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Kafida M, Karela M, Giakountis A. RNA-Independent Regulatory Functions of lncRNA in Complex Disease. Cancers (Basel) 2024; 16:2728. [PMID: 39123456 PMCID: PMC11311644 DOI: 10.3390/cancers16152728] [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: 07/06/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.
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Affiliation(s)
| | | | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
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2
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Yang W, Lin R, Guan S, Dang Y, He H, Huang X, Yang C. HNF1ɑ promotes colorectal cancer progression via HKDC1-mediated activation of AKT/AMPK signaling pathway. Gene 2024; 928:148752. [PMID: 38986750 DOI: 10.1016/j.gene.2024.148752] [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: 12/14/2023] [Revised: 06/24/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
The hepatocyte nuclear factor-1 (HNF1ɑ) is a transcription factor that contributes to several kinds of cancer progression. However, very little is known regarding the mechanisms underlying the activity of HNF1ɑ. We aimed to explore the role of HNF1ɑ in the progress of colorectal cancer (CRC) and elucidate its molecular mechanism. HNF1ɑ expression was upregulated in CRC samples and high expression of HNF1ɑ was associated with poor prognosis of CRC patients. HNF1α knockdown and overexpression inhibited and promoted proliferation, migration and invasion of CRC cells both in vitro and in vivo respectively. Mechanistically, HNF1ɑ increased the transcriptional activity of hexokinase domain component 1(HKDC1)promoter, thus activated AKT/AMPK signaling. Meanwhile, HKDC1 upregulation was important for the proliferation, migration and invasion of CRC cells and knockdown of HKDC1 significantly reversed the proliferation, migration and invasion induced by HNF1α overexpression. Taken together, HNF1ɑ contributes to CRC progression and metastasis through binding to HKDC1 and activating AKT/AMPK signaling. Targeting HNF1ɑ could be a potential therapeutic strategy for CRC patients.
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Affiliation(s)
- Weijin Yang
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China; Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Ruirong Lin
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China; Fujian Provincial Key Laboratory of Tumor Biotherapy, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, China
| | - Shen Guan
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Yuan Dang
- Innovation Center for Cancer Research, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, 350014, China
| | - Hongxin He
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Xinxiang Huang
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Chunkang Yang
- Department of Colorectal Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian 350014, China; Fujian Medical University, Fuzhou, Fujian 350122, China; Fujian Provincial Key Laboratory of Tumor Biotherapy, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350014, China.
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3
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Li LB, Yang LX, Liu L, Liu FR, Li AH, Zhu YL, Wen H, Xue X, Tian ZX, Sun H, Li PC, Zhao XG. Targeted inhibition of the HNF1A/SHH axis by triptolide overcomes paclitaxel resistance in non-small cell lung cancer. Acta Pharmacol Sin 2024; 45:1060-1076. [PMID: 38228910 PMCID: PMC11053095 DOI: 10.1038/s41401-023-01219-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/17/2023] [Indexed: 01/18/2024] Open
Abstract
Paclitaxel resistance is associated with a poor prognosis in non-small cell lung cancer (NSCLC) patients, and currently, there is no promising drug for paclitaxel resistance. In this study, we investigated the molecular mechanisms underlying the chemoresistance in human NSCLC-derived cell lines. We constructed paclitaxel-resistant NSCLC cell lines (A549/PR and H460/PR) by long-term exposure to paclitaxel. We found that triptolide, a diterpenoid epoxide isolated from the Chinese medicinal herb Tripterygium wilfordii Hook F, effectively enhanced the sensitivity of paclitaxel-resistant cells to paclitaxel by reducing ABCB1 expression in vivo and in vitro. Through high-throughput sequencing, we identified the SHH-initiated Hedgehog signaling pathway playing an important role in this process. We demonstrated that triptolide directly bound to HNF1A, one of the transcription factors of SHH, and inhibited HNF1A/SHH expression, ensuing in attenuation of Hedgehog signaling. In NSCLC tumor tissue microarrays and cancer network databases, we found a positive correlation between HNF1A and SHH expression. Our results illuminate a novel molecular mechanism through which triptolide targets and inhibits HNF1A, thereby impeding the activation of the Hedgehog signaling pathway and reducing the expression of ABCB1. This study suggests the potential clinical application of triptolide and provides promising prospects in targeting the HNF1A/SHH pathway as a therapeutic strategy for NSCLC patients with paclitaxel resistance. Schematic diagram showing that triptolide overcomes paclitaxel resistance by mediating inhibition of the HNF1A/SHH/ABCB1 axis.
