Expression Of Various Genes Research Articles

Rice small protein OsS1Fa1 participates in stress responses as an inner nuclear membrane protein

ABSTRACT The rice small protein OsS1Fa1, a homolog of spinach S1Fa, plays a significant role in drought tolerance, attributed to its transmembrane domain. In this study, we aim to further elucidate the potential roles of OsS1Fa1 in cold and biotic stresses as an inner nuclear membrane protein. Fluorescence analysis confirmed the localization of OsS1Fa1 to the inner nuclear membrane. Utilizing the bimolecular fluorescence complementation (BiFC) and bacterial infiltration assays with OsS1Fa1 and the inner nuclear membrane protein OsSUN1 (Rice Sad1 and UNC84 (SUN) domain containing 1 (SUN1)), we observed fluorescence detection within the inner nuclear membrane, indicating a direct interaction and colocalization between OsS1Fa1 and OsSUN1. Expression analysis revealed that overexpression of OsS1Fa1 induced the expression of various genes associated with cold and defense responses, including COLD-REGULATED 15A (COR15A), PATHOGENESIS-RELATED PROTEIN 1 (PR1), and PLANT DEFENSIN 1.2 (PDF1.2). Our findings collectively indicate that OsS1Fa1 plays crucial roles in both abiotic and biotic stress tolerance as an inner nuclear membrane protein.

Abstract IA023: Dual-drug ADC platform for effective and safe cancer treatment

Abstract Breast tumor heterogeneity presents significant treatment challenges, particularly in overcoming drug resistance and tumor relapse driven by heterogeneous gene expression variability. Antibody-drug conjugates (ADCs) have demonstrated therapeutic success, yet intratumor heterogeneity remains a hurdle. We investigated dual-drug ADCs as a promising approach to address this clinical challenge. Our conjugates achieved potent and antigen-specific cytotoxicity, favorable pharmacokinetic properties, and high tolerability. In xenograft models with heterogeneous HER2 expression, our anti-HER2 dual-drug ADC significantly outperformed co-administration of two separate single-drug ADCs, demonstrating enhanced capacity to surmount tumor heterogeneity and resistance. Additionally, we developed a novel glutamic acid-glycine-citrulline (EGCit) linker, which enhances ADC hydrophilicity and stability in circulation. This EGCit linker also resists neutrophil protease degradation, a factor implicated in ADC-associated neutropenia. Compared to currently approved ADCs, our EGCit-based ADC exhibited reduced blood and liver toxicity, alongside superior antitumor efficacy in preclinical xenograft studies. These findings underscore the potential of our technology platform for advancing safer, more effective treatments for breast and other refractory cancers. Citation Format: Kyoji Tsuchikama. Dual-drug ADC platform for effective and safe cancer treatment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr IA023.

Emergence of temporal noise hierarchy in co-regulated genes of multi-output feed-forward loop

Natural variations in gene expression, called noise, are fundamental to biological systems. The expression noise can be beneficial or detrimental to cellular functions. While the impact of noise on individual genes is well-established, our understanding of how noise behaves when multiple genes are co-expressed by shared regulatory elements within transcription networks remains elusive. This lack of understanding extends to how the architecture and regulatory features of these networks influence noise. To address this gap, we study the multi-output feed-forward loop motif. The motif is prevalent in bacteria and yeast and influences co-expression of multiple genes by shared transcription factors (TFs). Focusing on a two-output variant of the motif, the present study explores the interplay between its architecture, co-expression (symmetric and asymmetric) patterns of the two genes, and the associated noise dynamics. We employ a stochastic modeling approach to investigate how the binding affinities of the TFs influence symmetric and asymmetric expression patterns and the resulting noise dynamics in the co-expressed genes. This knowledge could guide the development of strategies for manipulating gene expression patterns through targeted modulation of TF binding affinities.

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns.

Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Genome-Wide Identification and Characterization of OSC Gene Family in Gynostemma pentaphyllum (Cucurbitaceae)

Gynostemma pentaphyllum is a traditional Chinese medicinal plant of considerable application value and commercial potential, primarily due to its production of various bioactive compounds, particularly dammarane-type triterpenoid saponins that are structurally analogous to ginsenosides. Oxidosqualene cyclase (OSC), a pivotal enzyme in the biosynthesis of triterpenoid metabolites in plants, catalyzes the conversion of oxidosqualene into triterpenoid precursors, which are essential components of the secondary metabolites found in G. pentaphyllum. To elucidate the role of OSC gene family members in the synthesis of gypenosides within G. pentaphyllum, this study undertook a comprehensive genome-wide identification and characterization of OSC genes within G. pentaphyllum and compared their expression levels across populations distributed over different geographical regions by both transcriptome sequencing and qRT-PCR experimental validation. The results identified a total of 11 members of the OSC gene family within the genome of G. pentaphyllum. These genes encode proteins ranging from 356 to 767 amino acids, exhibiting minor variations in their physicochemical properties, and are localized in peroxisomes, cytoplasm, plasma membranes, and lysosomes. All GpOSCs contain highly conserved DCTAE and QW sequences that are characteristic of the OSC gene family. A phylogenetic analysis categorized the GpOSCs into four distinct subfamilies. A cis-element analysis of the GpOSC promoters revealed a substantial number of abiotic stress-related elements, indicating that these genes may respond to drought conditions, low temperatures, and anaerobic environments, thus potentially contributing to the stress resistance observed in G. pentaphyllum. Expression analyses across different G. pentaphyllum populations demonstrated significant variability in OSC gene expression among geographically diverse samples of G. pentaphyllum, likely attributable to genetic variation or external factors such as environmental conditions and soil composition. These differences may lead to the synthesis of various types of gypenosides within geographically distinct G. pentaphyllum populations. The findings from this study enhance our understanding of both the evolutionary history of the OSC gene family in G. pentaphyllum and the biosynthetic mechanisms underlying triterpenoid compounds. This knowledge is essential for investigating molecular mechanisms involved in forming dammarane-type triterpenoid saponins as well as comprehending geographical variations within G. pentaphyllum populations. Furthermore, this research lays a foundation for employing plant genetic engineering techniques aimed at increasing gypenoside content.

034 Transcriptomic Analysis Identifies Gene Expression Variability Correlated with Clinical Outcomes to Azathioprine in Patients with Moderate-to-Severe Atopic Dermatitis

034 Transcriptomic Analysis Identifies Gene Expression Variability Correlated with Clinical Outcomes to Azathioprine in Patients with Moderate-to-Severe Atopic Dermatitis

Testing the evolutionary theory of inversion polymorphisms in the yellow monkeyflower (Mimulus guttatus)

Chromosomal inversions have been implicated in a remarkable range of natural phenomena, but it remains unclear how much they contribute to standing genetic variation. Here, we evaluate 64 inversions that segregate within a single natural population of the yellow monkeyflower (Mimulus guttatus). Nucleotide diversity patterns confirm low internal variation for the derived orientation (predicted by recent origin), elevated diversity between orientations (predicted by natural selection), and localized fluctuations (predicted by gene flux). Sequence divergence between orientations varies idiosyncratically by position, not following the suspension bridge pattern predicted if the breakpoints are the targets of selection. Genetic variation in gene expression is not inflated close to inversion breakpoints but is clearly partitioned between orientations. Like sequence variation, the pattern of expression variation suggests that the capture of coadapted alleles is more important than the breakpoints for the fitness effects of inversions. This work confirms several evolutionary predictions for inversion polymorphisms, but clarity emerges only by synthesizing estimates across many loci.

Cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation

Gene expression variation results from numerous sources including genetic, environmental, life stage, and even the environment experienced by previous generations. While the importance of each has been demonstrated in diverse organisms, their relative contributions remain understudied because few investigations have simultaneously determined each within a single experiment. Here we quantified genome-wide gene expression traits in Drosophila, quantified the contribution of multiple different sources of trait variation and determined the molecular mechanisms underlying observed variation. Our results show that there is a clear hierarchy in our data with genome and developmental stage contributing on average considerably more than current and finally previous generation environmental effects. We also determined the role of cis and trans-regulatory changes across different sources of trait variation, highlighting their importance in adaptation and environmental responses and showing unexpectedly that transgenerational effects herein were predominantly associated with changes in trans-regulation.

NeuroVar: an open-source tool for the visualization of gene expression and variation data for biomarkers of neurological diseases.

The expanding availability of large-scale genomic data and the growing interest in uncovering gene-disease associations call for efficient tools to visualize and evaluate gene expression and genetic variation data. Here, we developed a comprehensive pipeline that was implemented as an interactive Shiny application and a standalone desktop application. NeuroVar is a tool for visualizing genetic variation (single nucleotide polymorphisms and insertions/deletions) and gene expression profiles of biomarkers of neurological diseases. Data collection involved filtering biomarkers related to multiple neurological diseases from the ClinGen database. NeuroVar provides a user-friendly graphical user interface to visualize genomic data and is freely accessible on the project's GitHub repository (https://github.com/omicscodeathon/neurovar).

