1
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Liu H, Guan L, Su X, Zhao L, Shu Q, Zhang J. A broken network of susceptibility genes in the monocytes of Crohn's disease patients. Life Sci Alliance 2024; 7:e202302394. [PMID: 38925865 PMCID: PMC11208737 DOI: 10.26508/lsa.202302394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Su
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lijian Zhao
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Qing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Research, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
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2
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Fernández Aceñero MJ, Díaz del Arco C. Hereditary Gastrointestinal Tumor Syndromes: When Risk Comes with Your Genes. Curr Issues Mol Biol 2024; 46:6440-6471. [PMID: 39057027 PMCID: PMC11275188 DOI: 10.3390/cimb46070385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Despite recent campaigns for screening and the latest advances in cancer therapy and molecular biology, gastrointestinal (GI) neoplasms remain among the most frequent and lethal human tumors. Most GI neoplasms are sporadic, but there are some well-known familial syndromes associated with a significant risk of developing both benign and malignant GI tumors. Although some of these entities were described more than a century ago based on clinical grounds, the increasing molecular information obtained with high-throughput techniques has shed light on the pathogenesis of several of them. The vast amount of information gained from next-generation sequencing has led to the identification of some high-risk genetic variants, although others remain to be discovered. The opportunity for genetic assessment and counseling in these families has dramatically changed the management of these syndromes, though it has also resulted in significant psychological distress for the affected patients, especially those with indeterminate variants. Herein, we aim to summarize the most relevant hereditary cancer syndromes involving the stomach and colon, with an emphasis on new molecular findings, novel entities, and recent changes in the management of these patients.
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Affiliation(s)
- María Jesús Fernández Aceñero
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - Cristina Díaz del Arco
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
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3
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Brignola C, Pecoraro A, Danisi C, Iaccarino N, Di Porzio A, Romano F, Carotenuto P, Russo G, Russo A. uL3 Regulates Redox Metabolism and Ferroptosis Sensitivity of p53-Deleted Colorectal Cancer Cells. Antioxidants (Basel) 2024; 13:757. [PMID: 39061826 PMCID: PMC11274089 DOI: 10.3390/antiox13070757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Despite advancements in therapeutic strategies, the development of drug resistance and metastasis remains a serious concern for the efficacy of chemotherapy against colorectal cancer (CRC). We have previously demonstrated that low expression of ribosomal protein uL3 positively correlates with chemoresistance in CRC patients. Here, we demonstrated that the loss of uL3 increased the metastatic capacity of CRC cells in chick embryos. Metabolomic analysis revealed large perturbations in amino acid and glutathione metabolism in resistant uL3-silenced CRC cells, indicating that uL3 silencing dramatically triggered redox metabolic reprogramming. RNA-Seq data revealed a notable dysregulation of 108 genes related to ferroptosis in CRC patients. Solute Carrier Family 7 Member 11 (SLC7A11) is one of the most dysregulated genes; its mRNA stability is negatively regulated by uL3, and its expression is inversely correlated with uL3 levels. Inhibition of SLC7A11 with erastin impaired resistant uL3-silenced CRC cell survival by inducing ferroptosis. Of interest, the combined treatment erastin plus uL3 enhanced the chemotherapeutic sensitivity of uL3-silenced CRC cells to erastin. The antimetastatic potential of the combined strategy was evaluated in chick embryos. Overall, our study sheds light on uL3-mediated chemoresistance and provides evidence of a novel therapeutic approach, erastin plus uL3, to induce ferroptosis, establishing individualized therapy by examining p53, uL3 and SLC7A11 profiles in tumors.
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Affiliation(s)
- Chiara Brignola
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annalisa Pecoraro
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Camilla Danisi
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Francesca Romano
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Pietro Carotenuto
- TIGEM, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Naples, Italy;
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Corso Umberto I, 40, 80138 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annapina Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
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4
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Li D, Zhong C, Yang M, He L, Chang H, Zhu N, Celniker SE, Threadgill DW, Snijders AM, Mao JH, Yuan Y. Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer. Gut Microbes 2024; 16:2341647. [PMID: 38659246 PMCID: PMC11057575 DOI: 10.1080/19490976.2024.2341647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.
