AIM: To investigate the change in eukaryotic gene expression profile in Caco-2 cells after infection with strains of Escherichia coli and commensal probiotic bacteria. METHODS: A 19 200 gene/expressed sequence tag gen...AIM: To investigate the change in eukaryotic gene expression profile in Caco-2 cells after infection with strains of Escherichia coli and commensal probiotic bacteria. METHODS: A 19 200 gene/expressed sequence tag gene chip was used to examine expression of genes after infection of Caco-2 cells with strains of normal flora E. coli,Lactobacillus plantarum,and a combination of the two. RESULTS: The cDNA microarray revealed up-regulation of 155 and down-regulation of 177 genes by E. coli . L. plantarum up-regulated 45 and down-regulated 36 genes. During mixed infection,27 genes were up-regulated and 59 were down-regulated,with nullification of stimulatory/inhibitory effects on most of the genes. Expression of several new genes was noted in this group. CONCLUSION: The commensal bacterial strains used in this study induced the expression of a large number of genes in colonocyte-like cultured cells and changed the expression of several genes involved in important cellular processes such as regulation of transcription,protein biosynthesis,metabolism,cell adhesion,ubiquitination,and apoptosis. Such changes induced by the presence of probiotic bacteria may shape the physiologic and pathologic responses they trigger in the host.展开更多
AIM To identify chromosomal copy number aberrations(CNAs) in early-stage hepatocellular carcinoma(HCC) and analyze whether they are correlated with patient prognosis.METHODS One hundred and twenty patients with early-...AIM To identify chromosomal copy number aberrations(CNAs) in early-stage hepatocellular carcinoma(HCC) and analyze whether they are correlated with patient prognosis.METHODS One hundred and twenty patients with early-stage HCC were enrolled in our study, with the collection of formalin fixed, paraffin-embedded(FFPE) specimens and clinicopathological data. Tumor areas were marked by certified pathologists on a hematoxylin and eosinstained slide, and cancer and adjacent non-cancerous tissues underwent extraction of DNA, which was analyzed with the Affymetrix Onco Scan platform to assess CNAs and loss of heterozygosity(LOH). Ten individuals with nonmalignant disease were used as the control group. Another cohort consisting of 40 patients with stage Ⅰ/Ⅱ HCC were enrolled to analyze gene expression and to correlate findings with the Onco Scan data.RESULTS Copy number amplifications occurred at chromosomes 1 q21.1-q44 and 8 q12.3-24.3 and deletions were found at 4 q13.1-q35.2, 8 p 23.2-21.1, 16 q23.3-24.3, and 17 p13.3-12, while LOH commonly occurred at 1 p32.3, 3 p21.31, 8 p23.2-21.1, 16 q22.1-24.3, and 17 p 13.3-11 in early-stage HCC. Using Cox regression analysis, we also found that a higher percentage of genome change(≥ 60%) was an independent factor for worse prognosis in early-stage HCC(P = 0.031). Among the 875 genes in the Onco Scan Gene Chip, six were independent predictors of worse disease-free survival, of which three were amplified(MYC, ELAC2, and SYK) and three were deleted(GAK, MECOM, and WRN). Further, patients with HCC who exhibited ≥ 3 CNAs involving these six genes have worse outcomes compared to those who had < 3 CNAs(P < 0.001). Similarly, Asian patients with stage I HCC from The Cancer Genome Atlas harboring CNAs with these genes were also predicted to have poorer outcomes.CONCLUSION Patients with early-stage HCC and increased genome change or CNAs involving MYC, ELAC2, SYK, GAK, MECOM, or WRN are at risk for poorer outcome after resection.展开更多
Circulating tumor cells (CTC) are rarely detected in the blood of cancer patients, even though they are a direct harbinger of eventual patient demise. We developed an innovative CTC culture technology to allow more se...Circulating tumor cells (CTC) are rarely detected in the blood of cancer patients, even though they are a direct harbinger of eventual patient demise. We developed an innovative CTC culture technology to allow more sensitive isolation, expansion, and characterization of viable colonies from patient blood. In this assay, the entire leukocyte fraction from 10 ml of anticoagulated patient blood is placed into culture medium without any pre-selection. After 16 days in culture, CTC derived colonies are counted. As a proof-of-principle, blood samples from 58 Stage IIa-IV melanoma patients were tested. Ninety percent of these samples grew colonies. The colony numbers ranged from 0 - 308 (mean 63 ± 9.5 SEM). Ten normal volunteers had virtually no growth (mean 0.5 ± 1.4 colonies). Colonies were harvested using a micropipette for characterization. Tumor-cell containing spheroids were embedded in paraffin, sectioned, and stained with melanoma-specific mAb for histologic characterization. MITF proved to be the most consistent immunostain that identified melanoma cells in these colonies. A host-cell component in colonies was also identified using CD68 and CD43 mAb staining. Following enzymatic dissociation of colonies, a variety of immunostains were tested. Papanicolau staining proved most useful for identifying the abnormal nuclei of tumor cells. Flow cytometry could readily distinguish host and tumor cell populations based on DNA content and forward/side scatter in dissociated colonies. The stem cell marker ALDH1A1 associated with the aneuploid population, but CD45 was expressed on both diploid and aneuploid cells. The ability to repeatedly isolate CTC derived colonies from cancer patient blood samples opens the door to a novel type of long-term clinical monitoring. This novel CTC culture technology may prove useful to perform molecular characterization, assessment of treatment response, and testing of drug sensitivity and resistance in patients during treatment.展开更多
X-linked hypophosphatemia(XLH)represents the most common form of familial hypophosphatemia.Although significant advances have been made in the treatment of bone pathology,patients undergoing therapy continue to experi...X-linked hypophosphatemia(XLH)represents the most common form of familial hypophosphatemia.Although significant advances have been made in the treatment of bone pathology,patients undergoing therapy continue to experience significantly decreased oral health-related quality of life.The following study addresses this persistent oral disease by further investigating the effect of DMP1 expression on the differentiation of XLH dental pulp cells.Dental pulp cells were isolated from the third molars of XLH and healthy controls and stable transduction of full-length human DMP1 were achieved.RNA sequencing was performed to evaluate the genetic changes following the induction of odontogenic differentiation.RNAseq data shows the upregulation of inhibitors of the canonical Wnt pathway in XLH cells,while constitutive expression of full-length DMP1 in XLH cells reversed this effect during odontogenic differentiation.These results imply that inhibition of the canonical Wnt pathway may contribute to the pathophysiology of XLH and suggest a new therapeutic strategy for the management of oral disease.展开更多