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Affiliation(s)
- Ling-Bing Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Ling-Xiao Yang
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Lei Liu
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Fan-Rong Liu
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Alex H Li
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA
| | - Yi-Lin Zhu
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Hao Wen
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Xia Xue
- Department of Pharmacy, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Zhong-Xian Tian
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
- Key Laboratory of Chest Cancer, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China
| | - Hong Sun
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA
| | - Pei-Chao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China.
- Key Laboratory of Chest Cancer, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China.
| | - Xiao-Gang Zhao
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China.
- Key Laboratory of Chest Cancer, The Second Hospital, Cheeloo College of Medicine, Shandong University, Ji-nan, 250012, China.
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4
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Rao J, Sinn M, Pelzer U, Riess H, Oettle H, Demir IE, Friess H, Jäger C, Steiger K, Muckenhuber A. KRT81 and HNF1A expression in pancreatic ductal adenocarcinoma: investigation of predictive and prognostic value of immunohistochemistry-based subtyping. J Pathol Clin Res 2024; 10:e12377. [PMID: 38750616 PMCID: PMC11096282 DOI: 10.1002/2056-4538.12377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/19/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
Even after decades of research, pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease and responses to conventional treatments remain mostly poor. Subclassification of PDAC into distinct biological subtypes has been proposed by various groups to further improve patient outcome and reduce unnecessary side effects. Recently, an immunohistochemistry (IHC)-based subtyping method using cytokeratin-81 (KRT81) and hepatocyte nuclear factor 1A (HNF1A) could recapitulate some of the previously established molecular subtyping methods, while providing significant prognostic and, to a limited degree, also predictive information. We refined the KRT81/HNF1A subtyping method to classify PDAC into three distinct biological subtypes. The prognostic value of the IHC-based method was investigated in two primary resected cohorts, which include 269 and 286 patients, respectively. In the second cohort, we also assessed the predictive effect for response to erlotinib + gemcitabine. In both PDAC cohorts, the new HNF1A-positive subtype was associated with the best survival, the KRT81-positive subtype with the worst, and the double-negative with an intermediate survival (p < 0.001 and p < 0.001, respectively) in univariate and multivariate analyses. In the second cohort (CONKO-005), the IHC-based subtype was additionally found to have a potential predictive value for the erlotinib-based treatment effect. The revised IHC-based subtyping using KRT81 and HNF1A has prognostic significance for PDAC patients and may be of value in predicting treatment response to specific therapeutic agents.
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Affiliation(s)
- Jia Rao
- Institute of PathologyTechnical University of MunichMunichGermany
| | - Marianne Sinn
- Department of Haematology, Oncology and Tumour Immunology, CONKO‐Study‐GroupCharité – University Medicine BerlinBerlinGermany
- Department of Internal Medicine IIUniversity Medical Center of Hamburg‐EppendorfHamburgGermany
| | - Uwe Pelzer
- Department of Haematology, Oncology and Tumour Immunology, CONKO‐Study‐GroupCharité – University Medicine BerlinBerlinGermany
| | - Hanno Riess
- Department of Haematology, Oncology and Tumour Immunology, CONKO‐Study‐GroupCharité – University Medicine BerlinBerlinGermany
| | - Helmut Oettle
- Department of Haematology, Oncology and Tumour Immunology, CONKO‐Study‐GroupCharité – University Medicine BerlinBerlinGermany
| | - Ihsan E Demir
- Department of Surgery, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
- Else Kröner Clinician Scientist Professor for Translational Pancreatic SurgeryMunichGermany
| | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
| | - Carsten Jäger
- Department of Surgery, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
| | - Katja Steiger
- Institute of PathologyTechnical University of MunichMunichGermany
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Das A, Gkoutos GV, Acharjee A. Analysis of translesion polymerases in colorectal cancer cells following cetuximab treatment: A network perspective. Cancer Med 2024; 13:e6945. [PMID: 39102671 PMCID: PMC10809876 DOI: 10.1002/cam4.6945] [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: 10/15/2023] [Revised: 12/19/2023] [Accepted: 01/06/2024] [Indexed: 08/07/2024] Open
Abstract