Cardiac contractility modulation: from molecular patterns to tailored treatment in heart failure subgroups.

Cardiac contractility modulation (CCM) signals are non-excitatory signals that are applied during the myocyte's absolute refractory period. These signals have been demonstrated to have an inotropic effect without increasing myocardial oxygen consumption. This has been observed in both preclinical animal studies and randomized clinical trials. CCM influences the expression of various genes that are abnormally expressed in heart failure: it reverses fetal myocyte gene programming associated with heart failure and regulates the expression of genes associated with calcium cycling and myocardial contractile machinery. Clinical investigations have primarily focused on patients with heart failure and normal QRS duration where CCM has demonstrated its safety and effectiveness in reducing heart failure-related hospitalizations, as well as improving symptoms, functional capacity, and overall quality of life. Currently, for individuals experiencing symptomatic heart failure with an ejection fraction ranging from 25% to 45% and a QRS duration of less than 130 ms, who are not suitable candidates for cardiac resynchronization therapy, CCM offers a viable treatment option. Even though promising results in specific HF subgroups have been published, further studies are needed to understand the role of CCM in tailored treatment for heart failure. Moreover, the role of multimodality imaging in lead placement and prognostic stratification in CCM patients should be further investigated. This review aims to summarize the main pathophysiological evidence related to the use of CCM and to highlight its role as a possible additional weapon in tailored treatment for specific subgroups of patients with heart failure.

Physiological and Molecular Responses of Red Amaranth (Amaranthus cruentus L.) and Green Amaranth (Amaranthus hypochondriacus L.) to Salt Stress

AbstractSalinization, as a serious climate change phenomenon, continues to cause critical issues for soils and crops. Abundance of genetic diversity of plants could contribute in solving the impacts of salinity. However, the relations between physiological and molecular traits of plant species need deep investigation and interpretation. Pot experiments were conducted in the greenhouse to investigate the difference in behavior between two amaranth species when they were beforehand subjected to salinity-stress conditions, specifically on some specific physiological and molecular characteristics. After 45 days from transplanting, salt stress was induced using a 150 mM sodium chloride solution. Treatments were arranged in randomized complete block design using three replications. After 0, 2, 6, 10, and 24 h, samples were collected to evaluate physiological data as well as diversity of gene expression. The samples were immediately frozen in liquid nitrogen and stored in -80⁰ C ultralow temperature refrigerators. Findings revealed that the red amaranth species (Amaranthus cruentus) was more tolerant to saline stress than the green amaranth species (Amaranthus hypochondriacus). Result data revealed that malondialdehyde (MDA) content in the red amaranth increased after 2 h then decreased (after 6 and 10 h) before rising again after 24 h. In the green amaranth, MDA content initially decreased after 2 h before increasing and later decreasing in a zigzag pattern ending in an increase after 24 h. There was an initial steep rise in proline content of green amaranth after 2 h which continued to still rise moderately till 24 h. In the red amaranth the initial rise in proline continued after 2, 6 and 10 h before it stopped. Results also showed that red amaranth gave higher value of superoxide dismutase (SOD) activity as compared with green amaranth in all tested salinity exposure times. The investigation on the expression of four genes assessed through quantitative PCR indicated the efficiency of red amaranth in increasing the expression of SOS1, HKT1, NHX1, and DGR2 genes, which encode adaptation-related proteins under salinity stress. In summary, the current work demonstrated that red amaranth could be an efficient genetic resource in improving salt-tolerant genotypes belonging to Amaranthus genus.

Transcriptomic and Methylomic Analyses Show Significant Shifts in Biosynthetic Processes and Reduced Intrapopulation Gene Expression Variance in PAH-Adapted Atlantic Killifish.