Metastatic Merkel Cell carcinoma (MCC) is a highly unusual and aggressive skin cancer that presents as a small, pink to violet skin lesion and metastasizes early in its growth. Metastatic MCC is generally treated with...Metastatic Merkel Cell carcinoma (MCC) is a highly unusual and aggressive skin cancer that presents as a small, pink to violet skin lesion and metastasizes early in its growth. Metastatic MCC is generally treated with small cell lung cancer chemotherapy regimens, because the tumor consists of neuroendocrine cells, but patients generally do not have durable responses. The pathogenesis of MCC has recently been attributed to the Merkel Cell polyoma virus. This virus activates the cellular retinoblastoma oncoprotein and cell cycle machinery, triggering continual cellular proliferation. A 77-year-old man developed extensive MCC metastases, involving more than one fourth of his scalp and numerous cervical lymph nodes. Following failure of initial chemotherapy and radiation, effective palliation was achieved by using a sequence of electron-beam radiotherapy, low dose gemcitabine, and etoposide, resulting in significant periods of tumor regression and prolonged survival. A novel circulating tumor cell (CTC) culture assay was performed on four separate clinic visits during the treatment period. Tumor colonies were cultured from the patient’s peripheral blood and CTC colony counts were correlated with clinical treatment response. Not only did the patient respond to palliative cell cycle directed chemotherapy and electron beam radiation, but we demonstrated that CTC can be cultured from peripheral blood of MCC patients and serve as a predictive marker to monitor treatment response.展开更多
Genetically engineered mouse(GEM)models are commonly used in biomedical research.Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff.Beca...Genetically engineered mouse(GEM)models are commonly used in biomedical research.Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff.Because of these reasons,most research institutes set up centralized core facilities where custom GEMs are created for research groups.Researchers,on the other hand,when they begin thinking about generating GEMs for their research,several questions arise in their minds.For example,what type of model(s)would be best useful for my research,how do I design them,what are the latest technologies and tools available for developing my model(s),and finally how to breed GEMs in my research.As there are several considerations and options in mouse designs,and as it is an expensive and time-consuming endeavor,careful planning upfront can ensure the highest chance of success.In this article,we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s)for their work.展开更多
Islets from RIP-PDE3B mice, exhibiting β-cell specific overexpression of the cAMP/cGMP-degrading enzyme phosphodiesterase 3B (PDE3B) and dysregulated insulin secretion, were subjected to microarray analysis. We show ...Islets from RIP-PDE3B mice, exhibiting β-cell specific overexpression of the cAMP/cGMP-degrading enzyme phosphodiesterase 3B (PDE3B) and dysregulated insulin secretion, were subjected to microarray analysis. We show that osteopontin (OPN) mRNA is increased in a dose-dependent manner in islets from RIP-PDE3B mice, as compared to wild-type islets. In addition, in silico analysis shows that PDE3B and OPN are interacting. Furthermore, OPN interacts with protein kinase CK2 ina distinct submodule of the protein-protein interaction network. We studied PDE3B and OPN proteins and, in some cases, also PDE1B and PDE4C, under conditions of relevance for insulin secretion. In the presence of forskolin, PDE inhibitors, insulin, or a protein kinase CK2 inhibitor, similar alterations in protein levels of PDE3B and OPN are shown. In summary, results from using a number of strategies demonstrate a connection between PDE3B and OPNas well as a role for protein kinase CK2 inpancreatic β-cells.展开更多
Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was th...Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was therefore to search for DNA regions (copy number variations, CNVs) as biomarkers associated to genetic susceptibility for early risk predictions of colorectal cancer. Such sequence alterations could provide additional information on phenotypic grouping of patients. Material and Methods: High resolution 105K oligonucleotide microarrays were used in search for CNV loci in DNA from tumor-free colon mucosa at primary operations for colon cancer in 60 unselected patients in comparison to DNA in buffy coat cells from 44 confirmed tumor-free and healthy blood donors. Array-detected CNVs were confirmed by Multiplex ligation-dependent probe amplification (MLPA). Results: A total number of 205 potential CNVs were present in DNA from colon mucosa. 184 (90%) of the 205 potential CNVs had been identified earlier in mucosa DNA from healthy individuals as reported to the Database of Genomic Variants. Remaining 21 (10%) CNVs were potentially novel sites. Two CNVs (3q23 and 10q21.1) were significantly related to colon cancer, but not confirmed in buffy coat DNA from the cancer patients. Conclusion: Our study reveals two CNVs that indicate increased risk for colon cancer;These DNA alterations may have? been acquired by colon stem cells with subsequent appearance among epithelial mucosa cells. Impact: Certain mucosa CNV alterations may indicate individual susceptibility for malignant transformation in relationship to intestinal toxins and bacterial growth.展开更多
Exposure to disinfection by-products（DBP） such as trihalomethanes（THM） in swimming pools has been linked to adverse health effects in humans, but their biological mechanisms are unclear. We evaluated short-term ch...Exposure to disinfection by-products（DBP） such as trihalomethanes（THM） in swimming pools has been linked to adverse health effects in humans, but their biological mechanisms are unclear. We evaluated short-term changes in blood gene expression of adult recreational swimmers after swimming in a chlorinated pool. Volunteers swam 40 min in an indoor chlorinated pool. Blood samples were drawn and four THM（chloroform,bromodichloromethane, dibromochloromethane and bromoform） were measured in exhaled breath before and after swimming. Intensity of physical activity was measured as metabolic equivalents（METs）. Gene expression in whole blood m RNA was evaluated using Illumina Human HT-12v3 Expression-Bead Chip. Linear mixed models were used to evaluate the relationship between gene expression changes and THM exposure. Thirty-seven before-after pairs were analyzed. The median increase from baseline to after swimming were： 0.7 to 2.3 for MET, and 1.4 to 7.1 μg/m^3 for exhaled total THM（sum of the four THM）.Exhaled THM increased on average 0.94 μg/m^3 per 1 MET. While 1643 probes were differentially expressed post-exposure. Of them, 189 were also associated with exhaled levels of individual/total THM or MET after False Discovery Rate. The observed associations with the exhaled THM were low to moderate（Log-fold change range：-0.17 to 0.15）. In conclusion, we identified short-term gene expression changes associated with swimming in a pool that were minor in magnitude and their biological meaning was unspecific. The high collinearity between exhaled THM levels and intensity of physical activity precluded mutually adjusted models with both covariates. These exploratory results should be validated in future studies.展开更多
