bims-instec Biomed News
on Intestinal stem cells and chemoresistance in colon cancer and intestinal regeneration
Issue of 2022–08–14
fiveteen papers selected by
Maria-Virginia Giolito, IRFAC/UMR-S1113 INSERM
  1. Thyroid hormone signaling in the intestinal stem cells and their niche.
  2. Damage-induced regeneration of the intestinal stem cell pool through enteroblast mitosis in the Drosophila midgut.
  3. Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.
  4. Glutathione S-Transferase Alpha 4 Promotes Proliferation and Chemoresistance in Colorectal Cancer Cells.
  5. Retinoic Acid Promotes the In Vitro Growth, Patterning and Improves the Cellular Composition of Human Pluripotent Stem-Cell-Derived Intestinal Organoids.
  6. Targeting FAPα-expressing hepatic stellate cells overcomes resistance to anti-angiogenics in colorectal cancer liver metastasis models.
  7. Epithelial JAM-A is fundamental for intestinal wound repair in-vivo.
  8. Immunofluorescence staining of colorectal cancer patient-derived organoids.
  9. Patient-derived rectal cancer organoids-applications in basic and translational cancer research.
  10. Establishment of a circular RNA regulatory stemness-related gene pair signature for predicting prognosis and therapeutic response in colorectal cancer.
  11. Reprogrammed Lipid Metabolism and the Lipid-Associated Hallmarks of Colorectal Cancer.
  12. Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis.
  13. The emergence of the stem cell niche.
  14. Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms.
  15. Alteration in the Immune Microenvironment Based on APC Status in MSS/pMMR Colon Cancer.
  1. Cell Mol Life Sci. 2022 Aug 10. 79(9): 476
    Thyroid hormone signaling in the intestinal stem cells and their niche.
    Maria Virginia Giolito, Michelina Plateroti.
      Several studies emphasized the function of the thyroid hormones in stem cell biology. These hormones act through the nuclear hormone receptor TRs, which are T3-modulated transcription factors. Pioneer work on T3-dependent amphibian metamorphosis showed that the crosstalk between the epithelium and the underlying mesenchyme is absolutely required for intestinal maturation and stem cell emergence. With the recent advances of powerful animal models and 3D-organoid cultures, similar findings have now begun to be described in mammals, where the action of T3 and TRα1 control physiological and cancer-related stem cell biology. In this review, we have summarized recent findings on the multiple functions of T3 and TRα1 in intestinal epithelium stem cells, cancer stem cells and their niche. In particular, we have highlighted the regulation of metabolic functions directly linked to normal and/or cancer stem cell biology. These findings help explain other possible mechanisms by which TRα1 controls stem cell biology, beyond the more classical Wnt and Notch signaling pathways.
    Keywords:  Colon cancer; Intestinal epithelium; Stem cell; Stem cell niche; Thyroid hormone; Thyroid hormone receptor
    DOI:  https://doi.org/10.1007/s00018-022-04503-y
  2. EMBO J. 2022 Aug 11. e110834
    Damage-induced regeneration of the intestinal stem cell pool through enteroblast mitosis in the Drosophila midgut.
    Aiguo Tian, Virginia Morejon, Sarah Kohoutek, Yi-Chun Huang, Wu-Min Deng, Jin Jiang.
      Many adult tissues and organs including the intestine rely on resident stem cells to maintain homeostasis and regeneration. In mammals, the progenies of intestinal stem cells (ISCs) can dedifferentiate to generate ISCs upon ablation of resident stem cells. However, whether and how mature tissue cells generate ISCs under physiological conditions remains unknown. Here, we show that infection of the Drosophila melanogaster intestine with pathogenic bacteria induces entry of enteroblasts (EBs), which are ISC progenies, into the mitotic cycle through upregulation of epidermal growth factor receptor (EGFR)-Ras signaling. We also show that ectopic activation of EGFR-Ras signaling in EBs is sufficient to drive enteroblast mitosis cell autonomously. Furthermore, we find that the dividing enteroblasts do not gain ISC identity as a prerequisite to divide, and the regenerative ISCs are produced through EB mitosis. Taken together, our work uncovers a new role for EGFR-Ras signaling in driving EB mitosis and replenishing the ISC pool during fly intestinal regeneration, which may have important implications for tissue homeostasis and tumorigenesis in vertebrates.
