Song Li, Bing Cai, Jialiu Liu, Yan Xu, Chenhui Ding, Muhua Lai, Canquan Zhou, Yanwen Xu
<p>Dear Editor,</p><p>By taking advantage of parallel sequencing of genome and transcriptome (G&T-seq),<span><sup>1</sup></span> we demonstrated the distinct transcriptome profiles of human preimplantation blastocysts in perspectives of embryo digital karyotype, developmental speed and implantation competence. Our study provided valuable information for further research in the physiology behind human embryo development and laid the foundation for embryo selection from the view of the transcriptome.</p><p>Preimplantation genetic test for aneuploidy (PGT-A) serves as an important invasive method to select euploid embryos. However, even PGT-A cannot guarantee a successful pregnancy,<span><sup>2</sup></span> for almost 50% of euploid blastocysts could not result in a live birth. It means that there is still a big room to improve the capability of embryo selection besides aneuploidy screening. RNA sequencing might have the potential for assessing embryo competence.<span><sup>3, 4</sup></span> Here we investigated the distinct transcriptome profiles in human pre-implantation blastocysts with the application of G&T-seq (Figure 1A). We have verified this method in biopsied samples from 41 donated blastocysts in terms of the transcriptome consistency of samples from the same blastocyst, the prediction value of aneuploidies by transcriptome (Figure S1), as well as the lineage characteristic of inner cell mass (ICM) and trophectoderm (TE) (Figure S2), indicating the clinical safety and reproducibility of this method.</p><p>G&T-seq is a unique technology for studying the transcriptome of chromosomal mosaicism, taking advantage of separate genome sequencing and RNA sequencing. In comparisons of transcriptomes of 28 TE few-cell samples from eight mosaic embryos with 17 TE few-cell samples from five euploidies (Figure 1B), we identified 79 genes upregulated and 37 genes downregulated (Figure 1C). Notably, ectoderm and primitive endoderm genes, including <i>KLF4</i>, <i>TGFBR1</i>, <i>ITGB5</i> and <i>GATA6</i>, were significantly upregulated in TE of mosaic blastocysts (Figure 1D). Furthermore, upregulated genes were mainly enriched in embryonic development, stem cell proliferation, endoderm development and other pathways (Table S1), implying that there might be a lineage separation disorder in TE cells with chromosomal mosaicism, and the inadequately developed trophoblast may contribute to the adverse pregnancy outcomes of mosaic embryos.</p><p>Human blastocysts have different developmental speeds. It may take 5–7 days for an embryo to develop to the grade 4 stage according to the Gardner grading system, which is the stage allowing TE biopsy. Clinically, blastocysts biopsied on day 6 or day 7 (named D6 or D7 blastocyst) are defined as growth-retarded blastocysts with lower implantation potential compared with day 5 blastocysts. The reason for retarded development speed remains to be clarified. To investigate the transcriptome related to blastocyst
{"title":"Transcriptome profiles of human preimplantation blastocysts related to mosaicism, developmental speed and competence","authors":"Song Li, Bing Cai, Jialiu Liu, Yan Xu, Chenhui Ding, Muhua Lai, Canquan Zhou, Yanwen Xu","doi":"10.1002/ctm2.70196","DOIUrl":"10.1002/ctm2.70196","url":null,"abstract":"<p>Dear Editor,</p><p>By taking advantage of parallel sequencing of genome and transcriptome (G&T-seq),<span><sup>1</sup></span> we demonstrated the distinct transcriptome profiles of human preimplantation blastocysts in perspectives of embryo digital karyotype, developmental speed and implantation competence. Our study provided valuable information for further research in the physiology behind human embryo development and laid the foundation for embryo selection from the view of the transcriptome.</p><p>Preimplantation genetic test for aneuploidy (PGT-A) serves as an important invasive method to select euploid embryos. However, even PGT-A cannot guarantee a successful pregnancy,<span><sup>2</sup></span> for almost 50% of euploid blastocysts could not result in a live birth. It means that there is still a big room to improve the capability of embryo selection besides aneuploidy screening. RNA sequencing might have the potential for assessing embryo competence.