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Affiliation(s)
- Dan Li
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ZJ, China
| | - Chenhan Zhong
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mengyuan Yang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ning Zhu
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
- Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, ZJ, China
- Cancer Center, Zhejiang University, Hangzhou, ZJ, China
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5
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Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of various high fat diets on gene expression and the microbiome across the mouse intestines. Sci Rep 2023; 13:22758. [PMID: 38151490 PMCID: PMC10752901 DOI: 10.1038/s41598-023-49555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023] Open
Abstract
High fat diets (HFDs) have been linked to several diseases including obesity, diabetes, fatty liver, inflammatory bowel disease (IBD) and colon cancer. In this study, we examined the impact on intestinal gene expression of three isocaloric HFDs that differed only in their fatty acid composition-coconut oil (saturated fats), conventional soybean oil (polyunsaturated fats) and a genetically modified soybean oil (monounsaturated fats). Four functionally distinct segments of the mouse intestinal tract were analyzed using RNA-seq-duodenum, jejunum, terminal ileum and proximal colon. We found considerable dysregulation of genes in multiple tissues with the different diets, including those encoding nuclear receptors and genes involved in xenobiotic and drug metabolism, epithelial barrier function, IBD and colon cancer as well as genes associated with the microbiome and COVID-19. Network analysis shows that genes involved in metabolism tend to be upregulated by the HFDs while genes related to the immune system are downregulated; neurotransmitter signaling was also dysregulated by the HFDs. Genomic sequencing also revealed a microbiome altered by the HFDs. This study highlights the potential impact of different HFDs on gut health with implications for the organism as a whole and will serve as a reference for gene expression along the length of the intestines.
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Affiliation(s)
- Jose Martinez-Lomeli
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
| | - Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA.
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Paul Ruegger
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - James Borneman
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, 92521, USA
- Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA
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6
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Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of Various High Fat Diets on Gene Expression and the Microbiome Across the Mouse Intestines. RESEARCH SQUARE 2023:rs.3.rs-3401763. [PMID: 37886485 PMCID: PMC10602159 DOI: 10.21203/rs.3.rs-3401763/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
High fat diets (HFDs) have been linked to several diseases including obesity, diabetes, fatty liver, inflammatory bowel disease (IBD) and colon cancer. In this study, we examined the impact on intestinal gene expression of three isocaloric HFDs that differed only in their fatty acid composition - coconut oil (saturated fats), conventional soybean oil (polyunsaturated fats) and a genetically modified soybean oil (monounsaturated fats). Four functionally distinct segments of the mouse intestinal tract were analyzed using RNA-seq - duodenum, jejunum, terminal ileum and proximal colon. We found considerable dysregulation of genes in multiple tissues with the different diets, including those encoding nuclear receptors and genes involved in xenobiotic and drug metabolism, epithelial barrier function, IBD and colon cancer as well as genes associated with the microbiome and COVID-19. Network analysis shows that genes involved in metabolism tend to be upregulated by the HFDs while genes related to the immune system are downregulated; neurotransmitter signaling was also dysregulated by the HFDs. Genomic sequencing also revealed a microbiome altered by the HFDs. This study highlights the potential impact of different HFDs on gut health with implications for the organism as a whole and will serve as a reference for gene expression along the length of the intestines.
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7
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Zou D, Yang Y, Ji F, Lv R, Xu T, Hu C. DUOX2-Induced Oxidative Stress Inhibits Intestinal Angiogenesis through MMP3 in a Low-Birth-Weight Piglet Model. Antioxidants (Basel) 2023; 12:1800. [PMID: 37891879 PMCID: PMC10603984 DOI: 10.3390/antiox12101800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Intestinal vessels play a critical role in nutrient absorption, whereas the effect and mechanism of low birth weight (LBW) on its formation remain unclear. Here, twenty newborn piglets were assigned to the control (CON) group (1162 ± 98 g) and LBW group (724 ± 31 g) according to their birth weight. Results showed that the villus height and the activity of maltase in the jejunum were lower in the LBW group than in the CON group. LBW group exhibited a higher oxidative stress level and impaired mitochondrial function in the jejunum and was lower than the CON group in the intestinal vascular density. To investigate the role of oxidative stress in intestinal angiogenesis, H2O2 was employed to induce oxidative stress in porcine intestinal epithelial cells (IPEC-J2). The results showed that the conditioned media from IPEC-J2 with H2O2 treatment decreased the angiogenesis of porcine vascular endothelial cells (PVEC). Transcriptome analysis revealed that a higher expression level of dual oxidase 2 (DUOX2) was found in the intestine of LBW piglets. Knockdown of DUOX2 in IPEC-J2 increased the proliferation and decreased the oxidative stress level. In addition, conditioned media from IPEC-J2 with DUOX2-knockdown was demonstrated to promote the angiogenesis of PVEC. Mechanistically, the knockdown of DUOX2 decreased the reactive oxygen species (ROS) level, thus increasing the angiogenesis in a matrix metalloproteinase 3 (MMP3) dependent manner. Conclusively, our results indicated that DUOX2-induced oxidative stress inhibited intestinal angiogenesis through MMP3 in a LBW piglet model.