    Keywords:  Drosophila midgut; dedifferentiation; enteroblasts; regeneration; stem cells
    DOI:  https://doi.org/10.15252/embj.2022110834
  3. Sci Adv. 2022 Aug 12. 8(32): eabo2389
    Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.
    Sung Kook Chun, Bridget M Fortin, Rachel C Fellows, Amber N Habowski, Amandine Verlande, Wei A Song, Alisa L Mahieu, Austin E Y T Lefebvre, Jason N Sterrenberg, Leandro M Velez, Michelle A Digman, Robert A Edwards, Nicholas R Pannunzio, Marcus M Seldin, Marian L Waterman, Selma Masri.
      An alarming rise in young onset colorectal cancer (CRC) has been reported; however, the underlying molecular mechanism remains undefined. Suspected risk factors of young onset CRC include environmental aspects, such as lifestyle and dietary factors, which are known to affect the circadian clock. We find that both genetic disruption and environmental disruption of the circadian clock accelerate Apc-driven CRC pathogenesis in vivo. Using an intestinal organoid model, we demonstrate that clock disruption promotes transformation by driving Apc loss of heterozygosity, which hyperactivates Wnt signaling. This up-regulates c-Myc, a known Wnt target, which drives heightened glycolytic metabolism. Using patient-derived organoids, we show that circadian rhythms are lost in human tumors. Last, we identify that variance between core clock and Wnt pathway genes significantly predicts the survival of patients with CRC. Overall, our findings demonstrate a previously unidentified mechanistic link between clock disruption and CRC, which has important implications for young onset cancer prevention.
    DOI:  https://doi.org/10.1126/sciadv.abo2389
  4. Front Oncol. 2022 ;12 887127
    Glutathione S-Transferase Alpha 4 Promotes Proliferation and Chemoresistance in Colorectal Cancer Cells.
    Zhanhu Zhang, Lili Xu, Lin Huang, Tianqi Li, Jane Y Wang, Chunhua Ma, Xiaoyun Bian, Xiaoyan Ren, Haibo Li, Xingmin Wang.
      Glutathione S-transferase alpha 4 (GSTA4) is a phase II detoxifying enzyme that is overexpressed in colorectal cancer (CRC) and regulated by the oncogenic transcription factor AP-1. However, the role of GSTA4 in these CRC cells remains unclear. In this study, we investigated the roles of GSTA4 in the CRC cells by inactivating GSTA4 in HCT116 human CRC cells (Defined as HCT116ΔGSTA4) using the CRISPR/Cas9 gene editing. Cell proliferation, clonogenicity, and susceptibility to chemotherapeutic drugs were analyzed in vitro and in a xenograft model. The results showed that loss of GSTA4 significantly decreased cell proliferation and clonogenicity, whereas it increased intracellular reactive oxygen species and cell susceptibility to 5-fluorouracil (5-FU) and oxaliplatin. Additionally, exposure of HCT116ΔGSTA4 cells to 5-FU increased the expression of γH2AX, a hallmark of double-stranded DNA breaks. In contrast, no remarkably increased γH2AX was noted in oxaliplatin-treated HCT116ΔGSTA4 cells compared with HCT116 cells. Moreover, loss of GSTA4 blocked the AKT and p38 MAPK pathways, leading to proliferative suppression. Finally, the xenograft model showed decreased tumor size for HCT116ΔGSTA4 cells compared with HCT116 cells, confirming in vitro findings. These findings suggest that GSTA4 is capable of promoting proliferation, tumorigenesis, and chemoresistance and is a potential target for CRC therapy.
    Keywords:  chemoresistance; colorectal cancer; glutathione S-transferase alpha 4; proliferation; reactive oxygen species
    DOI:  https://doi.org/10.3389/fonc.2022.887127
  5. Int J Mol Sci. 2022 Aug 03. pii: 8624. [Epub ahead of print]23(15):
    Retinoic Acid Promotes the In Vitro Growth, Patterning and Improves the Cellular Composition of Human Pluripotent Stem-Cell-Derived Intestinal Organoids.