INTRODUCTION Adaptive mutagenesis observed in colorectal cancer (CRC) cells upon exposure to EGFR inhibitors contributes to the development of resistance and recurrence. Multiple investigations have indicated a parallel between cancer cells and bacteria in terms of exhibiting adaptive mutagenesis. This phenomenon entails a transient and coordinated escalation of error-prone translesion synthesis polymerases (TLS polymerases), resulting in mutagenesis of a magnitude sufficient to drive the selection of resistant phenotypes. METHODS In this study, we conducted a comprehensive pan-transcriptome analysis of the regulatory framework within CRC cells, with the objective of identifying potential transcriptome modules encompassing certain translesion polymerases and the associated transcription factors (TFs) that govern them. Our sampling strategy involved the collection of transcriptomic data from tumors treated with cetuximab, an EGFR inhibitor, untreated CRC tumors, and colorectal-derived cell lines, resulting in a diverse dataset. Subsequently, we identified co-regulated modules using weighted correlation network analysis with a minKMEtostay threshold set at 0.5 to minimize false-positive module identifications and mapped the modules to STRING annotations. Furthermore, we explored the putative TFs influencing these modules using KBoost, a kernel PCA regression model. RESULTS Our analysis did not reveal a distinct transcriptional profile specific to cetuximab treatment. Moreover, we elucidated co-expression modules housing genes, for example, POLK, POLI, POLQ, REV1, POLN, and POLM. Specifically, POLK, POLI, and POLQ were assigned to the "blue" module, which also encompassed critical DNA damage response enzymes, for example. BRCA1, BRCA2, MSH6, and MSH2. To delineate the transcriptional control of this module, we investigated associated TFs, highlighting the roles of prominent cancer-associated TFs, such as CENPA, HNF1A, and E2F7. CONCLUSION We found that translesion polymerases are co-regulated with DNA mismatch repair and cell cycle-associated factors. We did not, however, identified any networks specific to cetuximab treatment indicating that the response to EGFR inhibitors relates to a general stress response mechanism.
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Affiliation(s)
- Anubrata Das
- Institute of Cancer and Genomic Sciences, College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Georgios V. Gkoutos
- Institute of Cancer and Genomic Sciences, College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
- Institute of Translational MedicineUniversity Hospitals Birmingham NHS Foundation TrustBirminghamUK
- MRC Health Data Research UK (HDR UK)LondonUK
- Centre for Health Data ResearchUniversity of BirminghamBirminghamUK
- NIHR Experimental Cancer Medicine CentreBirminghamUK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
- Institute of Translational MedicineUniversity Hospitals Birmingham NHS Foundation TrustBirminghamUK
- MRC Health Data Research UK (HDR UK)LondonUK
- Centre for Health Data ResearchUniversity of BirminghamBirminghamUK
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6
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Fujino S, Miyoshi N, Ito A, Hayashi R, Yasui M, Matsuda C, Ohue M, Horie M, Yachida S, Koseki J, Shimamura T, Hata T, Ogino T, Takahashi H, Uemura M, Mizushima T, Doki Y, Eguchi H. Metastases and treatment-resistant lineages in patient-derived cancer cells of colorectal cancer. Commun Biol 2023; 6:1191. [PMID: 37996567 PMCID: PMC10667365 DOI: 10.1038/s42003-023-05562-y] [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: 01/25/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Circulating tumor cells (CTCs) play an important role in metastasis and recurrence. However, which cells comprise the complex tumor lineages in recurrence and are key in metastasis are unknown in colorectal cancer (CRC). CRC with high expression of POU5F1 has a poor prognosis with a high incidence of liver metastatic recurrence. We aim to reveal the key cells promoting metastasis and identify treatment-resistant lineages with established EGFP-expressing organoids in two-dimensional culture (2DOs) under the POU5F1 promotor. POU5F1-expressing cells are highly present in relapsed clinical patients' blood as CTCs. Sorted POU5F1-expressing cells from 2DOs have cancer stem cell abilities and abundantly form liver metastases in vivo. Single-cell RNA sequencing of 2DOs identifies heterogeneous populations derived from POU5F1-expressing cells and the Wnt signaling pathway is enriched in POU5F1-expressing cells. Characteristic high expression of CTLA4 is observed in POU5F1-expressing cells and immunocytochemistry confirms the co-expression of POU5F1 and CTLA4. Demethylation in some CpG islands at the transcriptional start sites of POU5F1 and CTLA4 is observed. The Wnt/β-catenin pathway inhibitor, XAV939, prevents the adhesion and survival of POU5F1-expressing cells in vitro. Early administration of XAV939 also completely inhibits liver metastasis induced by POU5F1-positive cells.
