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Bayasgalan T, Kanda M, Sato Y, Zhu H, Hamrah MH, Martinez FEG, Shinozuka T, Ito Y, Sasahara M, Shimizu D, Umeda S, Inokawa Y, Hattori N, Hayashi M, Tanaka C, Kodera Y. SPOCD1 Enhances Cancer Cell Activities and Serves as a Prognosticator in Esophageal Squamous Cell Carcinoma. Cancer Genomics Proteomics 2025; 22:306-325. [PMID: 39993802 PMCID: PMC11880929 DOI: 10.21873/cgp.20503] [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: 12/10/2024] [Revised: 01/02/2025] [Accepted: 01/13/2025] [Indexed: 02/26/2025] Open
Abstract
BACKGROUND/AIM Comprehensive transcriptome analysis has revealed SPOC Domain Containing 1 (SPOCD1) as a potential biomarker for esophageal squamous cell carcinoma (ESCC). However, the expression and oncological roles of SPOCD1 in ESCC remains underexplored. We aimed to evaluate the role of SPOCD1 in oncogenesis and prognosis of ESCC in vitro and in vivoMaterials and Methods: The Cancer Cell Line Encyclopedia (CCLE) database was utilized to evaluate correlations between SPOCD1 expression and oncogenes in ESCC. mRNA and protein levels were measured by qRT-PCR and Simple Western assays, respectively. siRNA-mediated knockdown and overexpression experiments assessed the effects of SPOCD1 expression on proliferation, migration, and invasion of ESCC cell lines. In vivo, siRNA knockdown effects on tumor growth were tested in mouse xenograft models. SPOCD1 mRNA levels in 164 resected tissues were correlated with clinicopathological parameters and survival, while a cohort of 177 patients was analyzed for protein expression and survival. RESULTS SPOCD1 mRNA expression varied widely among ESCC cell lines and correlated with epithelial-mesenchymal transition-related genes. Knockdown significantly suppressed proliferation, migration, and invasion (p<0.001), while overexpression increased proliferation (p<0.001). In vivo, siRNA knockdown reduced tumor growth compared to both si-control (p=0.005) and untransfected groups (p<0.001). High SPOCD1 mRNA expression was linked to poor disease-specific survival (p=0.009, HR=1.965, 95% CI=1.187-3.252) and disease-free survival (p=0.047, HR=1.602, 95% CI=1.007-2.549). Similarly, elevated protein levels were associated with unfavorable disease-specific (p=0.013, HR=1.860, 95% CI=1.137-3.041) and disease-free survival (p=0.032, HR=1.618, 95% CI=1.042-2.513). CONCLUSION SPOCD1 expression correlates with the aggressiveness of ESCC cells, and its expression levels in tumor tissues may serve as a prognostic factor for ESCC patients.
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Affiliation(s)
- Tuvshin Bayasgalan
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan;
| | - Yusuke Sato
- Department of Thoracic Surgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Haote Zhu
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mohammad Hussain Hamrah
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Takahiro Shinozuka
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Ito
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Sasahara
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Dai Shimizu
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichi Umeda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshikuni Inokawa
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norifumi Hattori
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masamichi Hayashi
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chie Tanaka
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Wang X, Yang Y, Zhou X, Yu S, Luo X, Lu L, Gao Z, Yang J. IFNγ regulates ferroptosis in KFs by inhibiting the expression of SPOCD1 through DNMT3A. Cell Death Discov 2025; 11:9. [PMID: 39820341 PMCID: PMC11739694 DOI: 10.1038/s41420-024-02257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 11/15/2024] [Accepted: 12/02/2024] [Indexed: 01/19/2025] Open
Abstract
Keloid is benign skin tumor, and their curing is relatively difficult due to the unclear mechanism of formation. Inducing ferroptosis of keloid fibroblasts (KFs) may become a new method for treating keloid. Here, we discover interferon (IFN)γ could induce KFs ferroptosis through inhibiting SPOC domain-containing protein 1 (SPOCD1), serving as a mode of action for CD8+T cell (CTL)-mediated keloid killing. Mechanistically, keloid IFNγ deficiency in combination with reduced DNMT3A increase the expression of SPOCD1, thereby promoting KFs' proliferation and inhibiting its ferroptosis. Moreover, keloid SPOCD1 deficiency attenuates KFs progression and extracellular matrix (ECM) deposition. Reducing IFNγ and SPOCD1 simultaneously can increase the positive rate of reactive oxygen species (ROS) and promote mitochondrial shrinkage. Ex-vivo explant keloid culture has also confirmed that the reduction of SPOCD1 helps to reduce the proliferation rate of KFs, inhibit the angiogenesis of keloid scars, and thus inhibit keloid formation. Thus, IFNγ signaling paired with SPOCD1 is a natural keloid ferroptosis promoting mechanism and a mode of action of CTLs. Targeting SPOCD1 pathway is a potential anti-keloid approach.