Environmental contaminants pose a significant selection pressure across taxa, potentiating evolved resistance to chemicals. However, rapid evolution may alter molecular and physiological homeostasis leading to trade-offs. To elucidate molecular underpinnings of evolved chemical resistance, we compared liver gene expression and methylation profiles in polycyclic aromatic hydrocarbon (PAH)-adapted Atlantic killifish (Fundulus heteroclitus) in the Republic site (RP), Elizabeth River, Virginia with PAH-sensitive Kings Creek (KC) fish. We found 1607 differentially expressed and 2252 alternatively spliced genes between RP and KC, with highly enriched genes involving lipid and amino acid metabolism, respectively. While 308 genes had differentially methylated regions, only 13 of these genes were differentially expressed. The aryl hydrocarbon receptor 2b gene (ahr2b) was differentially methylated and expressed, as well as alternatively spliced signifying its critical role in mediating PAH tolerance. Notably, the intrapopulation coefficient of variation (CoV) was lower in 82% of 17,566 expressed genes in RP fish compared to KC fish. Among other pathways, these genes with low CoV were highly enriched in bioenergetic processes inferring reduced metabolic physiological variation as a population in RP fish. Altered metabolic gene expression and overall reduced gene expression variance in RP fish warrant further studies on fitness trade-offs including altered susceptibility to other stressors associated with rapid adaptation to anthropogenic pressures.

Regional neural functional efficiency across schizophrenia, bipolar disorder, and major depressive disorder: a transdiagnostic resting-state fMRI study

Abstract Background Major psychiatric disorders (MPDs) are delineated by distinct clinical features. However, overlapping symptoms and transdiagnostic effectiveness of medications have challenged the traditional diagnostic categorisation. We investigate if there are shared and illness-specific disruptions in the regional functional efficiency (RFE) of the brain across these disorders. Methods We included 364 participants (118 schizophrenia [SCZ], 80 bipolar disorder [BD], 91 major depressive disorder [MDD], and 75 healthy controls [HCs]). Resting-state fMRI was used to caclulate the RFE based on the static amplitude of low-frequency fluctuation, regional homogeneity, and degree centrality and corresponding dynamic measures indicating variability over time. We used principal component analysis to obtain static and dynamic RFE values. We conducted functional and genetic annotation and enrichment analysis based on abnormal RFE profiles. Results SCZ showed higher static RFE in the cortico-striatal regions and excessive variability in the cortico-limbic regions. SCZ and MDD shared lower static RFE with higher dynamic RFE in sensorimotor regions than BD and HCs. We observed association between static RFE abnormalities with reward and sensorimotor functions and dynamic RFE abnormalities with sensorimotor functions. Differential spatial expression of genes related to glutamatergic synapse and calcium/cAMP signaling was more likely in the regions with aberrant RFE. Conclusions SCZ shares more regions with disrupted functional integrity, especially in sensorimotor regions, with MDD rather than BD. The neural patterns of these transdiagnostic changes appear to be potentially driven by gene expression variations relating to glutamatergic synapses and calcium/cAMP signaling. The aberrant sensorimotor, cortico-striatal, and cortico-limbic integrity may collectively underlie neurobiological mechanisms of MPDs.

Recent Therapeutic Advancements for Gaucher Disease

AbstractGaucher Disease (GD) is a well‐known lysosomal storage disease resulting from mutations in the GBA1 gene. GD exhibits a range of clinical manifestations, each with unique symptoms and severity levels. This review explores the genetic foundations of GD, highlighting the significance of Glucocerebrosidase (GCase) deficiency, resulting in the skeletal complications associated with GD, such as osteonecrosis, fractures, and bone pain, all of which significantly negatively influence the quality of life for patients. Over 700 mutations in the GBA1 gene are found to cause variations in gene expression in GD, indicating the disease's complexity and the need for continued research. Early diagnosis and prognosis evaluation depend heavily on diagnostic approaches integrating laboratory assessments, genetic testing, and clinical symptoms. Treatment strategies like enzyme replacement therapy (ERT) and substrate reduction therapy (SRT) have advanced, but issues like high costs and invasiveness still exist. This review focuses on novel therapeutic approaches that show promise in treating GD, including gene and cell‐based therapies, pharmacological chaperone therapy (PCT), and drug delivery via nanoparticles. Finally, discussions on current clinical trials, limitations of the advanced therapies, and future scope are summarized.

Analysis of genotype effects and inter-individual variability in iPSC-derived trisomy 21 neural progenitor cells.