    Na Qu, Braxton Jeffcoat, Pritiprasanna Maity, Rachael K Christensen, Jorge O Múnera.
      Human intestinal organoids (HIOs) generated from human pluripotent stem cells hold great promise for modeling human development and as a possible source of tissue for transplantation. HIOs generate all of the main epithelial and mesenchymal cell types found in the developing human intestine and mature into intestinal tissue with crypts and villi following transplantation into immunocompromised mice. However, incomplete in vitro patterning and the presence of contaminating neurons could hinder their use for regenerative medicine in humans. Based on studies in model organisms, we hypothesized that the treatment of HIOs with all trans retinoic acid (ATRA) would improve their in vitro growth and patterning. We found that ATRA not only improved the patterning of HIOs, ATRA also increased organoid forming efficiency, improved epithelial growth, enriched intestinal subepithelial myofibroblasts (ISEMFs) and reduced neuronal contamination in HIOs. Taken together, our studies demonstrate how the manipulation of a single developmental signaling pathway can be used to improve the survival, patterning and cellular composition of HIOs.
    Keywords:  hindgut; human intestinal organoids; human pluripotent stem cells; midgut; patterning; retinoic acid
    DOI:  https://doi.org/10.3390/ijms23158624
  6. J Clin Invest. 2022 Aug 11. pii: e157399. [Epub ahead of print]
    Targeting FAPα-expressing hepatic stellate cells overcomes resistance to anti-angiogenics in colorectal cancer liver metastasis models.
    Ming Qi, Shuran Fan, Maohua Huang, Jinghua Pan, Yong Li, Qun Miao, Wenyu Lyu, Xiaobo Li, Lijuan Deng, Shenghui Qiu, Tongzheng Liu, Weiqing Deng, Xiaodong Chu, Chang Jiang, Wenzhuo He, Liangping Xia, Yunlong Yang, Jian Hong, Qi Qi, Wenqian Yin, Xiangning Liu, Changzheng Shi, Minfeng Chen, Wencai Ye, Dongmei Zhang.
      Vessel co-option has been demonstrated to mediate colorectal cancer liver metastasis (CRCLM) resistance to anti-angiogenic therapy. The current mechanisms underlying vessel co-option have mainly focused on the "hijacker" tumor cells, whereas the function of the "hijackee" sinusoidal blood vessels has not been explored. Here, we found that the occurrence of vessel co-option in bevacizumab-resistant CRCLM xenografts was associated with increased expression of fibroblast activation protein alpha (FAPα) in the co-opted hepatic stellate cells (HSCs), which was dramatically attenuated in HSC-specific conditional Fap-knockout mice bearing CRCLM allografts. Mechanistically, bevacizumab treatment induced hypoxia to upregulate the expression of fibroblast growth factor-binding protein 1 (FGFBP1) in tumor cells. Gain- or loss-of-function experiments revealed that the bevacizumab-resistant tumor cell-derived FGFBP1 induced FAPα expression by enhancing the paracrine FGF2-FGFR1-ERK1/2-EGR1 signaling pathway in HSCs. FAPα promoted CXCL5 secretion in HSCs, which activated CXCR2 to promote the epithelial-mesenchymal transition of tumor cells and the recruitment of myeloid-derived suppressor cells. These findings were further validated in CRCLM patient-derived tumor tissues. Targeting FAPα+ HSCs effectively disrupted the co-opted sinusoidal blood vessels and overcame bevacizumab resistance. Our study highlights the role of FAPα+ HSCs in vessel co-option and provides an effective strategy to overcome the vessel co-option-mediated bevacizumab resistance.
    Keywords:  Colorectal cancer; Drug therapy; Gastroenterology; Pericytes; Therapeutics
    DOI:  https://doi.org/10.1172/JCI157399
  7. JCI Insight. 2022 Aug 09. pii: e158934. [Epub ahead of print]
    Epithelial JAM-A is fundamental for intestinal wound repair in-vivo.