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Affiliation(s)
- Xiuxia Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Yating Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Xianyu Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Shun Yu
- The Affiliated Hospital of Jiangnan University, Jiangsu, China
| | - Xusong Luo
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Lin Lu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Zhen Gao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Jun Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China.
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Lee SC, Peterson C, Wang K, Alaali L, Eshleman J, Mahoney NR, Li E, Eberhart CG, Campbell AA. Establishment and Characterization of Three Human Ocular Adnexal Sebaceous Carcinoma Cell Lines. Int J Mol Sci 2024; 25:10183. [PMID: 39337668 PMCID: PMC11432008 DOI: 10.3390/ijms251810183] [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: 08/16/2024] [Revised: 09/14/2024] [Accepted: 09/21/2024] [Indexed: 09/30/2024] Open
Abstract
Ocular adnexal sebaceous carcinoma (SebCA) represents one of the most clinically problematic periocular tumors, often requiring aggressive surgical resection. The pathobiology of this tumor remains poorly understood, and few models exist that are suitable for preclinical testing. The aim of this study was to establish new cell lines to serve as models for pathobiological and drug testing. With patient consent, freshly resected tumor tissue was cultured using conditional reprogramming cell conditions. Standard techniques were used to characterize the cell lines in terms of overall growth, clonogenicity, apoptosis, and differentiation in vitro. Additional analyses including Western blotting, short tandem repeat (STR) profiling, and next-generation sequencing (NGS) were performed. Drug screening using mitomycin-C (MMC), 5-fluorouricil (5-FU), and 6-Diazo-5-oxo-L-norleucine (DON) were performed. JHH-SebCA01, JHH-SebCA02, and JHH-SebCA03 cell lines were established from two women and one man undergoing surgical resection of eyelid tumors. At passage 15, they each showed a doubling time of two to three days, and all could form colonies in anchorage-dependent conditions, but not in soft agar. The cells contained cytoplasmic vacuoles consistent with sebaceous differentiation, and adipophilin protein was present in all three lines. STR profiling confirmed that all lines were derived from their respective patients. NGS of the primary tumors and their matched cell lines identified numerous shared mutations, including alterations similar to those previously described in SebCA. Treatment with MMC or 5-FU resulted in dose-dependent growth inhibition and the induction of both apoptosis and differentiation. MYC protein was abundant in all three lines, and the glutamine metabolism inhibitor DON, previously shown to target high MYC tumors, slowed the growth of all our SebCA models. Ocular adnexal SebCA cell lines can be established using conditional reprogramming cell conditions, and our three new models are useful for testing therapies and interrogating the functional role of MYC and other possible molecular drivers. Current topical chemotherapies promote both apoptosis and differentiation in SebCA cells, and these tumors appear sensitive to inhibition or MYC-associated metabolic changes.
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Affiliation(s)
- Su-Chan Lee
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.-C.L.)
| | - Cornelia Peterson
- Department of Comparative Pathobiology, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA;
| | - Kaixuan Wang
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lujain Alaali
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.-C.L.)
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Eshleman
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.-C.L.)
| | - Nicholas R. Mahoney
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Li
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charles G. Eberhart
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.-C.L.)