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Affiliation(s)
- Dongbin Zou
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
- College of Life Sciences, Hainan University, Haikou 571101, China
| | - Yun Yang
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengjie Ji
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
| | - Renlong Lv
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
| | - Tieshan Xu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
| | - Chengjun Hu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.Z.); (Y.Y.); (F.J.); (R.L.)
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Chen Y, Cai G, Jiang J, He C, Chen Y, Ding Y, Lu J, Zhao W, Yang Y, Zhang Y, Wu G, Wang H, Zhou Z, Teng L. Proteomic profiling of gastric cancer with peritoneal metastasis identifies a protein signature associated with immune microenvironment and patient outcome. Gastric Cancer 2023; 26:504-516. [PMID: 36930369 PMCID: PMC10284991 DOI: 10.1007/s10120-023-01379-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Peritoneal metastasis (PM) frequently occurs in patients with gastric cancer (GC) and is a major cause of mortality. Risk stratification for PM can optimize decision making in GC treatment. METHODS A total of 25 GC patients (13 with synchronous, 6 with metachronous PM and 6 PM-free) were included in this study. Quantitative proteomics by high-depth tandem mass tags labeling and whole-exome sequencing were conducted in primary GC and PM samples. Proteomic signature and prognostic model were established by machine learning algorithms in PM and PM-free GC, then validated in two external cohorts. Tumor-infiltrating immune cells in GC were analyzed by CIBERSORT. RESULTS Heterogeneity between paired primary and PM samples was observed at both genomic and proteomic levels. Compared to primary GC, proteome of PM samples was enriched in RNA binding and extracellular exosomes. 641 differently expressed proteins (DEPs) between primary GC of PM group and PM-free group were screened, which were enriched in extracellular exosome and cell adhesion pathways. Subsequently, a ten-protein signature was derived based on DEPs by machine learning. This signature was significantly associated with patient prognosis in internal cohort and two external proteomic datasets of diffuse and mixed type GC. Tumor-infiltrating immune cell analysis showed that the signature was associated with immune microenvironment of GC. CONCLUSIONS We characterized proteomic features that were informative for PM progression of GC. A protein signature associated with immune microenvironment and patient outcome was derived, and it could guide risk stratification and individualized treatment.
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Affiliation(s)
- Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Guoxin Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao He
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Wenyi Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yan Yang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Yiqin Zhang
- Department of Informatics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guanghao Wu
- School of Clinical Medicine, Hangzhou Normal University Medical College, Hangzhou, China
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, 310003, China.
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9
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Sun R, Yang Y, Lü W, Yang Y, Li Y, Liu Z, Diao D, Wang Y, Chang S, Lu M, Jiang Q, Dai B, Ma X, Zhao C, Lü M, Zhang J, Ding C, Li N, Zhang J, Xiao Z, Zhou D, Huang C. Single-cell transcriptomic analysis of normal and pathological tissues from the same patient uncovers colon cancer progression. Cell Biosci 2023; 13:62. [PMID: 36944972 PMCID: PMC10031920 DOI: 10.1186/s13578-023-01002-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
The aim of the present study was to elucidate the evolutionary trajectory of colon cells from normal colon mucosa, to adenoma, then to carcinoma in the same microenvironment. Normal colon, adenoma and carcinoma tissues from the same patient were analyzed by single-cell sequencing, which perfectly simulated the process of time-dependent colon cancer due to the same microenvironment. A total of 22 cell types were identified. Results suggest the presence of dominant clones of same cells including C2 goblet cell, epithelial cell subtype 1 (Epi1), enterocyte cell subset 0 (Entero0), and Entero5 in carcinoma. Epi1 and Entero0 were Co-enriched in antibacterial and IL-17 signaling, Entero5 was enriched in immune response and mucin-type O-glycan biosynthesis. We discovered new colon cancer related genes including AC007952.4, NEK8, CHRM3, ANO7, B3GNT6, NEURL1, ODC1 and KCNMA1. The function of TBC1D4, LTB, C2CD4A, AND GBP4/5 in T cells needs to be clarified. We used colon samples from the same person, which provide new information for colon cancer therapy.