    Shuling Fan, Kevin Boerner, Chithra K Muraleedharan, Asma Nusrat, Miguel Quiros, Charles A Parkos.
      Junctional adhesion molecule-A (JAM-A) is expressed in several cell types including epithelial and endothelial cells as well as some leukocytes. In intestinal epithelial cells (IEC), JAM-A localizes to cell junctions and plays a role in regulating barrier function. In vitro studies with model cell lines have shown that JAM-A contributes to IEC migration, however in vivo studies investigating the role of JAM-A in cell migration-dependent processes such as mucosal wound repair have not been performed. In this study, we developed an inducible intestinal epithelial-specific JAM-A knockdown mouse model (Jam-aER-ΔIEC). While acute induction of IEC-specific loss of JAM-A did not result in spontaneous colitis, such mice had significantly impaired mucosal healing after chemically induced colitis and after biopsy colonic wounding. In vitro primary cultures of JAM-A deficient IEC demonstrated impaired migration in wound healing assays. Mechanistic studies revealed that JAM-A stabilizes formation of protein signaling complexes containing Rap1A/Talin/β1-integrin at focal adhesions of migrating IECs. Loss of JAM-A in primary IEC led to decreased Rap1A activity and protein levels of Talin and β1-integrin and a reduction in focal adhesion structures. These findings suggest that epithelial JAM-A plays a critical role in controlling mucosal repair in vivo through dynamic regulation of focal adhesions.
    Keywords:  Cell Biology; Gastroenterology; Inflammatory bowel disease
    DOI:  https://doi.org/10.1172/jci.insight.158934
  8. Methods Cell Biol. 2022 ;pii: S0091-679X(22)00055-3. [Epub ahead of print]171 163-171
    Immunofluorescence staining of colorectal cancer patient-derived organoids.
    Joseph L Regan.
      Organoids recapitulate the cellular heterogeneity, functionality, architecture and molecular signature of the organ or diseased tissue from which they are derived. They thus provide a bridge between traditional 2D culture systems and animal models and have profoundly enhanced our ability to study organ development and disease in vitro. Fluorescence microscopy has been an essential method in characterizing the cellular and morphological composition of organoids and demonstrating that they faithfully recapitulate the in vivo tissue of origin. Here we provide a straightforward method for immunofluorescence staining and confocal microscopy imaging of colorectal cancer (CRC) patient-derived organoids (PDOs) in basement matrix. The method is applicable to other types of human organoids, and we have also successfully used it on organoids derived from the mouse mammary gland.
    Keywords:  Cancer; Cancer stem cells; Confocal microscopy; Fluorescence microscopy; Immunofluorescence staining; Matrigel; Organoids; Patient-derived organoids; Stem cells
    DOI:  https://doi.org/10.1016/bs.mcb.2022.04.008
  9. Front Oncol. 2022 ;12 922430
    Patient-derived rectal cancer organoids-applications in basic and translational cancer research.
    Yumeng Yan, Io Hong Cheong, Peizhan Chen, Xiaoguang Li, Xianli Wang, Hui Wang.
      Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and among the leading causes of death in both men and women. Rectal cancer (RC) is particularly challenging compared with colon cancer as the treatment after diagnosis of RC is more complex on account of its narrow anatomical location in the pelvis adjacent to the urogenital organs. More and more existing studies have begun to refine the research on RC and colon cancer separately. Early diagnosis and multiple treatment strategies optimize outcomes for individual patients. However, the need for more accurate and precise models to facilitate RC research is underscored due to the heterogeneity of clinical response and morbidity interrelated with radical surgery. Organoids generated from biopsies of patients have developed as powerful models to recapitulate many aspects of their primary tissue, consisting of 3-D self-organizing structures, which shed great light on the applications in both biomedical and clinical research. As the preclinical research models for RC are usually confused with colon cancer, research on patient-derived RC organoid models enable personalized analysis of cancer pathobiology, organizational function, and tumor initiation and progression. In this review, we discuss the various applications of patient-derived RC organoids over the past two years in basic cancer biology and clinical translation, including sequencing analysis, drug screening, precision therapy practice, tumor microenvironment studies, and genetic engineering opportunities.