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashley A. Campbell
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Bondar G, Mahapatra AD, Bao TM, Silacheva I, Hairapetian A, Vu T, Su S, Katappagari A, Galan L, Chandran J, Adamov R, Mancusi L, Lai I, Rahman A, Grogan T, Hsu JJ, Cappelletti M, Ping P, Elashoff D, Reed EF, Deng MC. An Exercise Immune Fitness Test to Unravel Disease Mechanisms-A Proof-of-Concept Heart Failure Study. J Clin Med 2024; 13:3200. [PMID: 38892912 PMCID: PMC11172881 DOI: 10.3390/jcm13113200] [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: 05/14/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Background: Cardiorespiratory fitness positively correlates with longevity and immune health. Regular exercise may provide health benefits by reducing systemic inflammation. In chronic disease conditions, such as chronic heart failure and chronic fatigue syndrome, mechanistic links have been postulated between inflammation, muscle weakness, frailty, catabolic/anabolic imbalance, and aberrant chronic activation of immunity with monocyte upregulation. We hypothesize that (1) temporal changes in transcriptome profiles of peripheral blood mononuclear cells during strenuous acute bouts of exercise using cardiopulmonary exercise testing are present in adult subjects, (2) these temporal dynamic changes are different between healthy persons and heart failure patients and correlate with clinical exercise-parameters and (3) they portend prognostic information. Methods: In total, 16 Heart Failure (HF) patients and 4 healthy volunteers (HV) were included in our proof-of-concept study. All participants underwent upright bicycle cardiopulmonary exercise testing. Blood samples were collected at three time points (TP) (TP1: 30 min before, TP2: peak exercise, TP3: 1 h after peak exercise). We divided 20 participants into 3 clinically relevant groups of cardiorespiratory fitness, defined by peak VO2: HV (n = 4, VO2 ≥ 22 mL/kg/min), mild HF (HF1) (n = 7, 14 < VO2 < 22 mL/kg/min), and severe HF (HF2) (n = 9, VO2 ≤ 14 mL/kg/min). Results: Based on the statistical analysis with 20-100% restriction, FDR correction (p-value 0.05) and 2.0-fold change across the three time points (TP1, TP2, TP3) criteria, we obtained 11 differentially expressed genes (DEG). Out of these 11 genes, the median Gene Expression Profile value decreased from TP1 to TP2 in 10 genes. The only gene that did not follow this pattern was CCDC181. By performing 1-way ANOVA, we identified 8/11 genes in each of the two groups (HV versus HF) while 5 of the genes (TTC34, TMEM119, C19orf33, ID1, TKTL2) overlapped between the two groups. We found 265 genes which are differentially expressed between those who survived and those who died. Conclusions: From our proof-of-concept heart failure study, we conclude that gene expression correlates with VO2 peak in both healthy individuals and HF patients, potentially by regulating various physiological processes involved in oxygen uptake and utilization during exercise. Multi-omics profiling may help identify novel biomarkers for assessing exercise capacity and prognosis in HF patients, as well as potential targets for therapeutic intervention to improve VO2 peak and quality of life. We anticipate that our results will provide a novel metric for classifying immune health.
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Affiliation(s)
- Galyna Bondar
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | | | - Tra-Mi Bao
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Irina Silacheva
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Adrian Hairapetian
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Thomas Vu
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Stephanie Su
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Ananya Katappagari
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Liana Galan
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Joshua Chandran
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Ruben Adamov
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Lorenzo Mancusi
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Isabel Lai
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Anca Rahman
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Tristan Grogan
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Jeffrey J. Hsu
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Monica Cappelletti
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Peipei Ping
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - David Elashoff
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Elaine F. Reed
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Mario C. Deng
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Gu R, Ge N, Huang B, Fu J, Zhang Y, Wang N, Xu Y, Li L, Peng X, Zou Y, Sun Y, Sun X. Impacts of vitrification on the transcriptome of human ovarian tissue in patients with gynecological cancer. Front Genet 2023; 14:1114650. [PMID: 37007967 PMCID: PMC10063885 DOI: 10.3389/fgene.2023.1114650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
Objective: This study investigated the effects of a vitrification/warming procedure on the mRNA transcriptome of human ovarian tissues.Design: Human ovarian tissues were collected and processed through vitrification (T-group) and then subjected to RNA sequencing (RNA-seq) analysis, HE, TdT-mediated dUTP nick-end labeling (TUNEL), and real-time quantitative PCR, and the results were compared to those of the fresh group (CK).Results: A total of 12 patients, aged 15–36 years old, with a mean anti-Müllerian hormone level of 4.57 ± 3.31 ng/mL were enrolled in this study. According to the HE and TUNEL results, vitrification effectively preserved human ovarian tissue. A total of 452 significantly dysregulated genes (|log2FoldChange| > 1 and p < 0.05) were identified between the CK and T groups. Among these, 329 were upregulated and 123 were downregulated. A total of 372 genes were highly enriched for 43 pathways (p < 0.05), which were mainly related to systemic lupus erythematous, cytokine–cytokine receptor interaction, the TNF signaling pathway, and the MAPK signaling pathway. IL10, AQP7, CCL2, FSTL3, and IRF7 were significantly upregulated (p < 0.01), while IL1RN, FCGBP, VEGFA, ACTA2, and ASPN were significantly downregulated in the T-group (p < 0.05) compared to the CK group, which agreed with the results of the RNA-seq analysis.Conclusion: These results showed (for the first time to the authors’ knowledge) that vitrification can induce changes in mRNA expression in human ovarian tissues. Further molecular studies on human ovarian tissues are required to determine whether altered gene expression could result in any downstream consequences.