Trisomy of human chromosome 21 (T21) gives rise to Down syndrome (DS), the most frequent live-born autosomal aneuploidy. T21 triggers genome-wide transcriptomic alterations that result in multiple atypical phenotypes with highly variable penetrance and expressivity in individuals with DS. Many of these phenotypes, including atypical neurodevelopment, emerge prenatally. To enable in vitro analyses of the cellular and molecular mechanisms leading to the neurological alterations associated with T21, we created and characterized a panel of genomically diverse T21 and euploid induced pluripotent stem cells (iPSCs). We subsequently differentiated these iPSCs to generate a panel of neural progenitor cells (NPCs). Alongside characterizing genotype effects from T21, we found that T21 NPCs showed inter-individual variability in growth rates, oxidative stress, senescence characteristics, and gene and protein expression. Pathway enrichment analyses of T21 NPCs identified vesicular transport, DNA repair, and cellular response to stress pathways. These results demonstrate T21-associated variability at the cellular level and suggest that cell lines from individuals with DS should not solely be analyzed as a homogenous population. Examining large cohorts of genetically diverse samples may more fully reveal the effects of aneuploidy on transcriptomic and phenotypic characteristics in T21 cell types. A panel of genomically diverse T21 and euploid induced pluripotent stem cells (iPSCs) were created and subsequently differentiated into neural progenitor cells (NPCs). T21 NPCs showed reduced growth, increased oxidative stress, and inter-individual variability in gene and protein expression. This inter-individual variability suggests that studies with large cohorts of genetically diverse T21 samples may more fully reveal the effects of aneuploidy.

Striatal dopamine gene network moderates the effect of early adversity on the risk for adult psychiatric and cardiometabolic comorbidity

Cardiometabolic and psychiatric disorders often co-exist and share common early life risk factors, such as low birth weight. However, the biological pathways linking early adversity to adult cardiometabolic/psychiatric comorbidity remain unknown. Dopamine (DA) neurotransmission in the striatum is sensitive to early adversity and influences the development of both cardiometabolic and psychiatric diseases. Here we show that a co-expression based polygenic score (ePGS) reflecting individual variations in the expression of the striatal dopamine transporter gene (SLC6A3) network significantly interacts with birth weight to predict psychiatric and cardiometabolic comorbidities in both adults (UK Biobank, N = 225,972) and adolescents (ALSPAC, N = 1188). Decreased birth weight is associated with an increased risk for psychiatric and cardiometabolic comorbidities, but the effect is dependent on a striatal SLC6A3 ePGS, that reflects individual variation in gene expression of genes coexpressed with the SLC6A3 gene in the striatum. Neuroanatomical analyses revealed that SNPs from the striatum SLC6A3 ePGS were significantly associated with prefrontal cortex gray matter density, suggesting a neuroanatomical basis for the link between early adversity and psychiatric and cardiometabolic comorbidity. Our study reveals that psychiatric and cardiometabolic diseases share common developmental pathways and underlying neurobiological mechanisms that includes dopamine signaling in the striatum.

Deciphering FUR-regulated gene networks in Klebsiella pneumoniae using FUR knockout mutant

Klebsiella pneumoniae is a nosocomial pathogen causing life-threatening infections worldwide. It possesses many virulence properties and the ferric uptake regulator (FUR) is the transcription factor that regulates the expression of various genes in K. pneumoniae. FUR binds to a conserved 19 bp sequence, called the FUR box, for either positive or negative regulation of the gene. FUR alters gene expression according to iron availability and also participates in virulence, colonization & toxin secretion in K. pneumoniae. FUR deletion mutant is an interesting model to understand the virulence factors. In the present study, we identified the genes containing putative FUR boxes (>50 % sequence homology) from the genome of K. pneumoniae M33. FUR deletion mutant for K. pneumoniae M33 was created using lambda red recombinase system using the plasmids- pACBSR-hyg, pMDIAI, and pFLP-hyg. The mutant (M33∆FUR) was characterized using various assays like CAS assay, string test, crystal violet assay to access siderophore production, capsule synthesis and biofilm formation respectively. FUR box was present upstream of 18 genes with distinct functions. In the FUR knockout mutant, M33∆FUR an increase in expression of iron transport and siderophore related genes feoC, fhuA, fepB and fes was observed whereas genes feoA, cirA, fecA, fepA and entC were down-regulated. Genes related to biofilm (fimA and mrkD) were downregulated whereas genes related to capsular polysaccharide (rcsA and rcsB) were upregulated upon FUR deletion. Among other genes murG and sucA were downregulated and priB and srlB were upregulated upon FUR deletion. This study shows that FUR regulates many genes involved in virulence, either positively or negatively.