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Affiliation(s)
- Ruifang Sun
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Middle Section of Century Avenue, Xianyang, Shaanxi, People's Republic of China.
| | - Weidong Lü
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yanqi Yang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhigang Liu
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Dongmei Diao
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Wang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Su'e Chang
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Chang'an Zhao
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Moqi Lü
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Juan Zhang
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Caixia Ding
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Na Li
- School of Pharmacy, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang, Henan, People's Republic of China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhengtao Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
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10
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Deng N, Zhang X, Zhang Y. BAIAP2L1 accelerates breast cancer progression and chemoresistance by activating AKT signaling through binding with ribosomal protein L3. Cancer Sci 2023; 114:764-780. [PMID: 36308067 PMCID: PMC9986062 DOI: 10.1111/cas.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022] Open
Abstract
BAI1-associated protein 2-like 1 (BAIAP2L1), also known as insulin receptor tyrosine kinase substrate, modulates the insulin network; however, its function in breast cancer has not been explored. Immunohistochemical analysis of 140 breast cancer specimens (77 triple-negative and 63 nontriple-negative cases) indicated that BAIAP2L1 expression was higher in breast cancer tissues (56/140, 40%) than in normal breast tissues (28.3%, 15/53; p < 0.001). BAIAP2L1 expression in breast cancer was correlated with triple-negative breast cancer (p = 0.0013), advanced TNM stage (p = 0.001), lymph node metastasis (p = 0.001), and poor patient prognosis (p = 0.001). BAIAP2L1 overexpression could accelerate breast cancer proliferation, invasion, and stemness in vivo and in vitro, possibly through the activation of AKT, Snail, and cyclin D1. Treatment with the AKT inhibitor LY294002 reduced the effects of BAIAP2L1 overexpression on breast cancer cells. BAIAP2L1 may bind to the AA202-288 of ribosomal protein L3 (RPL3) within its SRC homology 3 (SH3) domain, the loss of which may abolish the transduction of the AKT signaling pathway by promoting the degradation of PIK3CA. Moreover, BAIAP2L1 overexpression may induce chemotherapy resistance, with BAIAP2L1 expression being higher in patients with advanced Miller grades than those with lower grades. Our results indicated that BAIAP2L1 promotes breast cancer progression through the AKT signaling pathway by interacting with RPL3 through its SH3 domain.
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Affiliation(s)
- Ning Deng
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yong Zhang
- Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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11
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Lyons N, Giri R, Begun J, Clark DA, Proud D, He Y, Hooper J, Kryza T. Reactive oxygen species as mediators of disease progression and therapeutic response in colorectal cancer. Antioxid Redox Signal 2023. [PMID: 36792932 DOI: 10.1089/ars.2022.0127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Significance Reactive oxygen species (ROS) are critical to normal cellular function with redox homeostasis achieved by balancing ROS production with removal through detoxification mechanisms. Many of the conventional chemotherapies used to treat colorectal cancer (CRC) derive a proportion of their cytotoxicity from ROS generation and resistance to chemotherapy is associated with elevated detoxification mechanisms. Furthermore, cancer stem cells demonstrate elevated detoxification mechanisms making definitive treatment with existing chemotherapy challenging. In this article we review the roles of ROS in normal and malignant colonic cell biology and how existing and emerging therapies might harness ROS for therapeutic benefit. Recent advances Recent publications have elucidated the contribution of ROS to the cytotoxicity of conventional chemotherapy alongside the emerging approaches of photodynamic therapy (PDT), sonodynamic therapy (SDT) and radiodynamic therapy (RDT) in which ROS are generated in response to excitatory light, sound or X-ray stimuli to promote cancer cell apoptosis. Critical issues The majority of patients with metastatic CRC have a very poor prognosis with 5-year survival of approximately 13% making the need for new or more effective treatments an imperative. Future Directions Modulation of ROS through a combination of new and emerging therapies may improve the efficacy of current chemotherapy providing novel approaches to treat otherwise resistant disease.