    Keywords:  cancer modeling; organoids; patient-derived; precision medicine; rectal cancer; treatment prediction; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2022.922430
  10. Front Immunol. 2022 ;13 934124
    Establishment of a circular RNA regulatory stemness-related gene pair signature for predicting prognosis and therapeutic response in colorectal cancer.
    Qian Chen, Peng Tang, Huishen Huang, Xiaoqiang Qiu.
       Background: Colorectal cancer (CRC) is a common malignant tumor of the digestive tract with a poor prognosis. Cancer stem cells (CSCs) affect disease outcomes and treatment responses in CRC. We developed a circular RNA (circRNA) regulatory stemness-related gene pair (CRSRGP) signature to predict CRC patient prognosis and treatment effects.
    Methods: The circRNA, miRNA, and mRNA expression profiles and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. CRSRGPs were established based on stemness-related genes in the competing endogenous RNA (ceRNA) network. A CRSRGP signature was generated using the least absolute shrinkage and selection operator (Lasso) and Cox regression analysis of TCGA training set. The prognosis was predicted by generating a nomogram integrating the CRSRGP signature and clinicopathologic features. The model was validated in an external validation set (GSE17536). The antitumor drug sensitivity and immunotherapy responses of CRC patients in the high-risk group (HRG) and low-risk group (LRG) were evaluated by the pRRophetic algorithm and immune checkpoint analysis.
    Results: We established an 18-CRSRGP signature to predict the prognosis and treatment responses of CRC patients. In the training and external validation sets, risk scores were used to categorize CRC patients into the HRG and LRG. The Kaplan-Meier analysis showed a poor prognosis for patients in the HRG and that subgroups with different clinical characteristics had significantly different prognoses. A multivariate Cox analysis revealed that the CRSRGP signature was an independent prognostic factor. The nomogram integrating clinical features and the CRSRGP signature efficiently predicted CRC patient prognosis, outperformed the current TNM staging system, and had improved practical clinical value. Anticancer drug sensitivity predictions revealed that the tumors of patients in the HRG were more sensitive to pazopanib, sunitinib, gemcitabine, lapatinib, and cyclopamine. Analysis of immune checkpoint markers demonstrated that patients in the HRG were more likely to benefit from immunotherapy.
    Conclusion: An efficient, reliable tool for evaluating CRC patient prognosis and treatment response was established based on the 18-CRSRGP signature and nomogram.
    Keywords:  circRNA; colorectal cancer; immune; nomogram; stemness-related gene pair signature
    DOI:  https://doi.org/10.3389/fimmu.2022.934124
  11. Cancers (Basel). 2022 Jul 29. pii: 3714. [Epub ahead of print]14(15):
    Reprogrammed Lipid Metabolism and the Lipid-Associated Hallmarks of Colorectal Cancer.
    Timothy Salita, Yepy H Rustam, Dmitri Mouradov, Oliver M Sieber, Gavin E Reid.
      Lipids have diverse structures, with multifarious regulatory functions in membrane homeostasis and bioenergetic metabolism, in mediating functional protein-lipid and protein-protein interactions, as in cell signalling and proliferation. An increasing body of evidence supports the notion that aberrant lipid metabolism involving remodelling of cellular membrane structure and changes in energy homeostasis and signalling within cancer-associated pathways play a pivotal role in the onset, progression, and maintenance of colorectal cancer (CRC) and their tumorigenic properties. Recent advances in analytical lipidome analysis technologies have enabled the comprehensive identification and structural characterization of lipids and, consequently, our understanding of the role they play in tumour progression. However, despite progress in our understanding of cancer cell metabolism and lipidomics, the key lipid-associated changes in CRC have yet not been explicitly associated with the well-established 'hallmarks of cancer' defined by Hanahan and Weinberg. In this review, we summarize recent findings that highlight the role of reprogrammed lipid metabolism in CRC and use this growing body of evidence to propose eight lipid metabolism-associated hallmarks of colorectal cancer, and to emphasize their importance and linkages to the established cancer hallmarks.