Activating PIK3CA mutations,present in up to 40%of hormone receptor-positive(HR^(+)),human epidermal growth factor receptor 2-negative(Her2^(-))breast cancer(BC)patients,can be effectively targeted with the alpha isof...Activating PIK3CA mutations,present in up to 40%of hormone receptor-positive(HR^(+)),human epidermal growth factor receptor 2-negative(Her2^(-))breast cancer(BC)patients,can be effectively targeted with the alpha isoform-specific Pl3K inhibitor Alpelisib.This treatment significantly improves outcomes for HR^(+),Her2^(-),and PIK3CA-mutated metastatic BC patients.However,acquired resistance,often due to aberrant activation of the mTOR complex 1(mTORC1)pathway,remains a significant clinical challenge.Our study,using in vitro and orthotopic xenograft mouse models,demonstrates that constitutively active mTORC1 signaling renders PI3K inhibitor-resistant BC exquisitely sensitive to various drugs targeting cancer metabolism.Mechanistically,mTORC1 suppresses the induction of autophagy during metabolic perturbation,leading to energy stress,a critical depletion of aspartate,and ultimately cell death.Supporting this mechanism,BC cells with CRISPR/Cas9-engineered knockouts of canonical autophagy genes showed similar vulnerability to metaboliclly active drugs InBC patients,high mTORC1 activity,indicated by 4E-BP1^(T37/46) phosphorylation correlated with p62 accumulation,a sign of impaired autophagy.Together,these markers predicted poor overall survival in multiple BC subgroups.Our findings reveal that aberrant mTORC1 signaling,a common cause of PI3K inhibitor resistance in BC,creates a druggable metabolic vulnerability by suppressing autophagy.Additionall,the combination of 4E-BP1^(T37/46) phosphorylation and p62 accumulation serves as a biomarker for poor overall survival,suggesting their potential utility in identifying BC patients who may benefit from metabolic therapies.展开更多
Recent studies reveal a critical role of tumor cell-released extracellular vesicles(EVs)in pancreatic cancer(PC)progression.However,driver genes that direct EV function,the EV-recipient cells,and their cellular respon...Recent studies reveal a critical role of tumor cell-released extracellular vesicles(EVs)in pancreatic cancer(PC)progression.However,driver genes that direct EV function,the EV-recipient cells,and their cellular response to EV uptake remain to be identified.Therefore,we studied the role of Bcl-2-associated-anthanogene 6(BAG6),a regulator of EV biogenesis for cancer progression.We used a Cre recombinase/LoxP-based reporter system in combination with single-cell RNA sequencing to monitor in vivo EV uptake and tumor microenvironment(TME)changes in mouse models for pancreatic ductal adenocarcinoma(PDAC)in a Bag6 pro-or deficient background.In vivo data were validated using mouse and human organoids and patient samples.Our data demonstrated that Bag6-deficient subcutaneous and orthotopic PDAC tumors accelerated tumor growth dependent on EV release.Mechanistically,this was attributed to mast cell(MC)activation via EV-associated IL33.Activated MCs promoted tumor cell proliferation and altered the composition of the TME affecting fibroblast polarization and immune cell infiltration.Tumor cell proliferation and fibroblast polarization were mediated via the MC secretome containing high levels of PDGF and CD73.Patients with high BAG6 gene expression and high protein plasma level have a longer overall survival indicating clinical relevance.The current study revealed a so far unknown tumor-suppressing activity of BAG6 in PDAC.Bag6-deficiency allowed the release of EV-associated IL33 which modulate the TME via MC activation promoting aggressive tumor growth.MC depletion using imatinib diminished tumor growth providing a scientific rationale to consider imatinib for patients stratified with low BAG6 expression and high MC infiltration.展开更多
Although mechanisms of telomere protection are well-defined in differentiated cells,how stem cells sense and respond to telomere dysfunction,in particular telomeric double-strand breaks(DSBs),is poorly characterized.H...Although mechanisms of telomere protection are well-defined in differentiated cells,how stem cells sense and respond to telomere dysfunction,in particular telomeric double-strand breaks(DSBs),is poorly characterized.Here,we report the DNA damage signaling,cell cycle,and transcriptome changes in human induced pluripotent stem cells(iPSCs)in response to telomere-internal DSBs.We engineer human iPSCs with an inducible TRF1-FokI fusion protein to acutely induce DSBs at telomeres.Using this model,we demonstrate that TRF1-FokI DSBs activate an ATR-dependent DNA damage response,which leads to p53-independent cell cycle arrest in G2.Using CRISPR–Cas9 to cripple the catalytic domain of telomerase reverse transcriptase,we show that telomerase is largely dispensable for survival and lengthening of TRF1-FokI-cleaved telomeres,which instead are effectively repaired by robust homologous recombination(HR).In contrast to HR-based telomere maintenance in mouse embryonic stem cells,where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths,HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length,which is compatible with sustained survival of the cells over several days of TRF1-FokI induction.Our findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage.展开更多
Acute myeloid leukemia(AML)is a common hematological malignancy with overall poor prognosis.Exploring novel targets is urgent and necessary to improve the clinical outcome of relapsed and refractory(RR)AML patients.Th...Acute myeloid leukemia(AML)is a common hematological malignancy with overall poor prognosis.Exploring novel targets is urgent and necessary to improve the clinical outcome of relapsed and refractory(RR)AML patients.Through clinical specimens,animal models and cell-level studies,we explored the specific mechanism of 3-hydroxy-3-methylglutaryl coenzyme A synthase 1(HMGCS1)in AML and the mechanism of targeting HMGCS1 to attenuate cell proliferation,increase chemotherapy sensitivity and improve the occurrence and development of AML.Here,we reveal that HMGCS1 is overexpressed in RR patients and negatively related to overall survival(OS).Knocking out HMGCS1 in AML cells attenuated cell proliferation and increased chemotherapy sensitivity,while stable overexpression of HMGCS1 had the opposite effects.Mechanistically,we identified that knockout of HMGCS1 suppressed mitogen-activated protein kinase(MAPK)pathway activity,while overexpression of HMGCS1 could remarkably enhance the pathway.U0126,a MEK1 inhibitor,offset the effects of HMGCS1 overexpression,indicating that HMGCS1 promotes RR AML through the MAPK pathway.Further,we verified that hymeglusin,a specific inhibitor of HMGCS1,decreases cell growth both in AML cell lines and primary bone marrow cells of AML patients.Furthermore,combination of hymeglusin and the common chemotherapeutic drug cytarabine and adriamycin(ADR)had synergistic toxic effects on AML cells.Our study demonstrates the important role of HMGCS1 in AML,and targeting this protein is promising for the treatment of RR AML.展开更多
RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies...RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.展开更多