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Affiliation(s)
- Ruihuan Gu
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Naidong Ge
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Bin Huang
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jing Fu
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Department of Female Fertility Preservation, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ningyi Wang
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yan Xu
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lu Li
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Xiandong Peng
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yaoyu Zou
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yijuan Sun
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- *Correspondence: Yijuan Sun, ; Xiaoxi Sun,
| | - Xiaoxi Sun
- Department of Shanghai Ji’ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- *Correspondence: Yijuan Sun, ; Xiaoxi Sun,
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7
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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8
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529899. [PMID: 36945455 PMCID: PMC10028821 DOI: 10.1101/2023.02.24.529899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such regulation. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights for the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations. The TranNet method was implemented in python, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/TranNet .
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
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9
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Wang Z, Huang Z, Cao X, Zhang F, Cai J, Tang P, Yang C, Li S, Yu D, Yan Y, Shen B. A prognostic model based on necroptosis-related genes for prognosis and therapy in bladder cancer. BMC Urol 2023; 23:10. [PMID: 36709279 PMCID: PMC9883845 DOI: 10.1186/s12894-023-01175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/09/2023] [Indexed: 01/30/2023] Open
Abstract
Bladder cancer, one of the most prevalent malignant cancers, has high rate of recurrence and metastasis. Owing to genomic instability and high-level heterogeneity of bladder cancer, chemotherapy and immunotherapy drugs sensitivity and lack of prognostic markers, the prognosis of bladder cancer is unclear. Necroptosis is a programmed modality of necrotic cell death in a caspase-independent form. Despite the fact that necroptosis plays a critical role in tumor growth, cancer metastasis, and cancer patient prognosis, necroptosis-related gene sets have rarely been studied in bladder cancer. As a result, the development of new necroptosis-related prognostic indicators for bladder cancer patients is critical. Herein, we assessed the necroptosis landscape of bladder cancer patients from The Cancer Genome Atlas database and classified them into two unique necroptosis-related patterns, using the consensus clustering. Then, using five prognosis-related genes, we constructed a prognostic model (risk score), which contained 5 genes (ANXA1, DOK7, FKBP10, MAP1B and SPOCD1). And a nomogram model was also developed to offer the clinic with a more useful prognostic indicator. We found that risk score was significantly associated with clinicopathological characteristics, TIME, and tumor mutation burden in patients with bladder cancer. Moreover, risk score was a valid guide for immunotherapy, chemotherapy, and targeted drugs. In our study, DOK7 was chosen to further verify our prognosis model, and functional assays indicated that knockdown the expression of DOK7 could prompt bladder cancer proliferation and migration. Our work demonstrated the potential role of prognostic model based on necroptosis genes in the prognosis, immune landscape and response efficacy of immunotherapy of bladder cancer.