<span><sup>3, 4</sup></span> Here we investigated the distinct transcriptome profiles in human pre-implantation blastocysts with the application of G&T-seq (Figure 1A). We have verified this method in biopsied samples from 41 donated blastocysts in terms of the transcriptome consistency of samples from the same blastocyst, the prediction value of aneuploidies by transcriptome (Figure S1), as well as the lineage characteristic of inner cell mass (ICM) and trophectoderm (TE) (Figure S2), indicating the clinical safety and reproducibility of this method.</p><p>G&T-seq is a unique technology for studying the transcriptome of chromosomal mosaicism, taking advantage of separate genome sequencing and RNA sequencing. In comparisons of transcriptomes of 28 TE few-cell samples from eight mosaic embryos with 17 TE few-cell samples from five euploidies (Figure 1B), we identified 79 genes upregulated and 37 genes downregulated (Figure 1C). Notably, ectoderm and primitive endoderm genes, including <i>KLF4</i>, <i>TGFBR1</i>, <i>ITGB5</i> and <i>GATA6</i>, were significantly upregulated in TE of mosaic blastocysts (Figure 1D). Furthermore, upregulated genes were mainly enriched in embryonic development, stem cell proliferation, endoderm development and other pathways (Table S1), implying that there might be a lineage separation disorder in TE cells with chromosomal mosaicism, and the inadequately developed trophoblast may contribute to the adverse pregnancy outcomes of mosaic embryos.</p><p>Human blastocysts have different developmental speeds. It may take 5–7 days for an embryo to develop to the grade 4 stage according to the Gardner grading system, which is the stage allowing TE biopsy. Clinically, blastocysts biopsied on day 6 or day 7 (named D6 or D7 blastocyst) are defined as growth-retarded blastocysts with lower implantation potential compared with day 5 blastocysts. The reason for retarded development speed remains to be clarified. To investigate the transcriptome related to blastocyst ","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"15 2","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hanwool Jeon, Hayeong Kang, Jihyun Im, Suin Jo, Hyunchul Jung, Moinay Kim, Jae Hyun Kim, Eunyeup Lee, Soyoung Kim, Jeong Hoon Kim, Chang-Ki Hong, Young-Hoon Kim, Sang Woo Song, Jinha Park, Sang-Yeob Kim, Seungjoo Lee
<p>Dear Editor,</p><p>Glioblastoma (GBM), the most aggressive malignant tumour, is increasingly treated with immunotherapy.<span><sup>1-3</sup></span> The stimulator of interferon genes (STING) pathway<span><sup>4</sup></span> is key to tumour immunity and a studied target for immunotherapy.<span><sup>5</sup></span> This study explores the immune landscape of GBM, focusing on spatial relationships between tumour-associated immune cells (TAICs)<span><sup>6</sup></span> and STING-expressing cells, uncovering patterns linked to prognosis.</p><p>We studied 14 recurrent GBM patients using protein composition and Gene Ontology (GO) analysis and analyzed immune pathways in 69 newly diagnosed GBM patients undergoing standard therapy. Spatial analysis of cells was performed using QuPath, CytoMAP, and R, as illustrated in Figure 1A. From our proteomic analysis, we identified protein groups with marked upregulation in patients with favourable responses. A total of 99 proteins were highly upregulated in the favourable group, while 170 were more pronounced in the unfavourable group (Figure 1B). Clusters of downregulated and upregulated proteins were identified using the Benjamini-Hochberg False Discovery Rate. The expression of <b>TMEM173</b>, the gene encoding STING, was significantly elevated in the favourable group, as measured by protein expression using a mass spectrometer. The results were represented as an abundance ratio, and statistical significance was confirmed using the adjusted p-value. (Figure 1C). GO analysis showed that upregulated proteins in the favourable group were mainly linked to immune response activation. (Figure 1D). Pathways such as ‘regulation of innate immune response’ and ‘phagocytic respiratory burst’ were strongly linked to innate immune activation (Figure 1E). Additionally, pathways like ‘cell surface receptor signalling in immune response’, ‘T cell migration’ and ‘positive regulation of T cell receptor signalling’ were significantly linked to immune response activation (Figure 1F). <i>p</i>-Values were transformed to -log10 for statistical significance, with values above 1.3 considered significant. Table S1 provides the GO categories associated with immune response activation.</p><p>We used multiplex immunohistochemistry (IHC) to analyze immune cell distribution and protein markers in the TME. Markers included CD4<sup>+</sup> (helper T cells), CD8<sup>+</sup> (cytotoxic T cells), CD11c<sup>+</sup> (dendritic cells), TCRγ/δ<sup>+</sup> (γ/δ T cells), ATRX<sup>+</sup> (tumour cells) and DAPI<sup>+</sup> (nuclei), with STING as a primary marker of interest.</p><p>We explored correlations between immune cell populations identified by multiplex IHC and patient survival (Figure 2A). Tumour specimens were stained with multiplex immunofluorescence, and a pathologist selected regions of interest (ROIs), which were scanned at high magnification and analyzed with markers including ATRX, CD8, STING, DAPI, CD4, CD11c and TCRγ/δ. (Figure 2B