    Keywords:  CRC; cancer hallmarks; colorectal cancer; lipid metabolism; lipids; metabolomics
    DOI:  https://doi.org/10.3390/cancers14153714
  12. Nat Commun. 2022 Aug 08. 13(1): 4628
    Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis.
    Elle Koren, Alona Feldman, Marianna Yusupova, Avihay Kadosh, Egor Sedov, Roi Ankawa, Yahav Yosefzon, Waseem Nasser, Stefanie Gerstberger, Liam B Kimel, Noa Priselac, Samara Brown, Sam Sharma, Travis Gorenc, Ruby Shalom-Feuerstein, Hermann Steller, Tom Shemesh, Yaron Fuchs.
      The presence of distinct stem cells that maintain the interfollicular epidermis is highly debated. Here, we report a population of keratinocytes, marked by Thy1, in the basal layer of the interfollicular epidermis. We find that epidermal cells expressing differential levels of Thy1 display distinct transcriptional signatures. Thy1+ keratinocytes do not express T cell markers, express a unique transcriptional profile, cycle significantly slower than basal epidermal progenitors and display significant expansion potential in vitro. Multicolor lineage tracing analyses and mathematical modeling reveal that Thy1+ basal keratinocytes do not compete neutrally alike interfollicular progenitors and contribute long-term to both epidermal replenishment and wound repair. Importantly, ablation of Thy1+ cells strongly impairs these processes, thus indicating the non-redundant function of Thy1+ stem cells in the epidermis. Collectively, these results reveal a distinct stem cell population that plays a critical role in epidermal homeostasis and repair.
    DOI:  https://doi.org/10.1038/s41467-022-31629-1
  13. Trends Cell Biol. 2022 Aug 04. pii: S0962-8924(22)00173-8. [Epub ahead of print]
    The emergence of the stem cell niche.
    Michael R Hicks, April D Pyle.
      Stem cell niches are composed of dynamic microenvironments that support stem cells over a lifetime. The emerging niche is distinct from the adult because its main role is to support the progenitors that build organ systems in development. Emerging niches mature through distinct stages to form the adult niche and enable proper stem cell support. As a model of emerging niches, this review highlights how differences in the skeletal muscle microenvironment influence emerging versus satellite cell (SC) niche formation in skeletal muscle, which is among the most regenerative tissue systems. We contrast how stem cell niches regulate intrinsic properties between progenitor and stem cells throughout development to adulthood. We describe new applications for generating emerging niches from human pluripotent stem cells (hPSCs) using developmental principles and highlight potential applications for regeneration and therapeutics.
    Keywords:  niche emergence; niche rejuvenation and therapeutics; progenitor to stem cell maturation; skeletal muscle development
    DOI:  https://doi.org/10.1016/j.tcb.2022.07.003
  14. Gastroenterology. 2022 Aug 04. pii: S0016-5085(22)00827-7. [Epub ahead of print]
    Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms.
    Jibraan A Fawad, Deborah H Luzader, Gabriel F Hanson, Thomas J Moutinho, Craig A McKinney, Paul G Mitchell, Kathleen Brown-Steinke, Ajay Kumar, Miri Park, Suengwon Lee, David T Bolick, Greg L Medlock, Jesse Y Zhao, Andrew E Rosselot, C James Chou, Emily Eshleman, Theresa Alenghat, Christian I Hong, Jason A Papin, Sean R Moore.
       BACKGROUND & AIMS: The circadian clock orchestrates ∼24-hour oscillations of gastrointestinal epithelial structure and function that drive diurnal rhythms in gut microbiota. Here, we use experimental and computational approaches in intestinal organoids to reveal reciprocal effects of gut microbial metabolites on epithelial timekeeping by an epigenetic mechanism.
    METHODS: We cultured enteroids in media supplemented with sterile supernatants from the altered Schaedler Flora (ASF), a defined murine microbiota. Circadian oscillations of bioluminescent PER2 and Bmal1 were measured in the presence or absence of individual ASF supernatants. Separately, we applied machine learning to ASF metabolomics to identify phase-shifting metabolites.