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia.This symbiosis called nodulation i...Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia.This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria,as well as the initiation of nodule primordia from root cortical,endodermal,and pericycle cells,leading to the development of a new root organ,the nodule,where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant.Here,we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq(sNucRNA-seq)profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots.A gene expression map of the Medicago root was generated,comprising 25 clusters,which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes.A focus on root hair,cortex,endodermis,and pericycle cell types,showing the strongest differential regulation in response to a short-term(48 h)rhizobium inoculation,revealed not only known genes and functional pathways,validating the sNucRNA-seq approach,but also numerous novel genes and pathways,allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.展开更多
De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carri...De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,respectively.We then determined an efficient way to yield an optimal overall assembly using three different strategies.We first assembled brain and cell line transcriptome using a single k-mer length.Next we tested a range of values of k-mer length and coverage cutoff in assembling.Lastly,we combined the assembled contigs from a range of k values to generate a final assembly.By comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.展开更多
Colorectal cancer(CRC)is a predominant life-threatening cancer,with liver and peritoneal metastases as the primary causes of death.Intestinal inflammation,a known CRC risk factor,nurtures a local inflammatory environm...Colorectal cancer(CRC)is a predominant life-threatening cancer,with liver and peritoneal metastases as the primary causes of death.Intestinal inflammation,a known CRC risk factor,nurtures a local inflammatory environment enriched with tumor cells,endothelial cells,immune cells,cancer-associated fibroblasts,immunosuppressive cells,and secretory growth factors.The complex interactions of aberrantly expressed cytokines,chemokines,growth factors,and matrix-remodeling enzymes promote CRC pathogenesis and evoke systemic responses that affect disease outcomes.Mounting evidence suggests that these cytokines and chemokines play a role in the progression of CRC through immunosuppression and modulation of the tumor microenvironment,which is partly achieved by the recruitment of immunosuppressive cells.These cells impart features such as cancer stem cell-like properties,drug resistance,invasion,and formation of the premetastatic niche in distant organs,promoting metastasis and aggressive CRC growth.A deeper understanding of the cytokineand chemokine-mediated signaling networks that link tumor progression and metastasis will provide insights into the mechanistic details of disease aggressiveness and facilitate the development of novel therapeutics for CRC.Here,we summarized the current knowledge of cytokine-and chemokine-mediated crosstalk in the inflammatory tumor microenvironment,which drives immunosuppression,resistance to therapeutics,and metastasis during CRC progression.We also outlined the potential of this crosstalk as a novel therapeutic target for CRC.The major cytokine/chemokine pathways involved in cancer immunotherapy are also discussed in this review.展开更多
Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological health.However,collection of vaginal specimens is invasive and requires previous clinical training or the involveme...Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological health.However,collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained clinician.In contrast,urine sample collection is routine and noninvasive and does not require involvement of a clinician.We sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal microbiome.Paired urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic profiling.We examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes.A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal microbiomes.Moreover,the relative abundances of common vaginal taxa were linearly correlated with those in the paired urogenitalmicrobiomes.These similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginalmicrobiome with likely clinical applications.Finally,a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.展开更多
This work examines the physiologic basis of stress tolerance in bacterial strains of the genus Rhodanobacter that dominate in the acidic and highly metal contaminated near-source subsurface zone of the Oak Ridge Integ...This work examines the physiologic basis of stress tolerance in bacterial strains of the genus Rhodanobacter that dominate in the acidic and highly metal contaminated near-source subsurface zone of the Oak Ridge Integrated Field Research Challenge(ORIFRC)site.Tolerance of R.denitrificans to levels of different stresses were studied in synthetic groundwater medium and R2A broth.Two strains of R.denitrificans,strains 2APBS1T and 116-2,tolerate low to circumneutral pH(4–8),high Uranium(1 mmol/L),elevated levels of nitrate(400 mmol/L)and high NaCl(2.5%).A combination of physiologic traits,such as growth at low pH,increased growth in the presence of high organics concentration,and tolerance of high concentrations of nitrate,NaCl and heavy metals is likely responsible for dominance of Rhodanobacter at the ORIFRC site.Furthermore,extended incubation times and use of low carbon media,better approximating site groundwater conditions,are critical for accurate determination of stress responses.This study expands knowledge of the ecophysiology of bacteria from the genus Rhodanobacter and identifies methodological approaches necessary for acquiring accurate tolerance data.展开更多
基金Supported by the Department of Pediatrics and GCRC (M01- RR-16500), University of Maryland Baltimore, with partial funding from NIH grants UO1 HD 40574 and RO1 HD 053719
文摘AIM: To investigate the change in eukaryotic gene expression profile in Caco-2 cells after infection with strains of Escherichia coli and commensal probiotic bacteria. METHODS: A 19 200 gene/expressed sequence tag gene chip was used to examine expression of genes after infection of Caco-2 cells with strains of normal flora E. coli,Lactobacillus plantarum,and a combination of the two. RESULTS: The cDNA microarray revealed up-regulation of 155 and down-regulation of 177 genes by E. coli . L. plantarum up-regulated 45 and down-regulated 36 genes. During mixed infection,27 genes were up-regulated and 59 were down-regulated,with nullification of stimulatory/inhibitory effects on most of the genes. Expression of several new genes was noted in this group. CONCLUSION: The commensal bacterial strains used in this study induced the expression of a large number of genes in colonocyte-like cultured cells and changed the expression of several genes involved in important cellular processes such as regulation of transcription,protein biosynthesis,metabolism,cell adhesion,ubiquitination,and apoptosis. Such changes induced by the presence of probiotic bacteria may shape the physiologic and pathologic responses they trigger in the host.