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Affiliation(s)
- Zeyi Wang
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital of Nanjing Medical University, Shanghai, 200080 China
| | - Zhengnan Huang
- grid.24516.340000000123704535Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065 China
| | - Xiangqian Cao
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Fang Zhang
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Jinming Cai
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Pengfei Tang
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital of Nanjing Medical University, Shanghai, 200080 China
| | - Chenkai Yang
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Shengzhou Li
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Dong Yu
- grid.73113.370000 0004 0369 1660Department of Precision Medicine, Center of Translation Medicine, Naval Medical University, Shanghai, 200082 China
| | - Yilin Yan
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
| | - Bing Shen
- grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital of Nanjing Medical University, Shanghai, 200080 China ,grid.412478.c0000 0004 1760 4628Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080 China
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10
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Gan L, Yang C, Zhao L, Wang S, Gao Z, Ye Y. Prognostic Biomarker SPOCD1 and Its Correlation with Immune Infiltrates in Colorectal Cancer. Biomolecules 2023; 13:biom13020209. [PMID: 36830578 PMCID: PMC9953389 DOI: 10.3390/biom13020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
The biological role of the spen paralogue and orthologue C-terminal domain containing 1 (SPOCD1) has been investigated in human malignancies, but its function in colorectal cancer (CRC) is unclear. This study investigated the association between SPOCD1 expression and clinicopathological features of CRC cases, as well as its prognostic value and biological function based on large-scale databases and clinical samples. The results showed that the expression level of SPOCD1 was elevated in CRC, which was generally associated with shortened survival time and poor clinical indexes, including advanced T, N, and pathologic stages. Multivariate Cox regression analysis showed that elevated SPOCD1 expression was an independent factor for poor prognosis in CRC patients. Functional enrichment analysis of SPOCD1 and its co-expressed genes revealed that SPOCD1 could act as an oncogene by regulating gene expression in essential functions and pathways of tumorigenesis, such as extracellular matrix organization, chemokine signaling pathways, and calcium signaling pathways. In addition, immune cell infiltration results showed that SPOCD1 expression was associated with various immune cells, especially macrophages. Furthermore, our findings suggested a possible function for SPOCD1 in the polarization of macrophages from M1 to M2 in CRC. In conclusion, SPOCD1 is a promising diagnostic and prognostic marker for CRC, opening new avenues for research and treatment.
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Affiliation(s)
- Lin Gan
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Zhidong Gao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
- Correspondence: (Z.G.); (Y.Y.)
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
- Correspondence: (Z.G.); (Y.Y.)
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11
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Zhou D, Zhu F, Huang ZH, Zhang H, Fan LQ, Fan JY. SPOC domain-containing protein 1 regulates the proliferation and apoptosis of human spermatogonial stem cells through adenylate kinase 4. World J Stem Cells 2022; 14:822-838. [PMID: 36619695 PMCID: PMC9813840 DOI: 10.4252/wjsc.v14.i12.822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/07/2022] [Accepted: 11/30/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Spermatogonial stem cells (SSCs) are the origin of male spermatogenesis, which can reconstruct germ cell lineage in mice. However, the application of SSCs for male fertility restoration is hindered due to the unclear mechanisms of proliferation and self-renewal in humans.
AIM To investigate the role and mechanism of SPOC domain-containing protein 1 (SPOCD1) in human SSC proliferation.
METHODS We analyzed publicly available human testis single-cell RNA sequencing (RNA-seq) data and found that SPOCD1 is predominantly expressed in SSCs in the early developmental stages. Small interfering RNA was applied to suppress SPOCD1 expression to detect the impacts of SPOCD1 inhibition on SSC proliferation and apoptosis. Subsequently, we explored the target genes of SPOCD1 using RNA-seq and confirmed their role by restoring the expression of the target genes. In addition, we examined SPOCD1 expression in some non-obstructive azoospermia (NOA) patients to explore the correlation between SPOCD1 and NOA.
RESULTS The uniform manifold approximation and projection clustering and pseudotime analysis showed that SPOCD1 was highly expressed in the early stages of SSC, and immunohistological results showed that SPOCD1 was mainly localized in glial cell line-derived neurotrophic factor family receptor alpha-1 positive SSCs. SPOCD1 knockdown significantly inhibited cell proliferation and promoted apoptosis. RNA-seq results showed that SPOCD1 knockdown significantly downregulated genes such as adenylate kinase 4 (AK4). Overexpression of AK4 in SPOCD1 knockdown cells partially reversed the phenotypic changes, indicating that AK4 is a functional target gene of SPOCD1. In addition, we found a significant downregulation of SPOCD1 expression in some NOA patients, suggesting that the downregulation of SPOCD1 may be relevant for NOA.