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Affiliation(s)
- Shiki Fujino
- Department of Gastroenterology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
- Innovative Oncology Research and Translational Medicine, Osaka International Cancer Institute, Chuo-ku, Osaka, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan.
- Innovative Oncology Research and Translational Medicine, Osaka International Cancer Institute, Chuo-ku, Osaka, Japan.
| | - Aya Ito
- Innovative Oncology Research and Translational Medicine, Osaka International Cancer Institute, Chuo-ku, Osaka, Japan
| | - Rie Hayashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
- Innovative Oncology Research and Translational Medicine, Osaka International Cancer Institute, Chuo-ku, Osaka, Japan
| | - Masayoshi Yasui
- Department of Surgery, Osaka International Cancer Institute, Chuo-ku, Osaka, 541-8567, Japan
| | - Chu Matsuda
- Department of Surgery, Osaka International Cancer Institute, Chuo-ku, Osaka, 541-8567, Japan
| | - Masayuki Ohue
- Department of Surgery, Osaka International Cancer Institute, Chuo-ku, Osaka, 541-8567, Japan
| | - Masafumi Horie
- Department of Cancer Genome Informatics, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Jun Koseki
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Nagoya-City, Aichi, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Nagoya-City, Aichi, Japan
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita-City, Osaka, Japan
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7
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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8
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Xia R, Hu C, Ye Y, Zhang X, Li T, He R, Zheng S, Wen X, Chen R. HNF1A regulates oxaliplatin resistance in pancreatic cancer by targeting 53BP1. Int J Oncol 2023; 62:45. [PMID: 36825600 PMCID: PMC9990585 DOI: 10.3892/ijo.2023.5493] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
DNA double‑strand break repair is critically involved in oxaliplatin resistance in pancreatic ductal adenocarcinoma (PDAC). Hepatocyte nuclear factor 1 homeobox A (HNF1A) has received increased attention regarding its role in cancer progression. The present study explored the role of HNF1A in oxaliplatin resistance in PDAC. The results revealed that HNF1A expression was negatively associated with oxaliplatin chemoresistance in PDAC tissues and cell lines. HNF1A inhibition promoted the proliferation, colony formation and stemness of PDAC cells, and suppressed their apoptosis. Furthermore, HNF1A inhibition switched nonhomologous end joining to homologous recombination, thereby enhancing genomic stability and oxaliplatin resistance. Mechanistically, HNF1A transcriptionally activates p53‑binding protein 1 (53BP1) expression by directly interacting with the 53BP1 promoter region. Upregulation of HNF1A and 53BP1 induced significant inhibition of PDAC growth and oxaliplatin resistance in patient‑derived PDAC xenograft models and orthotopic models. In conclusion, the findings of the present study suggested that HNF1A/53BP1 may be a promising PDAC therapeutic target for overcoming oxaliplatin resistance.
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Affiliation(s)
- Renpeng Xia
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Chonghui Hu
- Department of Pancreas Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Yuancheng Ye
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xiang Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Tingting Li
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, P.R. China
| | - Rihua He
- Department of Pancreas Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Shangyou Zheng
- Department of Pancreas Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Xiaofeng Wen
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Rufu Chen
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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9
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Zheng Z, Wei J, Hou X, Jia F, Zhang Z, Guo H, Yuan F, He F, Ke Z, Wang Y, Zhao L. A High Hepatic Uptake of Conjugated Bile Acids Promotes Colorectal Cancer-Associated Liver Metastasis. Cells 2022; 11:cells11233810. [PMID: 36497071 PMCID: PMC9736302 DOI: 10.3390/cells11233810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The liver is the most common site for colorectal cancer (CRC)-associated metastasis. There remain unsatisfactory medications in liver metastasis given the incomplete understanding of pathogenic mechanisms. Herein, with an orthotopic implantation model fed either regular or high-fat diets (HFD), more liver metastases were associated with an expansion of conjugated bile acids (BAs), particularly taurocholic acid (TCA) in the liver, and an increased gene expression of Na+-taurocholate cotransporting polypeptide (NTCP). Such hepatic BA change was more apparently shown in the HFD group. In the same model, TCA was proven to promote liver metastases and induce a tumor-favorable microenvironment in the liver, characterizing a high level of fibroblast activation and increased proportions of myeloid-derived immune cells. Hepatic stellate cells, a liver-residing source of fibroblasts, were dose-dependently activated by TCA, and their conditioned medium significantly enhanced the migration capability of CRC cells. Blocking hepatic BA uptake with NTCP neutralized antibody can effectively repress TCA-triggered liver metastases, with an evident suppression of tumor microenvironment niche formation. This study points to a new BA-driven mechanism of CRC-associated liver metastases, suggesting that a reduction of TCA overexposure by limiting liver uptake is a potential therapeutic option for CRC-associated liver metastasis.