基金Supported by the Chang Gung Memorial Hospital in Taiwan,No.CMRPG 3C0951-3 and No.CMRPG 3A0671 to Yu MC,and No.CMRPD3F0011 to Tsai CN
文摘AIM To identify chromosomal copy number aberrations(CNAs) in early-stage hepatocellular carcinoma(HCC) and analyze whether they are correlated with patient prognosis.METHODS One hundred and twenty patients with early-stage HCC were enrolled in our study, with the collection of formalin fixed, paraffin-embedded(FFPE) specimens and clinicopathological data. Tumor areas were marked by certified pathologists on a hematoxylin and eosinstained slide, and cancer and adjacent non-cancerous tissues underwent extraction of DNA, which was analyzed with the Affymetrix Onco Scan platform to assess CNAs and loss of heterozygosity(LOH). Ten individuals with nonmalignant disease were used as the control group. Another cohort consisting of 40 patients with stage Ⅰ/Ⅱ HCC were enrolled to analyze gene expression and to correlate findings with the Onco Scan data.RESULTS Copy number amplifications occurred at chromosomes 1 q21.1-q44 and 8 q12.3-24.3 and deletions were found at 4 q13.1-q35.2, 8 p 23.2-21.1, 16 q23.3-24.3, and 17 p13.3-12, while LOH commonly occurred at 1 p32.3, 3 p21.31, 8 p23.2-21.1, 16 q22.1-24.3, and 17 p 13.3-11 in early-stage HCC. Using Cox regression analysis, we also found that a higher percentage of genome change(≥ 60%) was an independent factor for worse prognosis in early-stage HCC(P = 0.031). Among the 875 genes in the Onco Scan Gene Chip, six were independent predictors of worse disease-free survival, of which three were amplified(MYC, ELAC2, and SYK) and three were deleted(GAK, MECOM, and WRN). Further, patients with HCC who exhibited ≥ 3 CNAs involving these six genes have worse outcomes compared to those who had < 3 CNAs(P < 0.001). Similarly, Asian patients with stage I HCC from The Cancer Genome Atlas harboring CNAs with these genes were also predicted to have poorer outcomes.CONCLUSION Patients with early-stage HCC and increased genome change or CNAs involving MYC, ELAC2, SYK, GAK, MECOM, or WRN are at risk for poorer outcome after resection.
文摘Circulating tumor cells (CTC) are rarely detected in the blood of cancer patients, even though they are a direct harbinger of eventual patient demise. We developed an innovative CTC culture technology to allow more sensitive isolation, expansion, and characterization of viable colonies from patient blood. In this assay, the entire leukocyte fraction from 10 ml of anticoagulated patient blood is placed into culture medium without any pre-selection. After 16 days in culture, CTC derived colonies are counted. As a proof-of-principle, blood samples from 58 Stage IIa-IV melanoma patients were tested. Ninety percent of these samples grew colonies. The colony numbers ranged from 0 - 308 (mean 63 ± 9.5 SEM). Ten normal volunteers had virtually no growth (mean 0.5 ± 1.4 colonies). Colonies were harvested using a micropipette for characterization. Tumor-cell containing spheroids were embedded in paraffin, sectioned, and stained with melanoma-specific mAb for histologic characterization. MITF proved to be the most consistent immunostain that identified melanoma cells in these colonies. A host-cell component in colonies was also identified using CD68 and CD43 mAb staining. Following enzymatic dissociation of colonies, a variety of immunostains were tested. Papanicolau staining proved most useful for identifying the abnormal nuclei of tumor cells. Flow cytometry could readily distinguish host and tumor cell populations based on DNA content and forward/side scatter in dissociated colonies. The stem cell marker ALDH1A1 associated with the aneuploid population, but CD45 was expressed on both diploid and aneuploid cells. The ability to repeatedly isolate CTC derived colonies from cancer patient blood samples opens the door to a novel type of long-term clinical monitoring. This novel CTC culture technology may prove useful to perform molecular characterization, assessment of treatment response, and testing of drug sensitivity and resistance in patients during treatment.
基金our funding sources U.S.Department of Health&Human Services,NIH,NIDCR T32 DE018381[Multidisciplinary Oral Science Training Program]DE028193[E.G.]+1 种基金R01 DE031737 and DE 028531[A.G.]the Brodie Endowment Fund。
文摘X-linked hypophosphatemia(XLH)represents the most common form of familial hypophosphatemia.Although significant advances have been made in the treatment of bone pathology,patients undergoing therapy continue to experience significantly decreased oral health-related quality of life.The following study addresses this persistent oral disease by further investigating the effect of DMP1 expression on the differentiation of XLH dental pulp cells.Dental pulp cells were isolated from the third molars of XLH and healthy controls and stable transduction of full-length human DMP1 were achieved.RNA sequencing was performed to evaluate the genetic changes following the induction of odontogenic differentiation.RNAseq data shows the upregulation of inhibitors of the canonical Wnt pathway in XLH cells,while constitutive expression of full-length DMP1 in XLH cells reversed this effect during odontogenic differentiation.These results imply that inhibition of the canonical Wnt pathway may contribute to the pathophysiology of XLH and suggest a new therapeutic strategy for the management of oral disease.
文摘Metastatic Merkel Cell carcinoma (MCC) is a highly unusual and aggressive skin cancer that presents as a small, pink to violet skin lesion and metastasizes early in its growth. Metastatic MCC is generally treated with small cell lung cancer chemotherapy regimens, because the tumor consists of neuroendocrine cells, but patients generally do not have durable responses. The pathogenesis of MCC has recently been attributed to the Merkel Cell polyoma virus. This virus activates the cellular retinoblastoma oncoprotein and cell cycle machinery, triggering continual cellular proliferation. A 77-year-old man developed extensive MCC metastases, involving more than one fourth of his scalp and numerous cervical lymph nodes. Following failure of initial chemotherapy and radiation, effective palliation was achieved by using a sequence of electron-beam radiotherapy, low dose gemcitabine, and etoposide, resulting in significant periods of tumor regression and prolonged survival. A novel circulating tumor cell (CTC) culture assay was performed on four separate clinic visits during the treatment period. Tumor colonies were cultured from the patient’s peripheral blood and CTC colony counts were correlated with clinical treatment response. Not only did the patient respond to palliative cell cycle directed chemotherapy and electron beam radiation, but we demonstrated that CTC can be cultured from peripheral blood of MCC patients and serve as a predictive marker to monitor treatment response.
