the infected cells. By use of two recombinant adenoviral vectors containing genomic fragments of the SC gene, which is androgen responsive in the lacrimal gland, we could demonstrate the functionality of the sc promoter as well as its androgen regulation in this culture system.

Development of a homologous transformation system for the opportunistic human pathogen Aspergillus fumigatus based on the sC gene encoding ATP sulfurylase.

The development of a homologous transformation system for the opportunistic human pathogenic fungus Aspergillus fumigatus is described. The system is based on the sC gene encoding ATP sulfurylase. Several A. fumigatus sC mutant strains were readily isolated by strong selection for selenate resistance. The coding region plus upstream and downstream regulatory sequences of the A. fumigatus sC gene were cloned by inverse PCR and then sequenced. Sequencing of the sC cDNA revealed the presence of five introns located within the first half of the gene. The A. fumigatus sC gene encodes a protein of 574 amino acids which is highly similar to ATP sulfurylases from the filamentous fungal species Aspergillus nidulans, Aspergillus terreus and Penicillium chrysogenum. By contrast, ATP sulfurylases from the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe lack the C-terminal adenosine-5'-phosphosulfate kinase-like domain present in the filamentous fungal orthologues. A 3.8-kb DNA fragment amplified by PCR and containing the sC gene plus 5' and 3' flanking regions was cloned into pUC19 to give the vector pSCFUM. Transformation of two different sC mutant isolates with the plasmid pSCFUM established the functionality of this new homologous transformation system. Molecular analysis of sC+ transformants showed that up to 44% of transformed clones contained one or more copies of the entire plasmid integrated at the sC locus. This result also demonstrates the utility of the sC marker for targeting specific genetic constructs to the A. fumigatus sC locus, facilitating studies of gene regulation and function.

The first exon of the human sc gene contains an androgen responsive unit and an interferon regulatory factor element

Secretory component (SC) plays a key role in the transport of IgA and IgM to the lumina of many glands. The gene is constitutively expressed, but can be modulated by hormonal and immunological stimuli. Recently, the promoter and the first exon of the human sc gene have been cloned. The first exon contains a putative androgen/glucocorticoid response element (ARE/GRE) and an Interferon Regulatory Factor Element (IRF-E). Here we show that the ARE/GRE can bind the DNA-binding domain (DBD) of both the androgen (AR) and glucocorticoid receptor (GR) with a preference for the AR-DBD. In transient transfection experiments, this element confers higher responsiveness to androgens than to glucocorticoids. The IRF-E can function as an IRF-2, but surprisingly not as an IRF-1 responsive element. We postulate that these two regulatory elements play a key role in the complex regulation of the sc gene in vivo.

Different regulatory pathways employed in cytokine-enhanced expression of secretory component and epithelial HLA class I genes.

The transmembrane secretory component (SC, or pIg receptor) plays a crucial role in mucosal immunity by translocating dimeric IgA and pentameric IgM through exocrine epithelia. This receptor is up-regulated by cytokines in parallel with increased epithelial HLA expression. By use of the human epithelial cell line HT-29m3, we show that IFN-gamma, TNF-alpha and IL-4 activate transcription of the SC gene. This activation was slow, suggesting mediation via newly synthesized protein factors. IFN-gamma and TNF-alpha, but not IL-4, also up-regulated expression of HLA class I genes. However, this gene induction was rapid and did not depend on new protein synthesis. Nuclear run-on experiments showed that the transcription rate of HLA class I genes nearly peaked after only 30 min of IFN-gamma or TNF-alpha stimulation, whereas the SC transcription rate did not peak until after 20-36 h of IFN-gamma, TNF-alpha or IL-4 stimulation. Gel electrophoresis mobility shift assays demonstrated binding of nuclear proteins from cytokine-stimulated HT-29 cells to consensus elements in the promoter of the SC gene, involving the binding site for the nuclear factor-kappaB p50 subunit after TNF-alpha stimulation, and IFN-stimulated response element after IFN-gamma stimulation (and weakly after TNF-alpha. Our observations in vitro likely parallel events in vivo by which activated mucosal T cells and macrophages enhance pIg receptor-mediated external transport of secretory IgA and IgM and up-regulate epithelial HLA expression.