{"title":"Spatial distribution of immune cells and their proximity to STING+ cells are associated with survival in glioblastoma","authors":"Hanwool Jeon, Hayeong Kang, Jihyun Im, Suin Jo, Hyunchul Jung, Moinay Kim, Jae Hyun Kim, Eunyeup Lee, Soyoung Kim, Jeong Hoon Kim, Chang-Ki Hong, Young-Hoon Kim, Sang Woo Song, Jinha Park, Sang-Yeob Kim, Seungjoo Lee","doi":"10.1002/ctm2.70187","DOIUrl":"10.1002/ctm2.70187","url":null,"abstract":"<p>Dear Editor,</p><p>Glioblastoma (GBM), the most aggressive malignant tumour, is increasingly treated with immunotherapy.<span><sup>1-3</sup></span> The stimulator of interferon genes (STING) pathway<span><sup>4</sup></span> is key to tumour immunity and a studied target for immunotherapy.<span><sup>5</sup></span> This study explores the immune landscape of GBM, focusing on spatial relationships between tumour-associated immune cells (TAICs)<span><sup>6</sup></span> and STING-expressing cells, uncovering patterns linked to prognosis.</p><p>We studied 14 recurrent GBM patients using protein composition and Gene Ontology (GO) analysis and analyzed immune pathways in 69 newly diagnosed GBM patients undergoing standard therapy. Spatial analysis of cells was performed using QuPath, CytoMAP, and R, as illustrated in Figure 1A. From our proteomic analysis, we identified protein groups with marked upregulation in patients with favourable responses. A total of 99 proteins were highly upregulated in the favourable group, while 170 were more pronounced in the unfavourable group (Figure 1B). Clusters of downregulated and upregulated proteins were identified using the Benjamini-Hochberg False Discovery Rate. The expression of <b>TMEM173</b>, the gene encoding STING, was significantly elevated in the favourable group, as measured by protein expression using a mass spectrometer. The results were represented as an abundance ratio, and statistical significance was confirmed using the adjusted p-value. (Figure 1C). GO analysis showed that upregulated proteins in the favourable group were mainly linked to immune response activation. (Figure 1D). Pathways such as ‘regulation of innate immune response’ and ‘phagocytic respiratory burst’ were strongly linked to innate immune activation (Figure 1E). Additionally, pathways like ‘cell surface receptor signalling in immune response’, ‘T cell migration’ and ‘positive regulation of T cell receptor signalling’ were significantly linked to immune response activation (Figure 1F). <i>p</i>-Values were transformed to -log10 for statistical significance, with values above 1.3 considered significant. Table S1 provides the GO categories associated with immune response activation.</p><p>We used multiplex immunohistochemistry (IHC) to analyze immune cell distribution and protein markers in the TME. Markers included CD4<sup>+</sup> (helper T cells), CD8<sup>+</sup> (cytotoxic T cells), CD11c<sup>+</sup> (dendritic cells), TCRγ/δ<sup>+</sup> (γ/δ T cells), ATRX<sup>+</sup> (tumour cells) and DAPI<sup>+</sup> (nuclei), with STING as a primary marker of interest.</p><p>We explored correlations between immune cell populations identified by multiplex IHC and patient survival (Figure 2A). Tumour specimens were stained with multiplex immunofluorescence, and a pathologist selected regions of interest (ROIs), which were scanned at high magnification and analyzed with markers including ATRX, CD8, STING, DAPI, CD4, CD11c and TCRγ/δ. (Figure 2B","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"15 2","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sally E. Claridge, Shalini Nath, Anneliese Baum, Richard Farias, Julie-Ann Cavallo, Nile M. Rizvi, Lamberto De Boni, Eric Park, Genesis Lara Granados, Matthew Hauesgen, Ruben Fernandez-Rodriguez, Eda Nur Kozan, Evgeny Kanshin, Khoi Q. Huynh, Peng-Jen Chen, Kenneth Wu, Beatrix Ueberheide, Juan Miguel Mosquera, Fred R. Hirsch, Robert J. DeVita, Olivier Elemento, Chantal Pauli, Zhen-Qiang Pan, Benjamin D. Hopkins