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Affiliation(s)
- Nicholas Lyons
- The University of Queensland, 1974, Mater Research, Woolloongabba, Queensland, Australia;
| | - Rabina Giri
- The University of Queensland, 1974, Mater Research, Woolloongabba, Queensland, Australia;
| | - Jakob Begun
- The University of Queensland, 1974, Mater Research, Woolloongabba, Queensland, Australia;
| | - David A Clark
- Royal Brisbane and Women's Hospital, 3883, Surgery, Herston, Queensland, Australia;
| | - David Proud
- Austin Hospital, 96043, Surgery, Heidelberg, Victoria, Australia;
| | - Yaowu He
- The University of Queensland, 1974, Mater Research, Woolloongabba, Queensland, Australia;
| | - John Hooper
- The University of Queensland, 1974, Mater Research, Translational Research Institute, 37 Kent Street, Woolloongabba, Queensland, Australia, 4102;
| | - Thomas Kryza
- The University of Queensland, 1974, Mater Research, Woolloongabba, Queensland, Australia;
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12
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Ansari-Pour N, Samur M, Flynt E, Gooding S, Towfic F, Stong N, Estevez MO, Mavrommatis K, Walker B, Morgan G, Munshi N, Avet-Loiseau H, Thakurta A. Whole-genome analysis identifies novel drivers and high-risk double-hit events in relapsed/refractory myeloma. Blood 2023; 141:620-633. [PMID: 36223594 PMCID: PMC10163277 DOI: 10.1182/blood.2022017010] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Large-scale analyses of genomic data from patients with newly diagnosed multiple myeloma (ndMM) have been undertaken, however, large-scale analysis of relapsed/refractory MM (rrMM) has not been performed. We hypothesize that somatic variants chronicle the therapeutic exposures and clonal structure of myeloma from ndMM to rrMM stages. We generated whole-genome sequencing (WGS) data from 418 tumors (386 patients) derived from 6 rrMM clinical trials and compared them with WGS from 198 unrelated patients with ndMM in a population-based case-control fashion. We identified significantly enriched events at the rrMM stage, including drivers (DUOX2, EZH2, TP53), biallelic inactivation (TP53), noncoding mutations in bona fide drivers (TP53BP1, BLM), copy number aberrations (CNAs; 1qGain, 17pLOH), and double-hit events (Amp1q-ISS3, 1qGain-17p loss-of-heterozygosity). Mutational signature analysis identified a subclonal defective mismatch repair signature enriched in rrMM and highly active in high mutation burden tumors, a likely feature of therapy-associated expanding subclones. Further analysis focused on the association of genomic aberrations enriched at different stages of resistance to immunomodulatory agent (IMiD)-based therapy. This analysis revealed that TP53, DUOX2, 1qGain, and 17p loss-of-heterozygosity increased in prevalence from ndMM to lenalidomide resistant (LENR) to pomalidomide resistant (POMR) stages, whereas enrichment of MAML3 along with immunoglobulin lambda (IGL) and MYC translocations distinguished POM from the LEN subgroup. Genomic drivers associated with rrMM are those that confer clonal selective advantage under therapeutic pressure. Their role in therapy evasion should be further evaluated in longitudinal patient samples, to confirm these associations with the evolution of clinical resistance and to identify molecular subsets of rrMM for the development of targeted therapies.