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Affiliation(s)
- Zongmei Zheng
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiao Wei
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xinxin Hou
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Fengjing Jia
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhaozhou Zhang
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Haidong Guo
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Fuwen Yuan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Feng He
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zunji Ke
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yan Wang
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (Y.W.); (L.Z.)
| | - Ling Zhao
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (Y.W.); (L.Z.)
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Doescher J, von Witzleben A, Boukas K, Weissinger SE, Thomas GJ, Laban S, Thomas J, Hoffmann TK, Ottensmeier CH. Changes in Gene Expression Patterns in the Tumor Microenvironment of Head and Neck Squamous Cell Carcinoma Under Chemoradiotherapy Depend on Response. Front Oncol 2022; 12:862694. [PMID: 35433484 PMCID: PMC9012140 DOI: 10.3389/fonc.2022.862694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/14/2022] [Indexed: 12/24/2022] Open
Abstract
Chemoradiotherapy (CRT) is a standard treatment for advanced head and neck squamous cell carcinoma (HNSCC). Unfortunately, not all patients respond to this therapy and require further treatment, either salvage surgery or palliative therapy. The addition of immunotherapy to CRT is currently being investigated and early results describe a mixed response. Therefore, it is important to understand the impact of CRT on the tumor microenvironment (TME) to be able to interpret the results of the clinical trials. Paired biopsies from 30 HNSCC patients were collected before and three months after completion of primary CRT and interrogated for the expression of 1392 immune- and cancer-related genes. There was a relevant difference in the number of differentially expressed genes between the total cohort and patients with residual disease. Genes involved in T cell activation showed significantly reduced expression in these tumors after therapy. Furthermore, gene enrichment for several T cell subsets confirmed this observation. The analysis of tissue resident memory T cells (TRM) did not show a clear association with impaired response to therapy. CRT seems to lead to a loss of T cells in patients with incomplete response that needs to be reversed. It is not clear whether the addition of anti-PD-1 antibodies alone to CRT can prevent treatment failure, as no upregulation of the targets was measurable in the TME.
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Affiliation(s)
- Johannes Doescher
- Translational Immunology Group, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- *Correspondence: Johannes Doescher,
| | - Adrian von Witzleben
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Konstantinos Boukas
- Wessex Investigational Sciences Hub, University of Southampton, Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | | | - Gareth J. Thomas
- Wessex Investigational Sciences Hub, University of Southampton, Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Simon Laban
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Jaya Thomas
- Wessex Investigational Sciences Hub, University of Southampton, Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Thomas K. Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Christian H. Ottensmeier
- Translational Immunology Group, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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11
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Haque E, Teeli AS, Winiarczyk D, Taguchi M, Sakuraba S, Kono H, Leszczyński P, Pierzchała M, Taniguchi H. HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks. Genes (Basel) 2022; 13:genes13030413. [PMID: 35327967 PMCID: PMC8949677 DOI: 10.3390/genes13030413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatocyte nuclear factor 1A (HNF1A) is the master regulator of liver homeostasis and organogenesis and regulates many aspects of hepatocyte functions. It acts as a tumor suppressor in the liver, evidenced by the increased proliferation in HNF1A knockout (KO) hepatocytes. Hence, we postulated that any loss-of-function variation in the gene structure or composition (mutation) could trigger dysfunction, including disrupted transcriptional networks in liver cells. From the International Cancer Genome Consortium (ICGC) database of cancer genomes, we identified several HNF1A mutations located in the functional Pit-Oct-Unc (POU) domain. In our biochemical analysis, we found that the HNF1A POU-domain mutations Y122C, R229Q and V259F suppressed HNF4A promoter activity and disrupted the binding of HNF1A to its target HNF4A promoter without any effect on the nuclear localization. Our results suggest that the decreased transcriptional activity of HNF1A mutants