基金We thank D.D.Meigs(University of Nebraska Medical Center)and Tonya Cejka(freelance English editor)for editing assistance.C.B.G.is funded by NIH grants R35HG010719,R21GM129559,R21AI143394 and R21DA046831.M.O.is funded by 2016–2017 Tokai University School of Medicine Project Research,the Research Aid from the Institute of Medical Sciences in Tokai University,Grant-in-Aid for Scientific Research(25290035)from MEXTa Grant-in-Aid for Challenging Exploratory Research(15K14371)from JSPS.
文摘Genetically engineered mouse(GEM)models are commonly used in biomedical research.Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff.Because of these reasons,most research institutes set up centralized core facilities where custom GEMs are created for research groups.Researchers,on the other hand,when they begin thinking about generating GEMs for their research,several questions arise in their minds.For example,what type of model(s)would be best useful for my research,how do I design them,what are the latest technologies and tools available for developing my model(s),and finally how to breed GEMs in my research.As there are several considerations and options in mouse designs,and as it is an expensive and time-consuming endeavor,careful planning upfront can ensure the highest chance of success.In this article,we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s)for their work.
文摘Islets from RIP-PDE3B mice, exhibiting β-cell specific overexpression of the cAMP/cGMP-degrading enzyme phosphodiesterase 3B (PDE3B) and dysregulated insulin secretion, were subjected to microarray analysis. We show that osteopontin (OPN) mRNA is increased in a dose-dependent manner in islets from RIP-PDE3B mice, as compared to wild-type islets. In addition, in silico analysis shows that PDE3B and OPN are interacting. Furthermore, OPN interacts with protein kinase CK2 ina distinct submodule of the protein-protein interaction network. We studied PDE3B and OPN proteins and, in some cases, also PDE1B and PDE4C, under conditions of relevance for insulin secretion. In the presence of forskolin, PDE inhibitors, insulin, or a protein kinase CK2 inhibitor, similar alterations in protein levels of PDE3B and OPN are shown. In summary, results from using a number of strategies demonstrate a connection between PDE3B and OPNas well as a role for protein kinase CK2 inpancreatic β-cells.
基金Supported in parts by grants from the Swedish Cancer Society(CAN 2010/255),the Swedish Research Council(08712),Tore Nilson Foundation,Assar Gabrielsson Foundation(AB Volvo),Jubileumskliniken Foundation,IngaBritt&Arne Lundberg Research Foundation,Swedish and Gothenburg Medical Societies and the Medical Faculty,University of Gothenburg,VGR 19/00,1019/00.
文摘Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was therefore to search for DNA regions (copy number variations, CNVs) as biomarkers associated to genetic susceptibility for early risk predictions of colorectal cancer. Such sequence alterations could provide additional information on phenotypic grouping of patients. Material and Methods: High resolution 105K oligonucleotide microarrays were used in search for CNV loci in DNA from tumor-free colon mucosa at primary operations for colon cancer in 60 unselected patients in comparison to DNA in buffy coat cells from 44 confirmed tumor-free and healthy blood donors. Array-detected CNVs were confirmed by Multiplex ligation-dependent probe amplification (MLPA). Results: A total number of 205 potential CNVs were present in DNA from colon mucosa. 184 (90%) of the 205 potential CNVs had been identified earlier in mucosa DNA from healthy individuals as reported to the Database of Genomic Variants. Remaining 21 (10%) CNVs were potentially novel sites. Two CNVs (3q23 and 10q21.1) were significantly related to colon cancer, but not confirmed in buffy coat DNA from the cancer patients. Conclusion: Our study reveals two CNVs that indicate increased risk for colon cancer;These DNA alterations may have? been acquired by colon stem cells with subsequent appearance among epithelial mucosa cells. Impact: Certain mucosa CNV alterations may indicate individual susceptibility for malignant transformation in relationship to intestinal toxins and bacterial growth.
基金funded by the projects SAF2005-07643-C03-01/02/03 and SAF2007-62719 by Spanish Health Ministry grantsby FIS CP06/00341, FI06/00651 and CP01/3058 from the Fondo de Investigación Sanitaria (FIS), Ministerio de Sanidad+3 种基金from the Plan Nacional, Ministerio de Educación y Cienciasupported by the Instituto de Salud Carlos Ⅲ (CP06/00341)supported by a predoctoral fellowship (FI06/00651) from the Spanish Health Ministrysupported by a Colciencias International PhD Scholarship (Grant: 529/2011),from the Fund for science and technology of Colombian Ministry of Education
文摘Exposure to disinfection by-products（DBP） such as trihalomethanes（THM） in swimming pools has been linked to adverse health effects in humans, but their biological mechanisms are unclear. We evaluated short-term changes in blood gene expression of adult recreational swimmers after swimming in a chlorinated pool. Volunteers swam 40 min in an indoor chlorinated pool. Blood samples were drawn and four THM（chloroform,bromodichloromethane, dibromochloromethane and bromoform） were measured in exhaled breath before and after swimming. Intensity of physical activity was measured as metabolic equivalents（METs）. Gene expression in whole blood m RNA was evaluated using Illumina Human HT-12v3 Expression-Bead Chip. Linear mixed models were used to evaluate the relationship between gene expression changes and THM exposure. Thirty-seven before-after pairs were analyzed. The median increase from baseline to after swimming were： 0.7 to 2.3 for MET, and 1.4 to 7.1 μg/m^3 for exhaled total THM（sum of the four THM）.Exhaled THM increased on average 0.94 μg/m^3 per 1 MET. While 1643 probes were differentially expressed post-exposure. Of them, 189 were also associated with exhaled levels of individual/total THM or MET after False Discovery Rate. The observed associations with the exhaled THM were low to moderate（Log-fold change range：-0.17 to 0.15）. In conclusion, we identified short-term gene expression changes associated with swimming in a pool that were minor in magnitude and their biological meaning was unspecific. The high collinearity between exhaled THM levels and intensity of physical activity precluded mutually adjusted models with both covariates. These exploratory results should be validated in future studies.
基金support provided by the Core Facilities for Metabolomics,Flow Cytometry,Cellular Imaging,Preclinical Imagingthe animal facility at Philipps-University of Marburg.N.G.was supported by the Clinician Scientist program(SUCCESS-program)of the Philipps-University of Marburg,the University Cancer Center(UCT)Frankfurt-Marburg+6 种基金the University Hospital of Giessen and Marburg(UKGM)research grants of the Deutsche Forschungsgemeinschaft(GRK 2573/2-2024)University Medical Center Giessen and Marburg(UKGM)(3/2022 MR to N.G.)von Behring-Rontgen-Stiftung(70_0027 to N.G.)Stiftung P.E.Kempkes(01/2021 to N.G.)Medizinstiftung(04/2021 to N.G.)M.F.F.reports funding from the Deutsche Forschungsgemeinschaft(INST 90/1048-1 FUGG).