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Affiliation(s)
- Naser Ansari-Pour
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Sarah Gooding
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | | | - Maria Ortiz Estevez
- Predictive Sciences, BMS Center for Innovation and Translational Research Europe, A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Brian Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Gareth Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Boston, MA
- VA Boston Healthcare System, West Roxbury, MA
- Harvard Medical School, Boston, MA
| | | | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Bristol Myers Squibb, Summit, NJ
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Disease, University of Oxford, Oxford, United Kingdom
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13
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[Silenced ANP32A inhibits the growth, invasion and migration of colorectal cancer in vitro via the inactivation of AKT pathway]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:52-59. [PMID: 36856210 DOI: 10.12122/j.issn.1673-4254.2023.01.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To investigate the effect of ANP32A silencing on invasion and migration of colon cancer cells and the influence of the activity of AKT signaling pathway on this effect. METHODS Colorectal cancer HCT116 and SW480 were transfected with a small interfering RNA targeting ANP32A via a lentiviral vector. At 24, 48 and 72 h after the transfection, the changes in cell proliferation and AKT activity in the cells were detected using MTT assay and Western blotting, respectively. HCT116 and SW480 cells were treated with the AKT agonist SC79 or its inhibitor MK2206 for 24, 48, 72 and 96 h, and the changes in cell migration and invasion ability were analyzed using Transwell chamber assay and cell proliferation was assessed using MTT assay. The effects of SC79 and MK2206 on migration and invasion abilities of HCT116 and SW480 cells with or without ANP32A silencing were examined using wound healing and Transwell chamber assays, and the changes in the expression of metadherin (MTDH), a factor associated with cells invasion and migration, was detected with Western blotting. RESULTS Lentivirus-mediated ANP32A silencing significantly down-regulated the activity of AKT and inhibited the proliferation of both HCT116 and SW480 cells (P < 0.01). The application of AKT inhibitor MK2206 obviously inhibited the proliferation, invasion and migration of the colorectal cancer cells (P < 0.05), while the AKT agonist SC79 significantly promoted the invasion and migration of the cells (P < 0.01). In HCT116 and SW480 cells with ANP32A silencing, treatment with MK2206 strongly enhanced the inhibitory effects of ANP32A silencing on cell invasion and migration (P < 0.05) and the expression of MTDH, while SC79 partially reversed these inhibitory effects (P < 0.01). CONCLUSION ANP32A silencing inhibits invasion and migration of colorectal cancer cells possibly by inhibiting the activation of the AKT signaling pathway.
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14
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Sun X, Sun P, Sui Y, Tan C, Chen Y. Prognostic model based on six feature genes of intestinal flora subtypes predicts survival in colon cancer. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2126898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Xiao Sun
- Department of Gastrointestinal Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People’s Republic of China
| | - Peng Sun
- Department of Gastrointestinal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, People’s Republic of China
| | - Yi Sui
- Department of IVD Medical Marketing, 3D Medicine Inc., Shanghai, People’s Republic of China
| | - Canliang Tan
- Departmemt of General Surgery, the Third Affilliated Hospital of Southern Medical University, Guangzhou, People’s Republic of China
| | - Yinggang Chen
- Department of Gastrointestinal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, People’s Republic of China
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15
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Dual Oxidase 2 (DUOX2) as a Proteomic Biomarker for Predicting Treatment Response to Chemoradiation Therapy for Locally Advanced Rectal Cancer: Using High-Throughput Proteomic Analysis and Machine Learning Algorithm. Int J Mol Sci 2022; 23:ijms232112923. [DOI: 10.3390/ijms232112923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput mass-spectrometry-based quantitative proteomic analysis was performed using formalin-fixed, paraffin-embedded (FFPE) biopsy samples obtained before treatment from 13 patients with locally advanced rectal cancer (LARC), who were treated with concurrent chemoradiation therapy (CCRT) followed by surgery. Patients were divided into complete responder (CR) and non-complete responder (nCR) groups. Immunohistochemical (IHC) staining of 79 independent FFPE tissue samples was performed to validate the predictive ability of proteomic biomarker candidates. A total of 3637 proteins were identified, and the expression of 498 proteins was confirmed at significantly different levels (differentially expressed proteins—DEPs) between two groups. In Gene Ontology enrichment analyses, DEPs enriched in biological processes in the CR group included proteins linked to cytoskeletal organization, immune response processes, and vesicle-associated protein transport processes, whereas DEPs in the nCR group were associated with biosynthesis, transcription, and translation processes. Dual oxidase 2 (DUOX2) was selected as the most predictive biomarker in machine learning algorithm analysis. Further IHC validation ultimately confirmed DUOX2 as a potential biomarker for predicting the response of nCR to CCRT. In conclusion, this study suggests that the treatment response to RT may be affected by the pre-treatment tumor microenvironment. DUOX2 is a potential biomarker for the early prediction of nCR after CCRT.