is due to impaired DNA binding. Through structural simulation analysis, we found that a V259F mutation was likely to affect DNA interaction by inducing large conformational changes in the N-terminal region of HNF1A. The results suggest that POU-domain mutations of HNF1A downregulate HNF4A gene expression. Therefore, to mimic the HNF1A mutation phenotype in transcription networks, we performed siRNA-mediated knockdown (KD) of HNF4A. Through RNA-Seq data analysis for the HNF4A KD, we found 748 differentially expressed genes (DEGs), of which 311 genes were downregulated (e.g., HNF1A, ApoB and SOAT2) and 437 genes were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed that the DEGs were involved in several signaling pathways (e.g., lipid and cholesterol metabolic pathways). Protein–protein network analysis suggested that the downregulated genes were related to lipid and cholesterol metabolism pathways, which are implicated in hepatocellular carcinoma (HCC) development. Our study demonstrates that mutations of HNF1A in the POU domain result in the downregulation of HNF1A target genes, including HNF4A, and this may trigger HCC development through the disruption of HNF4A–HNF1A transcriptional networks.
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Affiliation(s)
- Effi Haque
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Aamir Salam Teeli
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Dawid Winiarczyk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Shun Sakuraba
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum Science and Technology, Kizugawa 619-0215, Japan; (M.T.); (S.S.); (H.K.)
| | - Paweł Leszczyński
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (E.H.); (A.S.T.); (D.W.); (P.L.); (M.P.)
- Correspondence: ; Tel.: +48-22-736-70-95
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12
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Barata T, Vieira V, Rodrigues R, Neves RPD, Rocha M. Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells. Comput Biol Med 2021; 142:105177. [PMID: 35026576 DOI: 10.1016/j.compbiomed.2021.105177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023]
Abstract
Cancer Stem Cells (CSCs) contribute to cancer aggressiveness, metastasis, chemo/radio-therapy resistance, and tumor recurrence. Recent studies emphasized the importance of metabolic reprogramming of CSCs for the maintenance and progression of the cancer phenotype through both the fulfillment of the energetic requirements and the supply of substrates fundamental for fast-cell growth, as well as through metabolite-induced epigenetic regulation. Therefore, it is of paramount importance to develop therapeutic strategies tailored to target the metabolism of CSCs. In this work, we built computational Genome-Scale Metabolic Models (GSMMs) for CSCs of different tissues. Flux simulations were then used to predict metabolic phenotypes, identify potential therapeutic targets, and spot already-known Transcription Factors (TFs), miRNAs and antimetabolites that could be used as part of drug repurposing strategies against cancer. Results were in accordance with experimental evidence, provided insights of new metabolic mechanisms for already known agents, and allowed for the identification of potential new targets and compounds that could be interesting for further in vitro and in vivo validation.
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Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - Vítor Vieira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Rúben Rodrigues
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal.
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; Department of Informatics, University of Minho.
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Khashefizadeh A. Hepatocyte nuclear factor 1A-antisense: Review of its role in the carcinogenesis. Pathol Res Pract 2021; 227:153623. [PMID: 34563755 DOI: 10.1016/j.prp.2021.153623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Hepatocyte nuclear factor 1A-antisense (HNF1A-AS) is an RNA gene classified as a long non-coding RNA (lncRNA). This gene is located on 12q24.31 and produces at least seven transcripts. This lncRNA contributes in the pathogenesis of cancer via HNF1A-dependent and -independent routes. Moreover, the role of this lncRNA in this process is context-dependent. The bulk of evidence from cell line, in vivo and clinical studies propose HNF1A-AS as an oncogenic lncRNA. However, in hepatic cancer, gastric cancer and laryngeal cancer, opposite results have been reported. In the current review, we explain the impact of HNF1A-AS in the pathoetiology of cancers. In order to appraise the importance of available evidence on this topic, we have classified evidence to preclinical models (cell liens and animal models) and investigations in tissues obtained from human subjects.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Alireza Khashefizadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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