文摘Activating PIK3CA mutations,present in up to 40%of hormone receptor-positive(HR^(+)),human epidermal growth factor receptor 2-negative(Her2^(-))breast cancer(BC)patients,can be effectively targeted with the alpha isoform-specific Pl3K inhibitor Alpelisib.This treatment significantly improves outcomes for HR^(+),Her2^(-),and PIK3CA-mutated metastatic BC patients.However,acquired resistance,often due to aberrant activation of the mTOR complex 1(mTORC1)pathway,remains a significant clinical challenge.Our study,using in vitro and orthotopic xenograft mouse models,demonstrates that constitutively active mTORC1 signaling renders PI3K inhibitor-resistant BC exquisitely sensitive to various drugs targeting cancer metabolism.Mechanistically,mTORC1 suppresses the induction of autophagy during metabolic perturbation,leading to energy stress,a critical depletion of aspartate,and ultimately cell death.Supporting this mechanism,BC cells with CRISPR/Cas9-engineered knockouts of canonical autophagy genes showed similar vulnerability to metaboliclly active drugs InBC patients,high mTORC1 activity,indicated by 4E-BP1^(T37/46) phosphorylation correlated with p62 accumulation,a sign of impaired autophagy.Together,these markers predicted poor overall survival in multiple BC subgroups.Our findings reveal that aberrant mTORC1 signaling,a common cause of PI3K inhibitor resistance in BC,creates a druggable metabolic vulnerability by suppressing autophagy.Additionall,the combination of 4E-BP1^(T37/46) phosphorylation and p62 accumulation serves as a biomarker for poor overall survival,suggesting their potential utility in identifying BC patients who may benefit from metabolic therapies.
基金This work was supported by grants from Deutsche Forschungsgemeinschaft(KFO325,project 329116008 and GRK2573,project 416910386 to EPvS)Hessisches Ministerium fur Wissenschaft und Kunst(LOEWE iCANx to EPvS)+1 种基金from von Behring-RontgenStiftung(66-0024 to VP and BD)Open Access funding enabled and organized by Projekt DEAL.
文摘Recent studies reveal a critical role of tumor cell-released extracellular vesicles(EVs)in pancreatic cancer(PC)progression.However,driver genes that direct EV function,the EV-recipient cells,and their cellular response to EV uptake remain to be identified.Therefore,we studied the role of Bcl-2-associated-anthanogene 6(BAG6),a regulator of EV biogenesis for cancer progression.We used a Cre recombinase/LoxP-based reporter system in combination with single-cell RNA sequencing to monitor in vivo EV uptake and tumor microenvironment(TME)changes in mouse models for pancreatic ductal adenocarcinoma(PDAC)in a Bag6 pro-or deficient background.In vivo data were validated using mouse and human organoids and patient samples.Our data demonstrated that Bag6-deficient subcutaneous and orthotopic PDAC tumors accelerated tumor growth dependent on EV release.Mechanistically,this was attributed to mast cell(MC)activation via EV-associated IL33.Activated MCs promoted tumor cell proliferation and altered the composition of the TME affecting fibroblast polarization and immune cell infiltration.Tumor cell proliferation and fibroblast polarization were mediated via the MC secretome containing high levels of PDGF and CD73.Patients with high BAG6 gene expression and high protein plasma level have a longer overall survival indicating clinical relevance.The current study revealed a so far unknown tumor-suppressing activity of BAG6 in PDAC.Bag6-deficiency allowed the release of EV-associated IL33 which modulate the TME via MC activation promoting aggressive tumor growth.MC depletion using imatinib diminished tumor growth providing a scientific rationale to consider imatinib for patients stratified with low BAG6 expression and high MC infiltration.
基金supported by the NIH(R01HL148821 and F31CA260918)University of Pennsylvania Abramson Cancer Center(Patel Scholar Award)Pennsylvania Department of Health(Health Research Formula Fund).
文摘Although mechanisms of telomere protection are well-defined in differentiated cells,how stem cells sense and respond to telomere dysfunction,in particular telomeric double-strand breaks(DSBs),is poorly characterized.Here,we report the DNA damage signaling,cell cycle,and transcriptome changes in human induced pluripotent stem cells(iPSCs)in response to telomere-internal DSBs.We engineer human iPSCs with an inducible TRF1-FokI fusion protein to acutely induce DSBs at telomeres.Using this model,we demonstrate that TRF1-FokI DSBs activate an ATR-dependent DNA damage response,which leads to p53-independent cell cycle arrest in G2.Using CRISPR–Cas9 to cripple the catalytic domain of telomerase reverse transcriptase,we show that telomerase is largely dispensable for survival and lengthening of TRF1-FokI-cleaved telomeres,which instead are effectively repaired by robust homologous recombination(HR).In contrast to HR-based telomere maintenance in mouse embryonic stem cells,where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths,HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length,which is compatible with sustained survival of the cells over several days of TRF1-FokI induction.Our findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage.
基金supported by the National Natural Science Foundation of China to H.Z.(Grant Nos.81770184,81970143,and 82270167)and L.Z.(Grant No.81800174)the Talent Young Program of Guangdong Province(2021B1515020017),and the Leading Talents Program from The First Affiliated Hospital of Jinan University to H.Z.