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16
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Xing C, Yin H, Yao ZY, Xing XL. Prognostic Signatures Based on Ferroptosis- and Immune-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Front Oncol 2022; 11:774558. [PMID: 35087751 PMCID: PMC8787259 DOI: 10.3389/fonc.2021.774558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/09/2021] [Indexed: 01/01/2023] Open
Abstract
Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) are among the most common malignancies of the female genital tract. Ferroptosis and immunity regulate each other and play important roles in the progression of CESC. The present study aimed to screen ferroptosis- and immune-related differentially expressed genes (FI-DEGs) to identify suitable prognostic signatures for patients with CESC. We downloaded the RNAseq count data and corresponding clinical information of CESC patients from The Cancer Genome Atlas database; obtained recognized ferroptosis- and immune-related genes from the FerrDb and ImmPort databases, respectively; and screened for suitable prognostic signatures using a series of bioinformatics analyses. We identified eight FI-DEGs (CALCRL, CHIT1, DES, DUOX1, FLT1, HELLS, SCD, and SDC1) that were independently correlated with the overall survival of patients with CESC. The prediction model constructed using these eight FI-DEGs was also independently correlated with overall survival. Both the sensitivity and specificity of the prediction model constructed using these eight signatures were over 60%. The comprehensive index of ferroptosis and immune status was significantly correlated with the immunity of patients with CESC. In conclusion, the risk assessment model constructed with these eight FI-DEGs predicted the CESC outcomes. Therefore, these eight FI-DEGs could serve as prognostic signatures for CESC.
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Affiliation(s)
- Chaoqun Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
| | - Huiming Yin
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
| | - Zhi-Yong Yao
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Xiao-Liang Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China
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17
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Yang M, Zhao Y, Ding Y, Wang J, Tan Y, Xu D, Yuan Y. A truncated protein product of the germline variant of the DUOX2 gene leads to adenomatous polyposis. Cancer Biol Med 2021; 18:215-226. [PMID: 33628596 PMCID: PMC7877186 DOI: 10.20892/j.issn.2095-3941.2020.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Objective: In some patients with adenomatous polyposis, an identifiable pathogenic variant of known associated genes cannot be found. Researchers have studied this for decades; however, few new genes have been identified. Methods: Adenomatous polyposis coli (APC) negative polyposis patients were identified through next-generation sequencing and multiplex ligation-dependent probe amplification. Then, whole-exome sequencing (WES) was used to determine candidate genes harboring pathogenic variants. Functional experiments were performed to explore their effects. Subsequently, using Sanger sequencing, we found other polyposis patients carrying variants of the DUOX2 gene, encoding dual oxidase 2, and analyzed them. Results: From 88 patients with suspected familial adenomatous polyposis, 25 unrelated APC negative polyposis patients were identified. Based on the WES results of 3 patients and 2 healthy relatives from a family, the germline nonsense variant (c.1588A>T; p.K530X) of the DUOX2 gene was speculated to play a decisive role in the pedigree in relation to adenomatous polyposis. During functional experiments, we observed that the truncated protein, hDuox2 K530, was overexpressed in the adenoma in a carrier of the DUOX2 nonsense variant, causing abnormal cell proliferation through endoplasmic reticulum (ER) retention. In addition, we found two unrelated APC negative patients carrying DUOX2 missense variants (c.3329G>A, p.R1110Q; c.4027C>T, p.L1343F). Given the results of the in silico analysis, these two missense variants might exert a negative influence on the function of hDuox2. Conclusions: To our knowledge, this is the first study that reports the possible association of DUOX2 germline variants with adenomatous polyposis. With an autosomal dominant inheritance, it causes ER retention, inducing an unfolded protein response.
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Affiliation(s)
- Mengyuan Yang
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China.,Cancer Institute, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yingxin Zhao
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China.,Cancer Institute, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yuwei Ding
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Juan Wang
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China.,Cancer Institute, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yinuo Tan
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China.,Cancer Institute, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Dong Xu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ying Yuan
- Department of Medical Oncology, Zhejiang University School of Medicine, Hangzhou 310009, China.,Cancer Institute, Zhejiang University School of Medicine, Hangzhou 310009, China
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18
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Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
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Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
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