    RESULTS: Sterile filtrates from 3 of 7 ASF species (ASF360 Lactobacillus intestinalis, ASF361 Ligilactobacillus murinus, ASF502 Clostridium spp.) induced minimal alterations in circadian rhythms, whereas filtrates from 4 ASF species (ASF356 Clostridium spp., ASF492 Eubacterium plexicaudatum, ASF500 Pseudoflavonifactor spp., ASF519 Parabacteroides goldsteinii) induced profound, concentration-dependent phase shifts. Random forest classification identified short chain fatty acids (SCFA: butyrate, propionate, acetate, and isovalerate) production as a discriminating feature of ASF "shifters". Experiments with SCFAs confirmed machine learning predictions, with a median phase shift of 6.2 hours in murine enteroids. Pharmacological or botanical HDAC inhibitors yielded similar findings. Further, mithramycin A, an inhibitor of HDAC inhibition, reduced SCFA-induced phase shifts by 20% (P<0.05) and conditional knockout of HDAC3 in enteroids abrogated butyrate effects on Per2 expression. Key findings were reproducible in human Bmal1-luciferase enteroids, colonoids and Per2-luciferase Caco-2 cells.
    CONCLUSIONS: Gut microbe-generated SCFAs entrain intestinal epithelial circadian rhythms by an HDACi-dependent mechanism, with critical implications for understanding microbial and circadian network regulation of intestinal epithelial homeostasis.
    Keywords:  circadian rhythm; histone deacetylation; intestinal organoids; microbiome; short chain fatty acids
    DOI:  https://doi.org/10.1053/j.gastro.2022.07.051
  15. Dis Markers. 2022 ;2022 3592990
    Alteration in the Immune Microenvironment Based on APC Status in MSS/pMMR Colon Cancer.
    Haishan Lin, Bangwei Cao.
       Introduction: Immunotherapy is currently the most promising antitumor treatment approach. However, the colon cancer immunotherapy indication dMMR/MSI-H do not cover all colon cancer patients suitable for immunotherapy. We performed transcriptome-wide expression profile analyses of pMMR/MSS colon adenocarcinoma (COAD) specimens from TCGA database to identify a genetype signature associated with tumor immune microenvironment types (TIMTs).
    Methods: TCGA database was used to identify tumor genotypes suitable for antitumor immunotherapy. We analyzed RNA-sequencing profiles of 338 COAD targeted to the pMMR/MSS group from TCGA public dataset. The ESTIMATE and the CIBERSORT were used to analyze the pMMR/MSS COAD immune microenvironment between APC wild and APC mutation. Furthermore, we further verified the relationship between APC genotype and TIMTs and the efficacy of immunotherapy in 42 colon cancer specimens.
    Results: We identified that in APC-wt/MSS colon cancer, the expressions of PD-1, PD-L1, CTLA4, and CYT (GZMA and PRF1) were increased. The TMB, Immunoscore, and the proportion of CT8+ T cell infiltration also were identified increasing in these patients. And pathway enrichment analysis for differentially expressed genes (DEGs) between APC-wt and APC-mt MSS COAD was done to further explore their biological function. Similarly, the significant pathways for DEGs were mainly enriched in the immune response, extracellular matrix, and cell adhesion which involved in immune response. Specimens from 42 colon cancer patients, including 22 APC-mt/MSS and 20 APC-wt/MSS, were immunohistochemically evaluated for expression of CD8 and PD-L1. And APC-wt/MSS tumors showed significantly higher expression of CD8 and PD-L1 than APC-mt/MSS tumor. Moreover, APC-wt was compared with APC-mt MSS/pMMR colon cancer (DOR, 45% and 26.7%, respectively; P < 0.05).
    Conclusion: Based on the results, we found that more colon cancers of APC-wt/MSS are classified by TMIT I. And APC-wt/MSS colon cancer patients are more likely to benefit from antitumor immunotherapy.
    DOI:  https://doi.org/10.1155/2022/3592990
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