文摘Acute myeloid leukemia(AML)is a common hematological malignancy with overall poor prognosis.Exploring novel targets is urgent and necessary to improve the clinical outcome of relapsed and refractory(RR)AML patients.Through clinical specimens,animal models and cell-level studies,we explored the specific mechanism of 3-hydroxy-3-methylglutaryl coenzyme A synthase 1(HMGCS1)in AML and the mechanism of targeting HMGCS1 to attenuate cell proliferation,increase chemotherapy sensitivity and improve the occurrence and development of AML.Here,we reveal that HMGCS1 is overexpressed in RR patients and negatively related to overall survival(OS).Knocking out HMGCS1 in AML cells attenuated cell proliferation and increased chemotherapy sensitivity,while stable overexpression of HMGCS1 had the opposite effects.Mechanistically,we identified that knockout of HMGCS1 suppressed mitogen-activated protein kinase(MAPK)pathway activity,while overexpression of HMGCS1 could remarkably enhance the pathway.U0126,a MEK1 inhibitor,offset the effects of HMGCS1 overexpression,indicating that HMGCS1 promotes RR AML through the MAPK pathway.Further,we verified that hymeglusin,a specific inhibitor of HMGCS1,decreases cell growth both in AML cell lines and primary bone marrow cells of AML patients.Furthermore,combination of hymeglusin and the common chemotherapeutic drug cytarabine and adriamycin(ADR)had synergistic toxic effects on AML cells.Our study demonstrates the important role of HMGCS1 in AML,and targeting this protein is promising for the treatment of RR AML.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB945401, 2007CB108800)National Natural Science Foundation of China (Grant Nos. 30870575,31071162,31000590)Science and Technology Commission of Shanghai Municipality (Grant No. 11DZ2260300)
文摘RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.
基金Supported by grants to M.L.from the U.S.National Sclence Foundation (I0S#1854326 and 2127485),USDA-NIFA(2022-67013-36144)by the Center for Plant Science Innovation,and by the Department of Agronomy and Horticulture at the University of Nebraska-Lincoln.Work in F.F.labo-ratory was supported by the"Ecole Universitaire de Recherche"Saclay Plant Sciences(EUR-SPS).
文摘Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia.This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria,as well as the initiation of nodule primordia from root cortical,endodermal,and pericycle cells,leading to the development of a new root organ,the nodule,where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant.Here,we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq(sNucRNA-seq)profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots.A gene expression map of the Medicago root was generated,comprising 25 clusters,which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes.A focus on root hair,cortex,endodermis,and pericycle cell types,showing the strongest differential regulation in response to a short-term(48 h)rhizobium inoculation,revealed not only known genes and functional pathways,validating the sNucRNA-seq approach,but also numerous novel genes and pathways,allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB945401, 2007CB108800)National Natural Science Foundation of China (Grant Nos. 30870575, 31071162,31000590)the Science and Technology Commission of Shanghai Municipality (Grant No. 11DZ2260300)
文摘De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,respectively.We then determined an efficient way to yield an optimal overall assembly using three different strategies.We first assembled brain and cell line transcriptome using a single k-mer length.Next we tested a range of values of k-mer length and coverage cutoff in assembling.Lastly,we combined the assembled contigs from a range of k values to generate a final assembly.By comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.
基金Ramalingaswami Fellowship,Grant/Award Number:D.O.NO.BT/HRD/35/02/2006the Department of Biotechnology,&Core Research grant,Grant/Award Number:CRG/2021/003805+1 种基金Science and Engineering Research Board(SERB),Govt.of India,New DelhiSidra Medicine Precision Program,Grant/Award Numbers:5081012003,5081012002。
文摘Colorectal cancer(CRC)is a predominant life-threatening cancer,with liver and peritoneal metastases as the primary causes of death.Intestinal inflammation,a known CRC risk factor,nurtures a local inflammatory environment enriched with tumor cells,endothelial cells,immune cells,cancer-associated fibroblasts,immunosuppressive cells,and secretory growth factors.The complex interactions of aberrantly expressed cytokines,chemokines,growth factors,and matrix-remodeling enzymes promote CRC pathogenesis and evoke systemic responses that affect disease outcomes.Mounting evidence suggests that these cytokines and chemokines play a role in the progression of CRC through immunosuppression and modulation of the tumor microenvironment,which is partly achieved by the recruitment of immunosuppressive cells.These cells impart features such as cancer stem cell-like properties,drug resistance,invasion,and formation of the premetastatic niche in distant organs,promoting metastasis and aggressive CRC growth.A deeper understanding of the cytokineand chemokine-mediated signaling networks that link tumor progression and metastasis will provide insights into the mechanistic details of disease aggressiveness and facilitate the development of novel therapeutics for CRC.Here,we summarized the current knowledge of cytokine-and chemokine-mediated crosstalk in the inflammatory tumor microenvironment,which drives immunosuppression,resistance to therapeutics,and metastasis during CRC progression.We also outlined the potential of this crosstalk as a novel therapeutic target for CRC.The major cytokine/chemokine pathways involved in cancer immunotherapy are also discussed in this review.
基金supported by grants UH3AI083263,U54HD080784 and R01HD092415 fromthe National Institutes of Health and the GAPPS BMGF PPB grant from the Global Alliance to Prevent Prematurity and Stillbirth。
文摘Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological health.However,collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained clinician.In contrast,urine sample collection is routine and noninvasive and does not require involvement of a clinician.We sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal microbiome.Paired urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic profiling.We examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes.A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal microbiomes.Moreover,the relative abundances of common vaginal taxa were linearly correlated with those in the paired urogenitalmicrobiomes.These similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginalmicrobiome with likely clinical applications.Finally,a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.
基金the US Department of Energy(Grant Nos.DE-FG02-00ER62986 and DE-FG02-07ER64373 to J.E.K.)the Department of Biotechnology,Govt.of India(Grant No.BT/Coord.II/01/03/2016)for their support.Fellowship funding for one of the authors(Dr.Pooja Singh)by the Department of Science and Technology(DST),Government of India,is greatly acknowledged.
文摘This work examines the physiologic basis of stress tolerance in bacterial strains of the genus Rhodanobacter that dominate in the acidic and highly metal contaminated near-source subsurface zone of the Oak Ridge Integrated Field Research Challenge(ORIFRC)site.Tolerance of R.denitrificans to levels of different stresses were studied in synthetic groundwater medium and R2A broth.Two strains of R.denitrificans,strains 2APBS1T and 116-2,tolerate low to circumneutral pH(4–8),high Uranium(1 mmol/L),elevated levels of nitrate(400 mmol/L)and high NaCl(2.5%).A combination of physiologic traits,such as growth at low pH,increased growth in the presence of high organics concentration,and tolerance of high concentrations of nitrate,NaCl and heavy metals is likely responsible for dominance of Rhodanobacter at the ORIFRC site.Furthermore,extended incubation times and use of low carbon media,better approximating site groundwater conditions,are critical for accurate determination of stress responses.This study expands knowledge of the ecophysiology of bacteria from the genus Rhodanobacter and identifies methodological approaches necessary for acquiring accurate tolerance data.