Inhibition of Bruton's tyrosine kinase with PD-1 blockade modulates T cell activation in solid tumors.

BACKGROUNDInhibition of Bruton's tyrosine kinase with ibrutinib blocks the function of myeloid-derived suppressor cells (MDSC). The combination of ibrutinib and nivolumab was tested in patients with metastatic solid tumors.METHODSSixteen patients received ibrutinib 420 mg p.o. daily with nivolumab 240 mg i.v. on days 1 and 15 of a 28-day cycle. The effect of ibrutinib and nivolumab on MDSC, the immune profile, and cytokine levels were measured. Single-cell RNA-Seq and T cell receptor sequencing of immune cells was performed.RESULTSCommon adverse events were fatigue and anorexia. Four patients had partial responses and 4 had stable disease at 3 months (average 6.5 months, range 3.5-14.6). Median overall survival (OS) was 10.8 months. Seven days of Bruton's tyrosine kinase (BTK) inhibition significantly increased the proportion of monocytic-MDSC (M-MDSC) and significantly decreased chemokines associated with MDSC recruitment and accumulation (CCL2, CCL3, CCL4, CCL13). Single-cell RNA-Seq revealed ibrutinib-induced downregulation of genes associated with MDSC-suppressive function (TIMP1, CXCL8, VEGFA, HIF1A), reduced MDSC interactions with exhausted CD8+ T cells, and decreased TCR repertoire diversity. The addition of nivolumab significantly increased circulating NK and CD8+ T cells and increased CD8+ T cell proliferation. Exploratory analyses suggest that MDSC and T cell gene expression and TCR repertoire diversity were differentially affected by BTK inhibition according to patient response.CONCLUSIONIbrutinib and nivolumab were well tolerated and affected MDSC and T cell function in patients with solid metastatic tumors.TRIAL REGISTRATIONClinicalTrials.gov NCT03525925.FUNDINGNIH; National Cancer Institute Cancer; National Center for Advancing Translational Sciences; Pelotonia.

Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies

A comprehensive endoscopic small and large intestinal untargeted step biopsy procedure was conducted to compare gene expression between the normal intestinal mucosa of healthy individuals and that of patients with colorectal tumors. From 78 participants (healthy individuals [n = 17], patients with colorectal conventional adenomas [n = 6], patients with Tis–T1 colorectal cancer [n = 41], patients with T2–4 colorectal cancer [n = 14]), biopsies of normal mucosa of the terminal ileum, right-sided colon (cecum and ascending colon), and left-sided colorectum (descending colon, sigmoid colon, and rectum) were obtained using a lower gastrointestinal endoscope. RNA was extracted from all samples, and total transcriptome sequencing was performed. Transcriptome data from 388 samples was analyzed. DNA was also extracted from tumor biopsy tissues and analyzed for whole-exome sequencing. In healthy individuals, gene expression differed significantly among the terminal ileum, right-sided colon, and left-sided colorectum, presumably linked to embryological factors. There were differences in gene expression in the normal mucosa in colorectal cancer patients, compared to healthy controls. Patients with tumors, especially T2–4 colorectal cancer, showed considerable variation in gene expression in non-tumor tissues, even in the terminal ileum distant from the tumor site. Based on endoscopic biopsies, the results imply cancer-predisposing conditions in seemingly normal tissues. The present study points to the importance of small intestine and cancer-predisposing conditions in the colon of colorectal cancer patients, with possible implications for developing novel immunotherapy and other therapeutic modalities.

Simultaneous single-nucleus RNA sequencing and single-nucleus ATAC sequencing of neuroblastoma cell lines

Neuroblastoma is the most common extracranial solid tumor in children, and a leading cause of childhood cancer deaths. All neuroblastomas arise from neural crest-derived sympathetic neuronal progenitors, but numerous mutations, the most common of which is MYCN amplification, give rise to these lesions. Epigenetic aberrations also play a role in oncogenesis and tumor progression. To better understand biologic diversity of neuroblastomas, we performed joint single-nucleus ATAC sequencing and single-nucleus RNA sequencing on six neuroblastoma cell lines, three of which are MYCN amplified. After standard filtering for high-quality nuclei, we obtained chromatin accessibility and transcript abundance data from 41,733 neuroblastoma tumor cells. Preliminary analysis reveals significant diversity in chromatin landscape and gene expression across neuroblastoma cell lines. This dataset is a valuable resource for studying the transcriptional and epigenetic mechanisms of this deadly childhood disease.