CONCLUSION Our study broadens the understanding of human SSC fate determination and may offer new theories on the etiology of male infertility.
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Affiliation(s)
- Dai Zhou
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- College of Life Sciences, Hunan Normal University, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Fang Zhu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
| | - Zeng-Hui Huang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Huan Zhang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Li-Qing Fan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Jing-Yu Fan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
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12
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Zhao Z, Wang C, Chu P, Lu X. Key Genes Associated with Tumor-Infiltrating Non-regulatory CD4- and CD8-Positive T Cells in Microenvironment of Hepatocellular Carcinoma. Biochem Genet 2022; 60:1762-1780. [PMID: 35092558 PMCID: PMC9470630 DOI: 10.1007/s10528-021-10175-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
The immune microenvironment in hepatocellular carcinoma (HCC), especially T-cell infiltration, plays a key role in the prognosis and drug sensitivity of HCC. Our study aimed to analyze genes related to non-regulatory CD4+ and CD8+ T cell in HCC. Data of HCC samples were downloaded from The Cancer Genome Atlas (TCGA) database. According to stromal and immune score retrieved by Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) algorithm, differentiated expressed genes (DEGs) between high and low stromal/immune scoring groups were collected. Using Cibersort algorithm, abundance of immune cells was calculated and genes related with CD4+ and CD8+ T cells were selected. Protein-protein interaction (PPI) networks and networks of microRNA (miRNA)-target gene interactions were illustrated, in which CD4+ and CD8+ T cell-related core genes were selected. Finally, Cox regression test and Kaplan-Meier (K-M) survival analysis were conducted. Totally, 1579 DEGs were identified, where 103 genes and 407 genes related with CD4+ and CD8+ T cell were selected, respectively. Each of 30 core genes related to CD4+ T cells and CD8+ T cells were selected by PPI network. Four genes each related with the two types of T cells had a significant impact on prognosis of HCC patients. Amongst, KLRB1 and IL18RAP were final two genes related to both two kinds of T cells and associated with overall survival of the HCC patients.
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Affiliation(s)
- Zijun Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Wangfujing, Beijing, 100730, China
| | - Chaonan Wang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peishan Chu
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Lu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Wangfujing, Beijing, 100730, China.
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13
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Nishi K, Fu W, Kiyama R. Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity. PLoS One 2022; 17:e0273164. [PMID: 35976950 PMCID: PMC9385026 DOI: 10.1371/journal.pone.0273164] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Estrogen action is mediated by various genes, including estrogen-responsive genes (ERGs). ERGs have been used as reporter-genes and markers for gene expression. Gene expression profiling using a set of ERGs has been used to examine statistically reliable transcriptomic assays such as DNA microarray assays and RNA sequencing (RNA-seq). However, the quality of ERGs has not been extensively examined. Here, we obtained a set of 300 ERGs that were newly identified by six sets of RNA-seq data from estrogen-treated and control human breast cancer MCF-7 cells. The ERGs exhibited statistical stability, which was based on the coefficient of variation (CV) analysis, correlation analysis, and examination of the functional association with estrogen action using database searches. A set of the top 30 genes based on CV ranking were further evaluated quantitatively by RT-PCR and qualitatively by a functional analysis using the GO and KEGG databases and by a mechanistic analysis to classify ERα/β-dependent or ER-independent types of transcriptional regulation. The 30 ERGs were characterized according to (1) the enzymes, such as metabolic enzymes, proteases, and protein kinases, (2) the genes with specific cell functions, such as cell-signaling mediators, tumor-suppressors, and the roles in breast cancer, (3) the association with transcriptional regulation, and (4) estrogen-responsiveness. Therefore, the ERGs identified here represent various cell functions and cell signaling pathways, including estrogen signaling, and thus, may be useful to evaluate estrogenic activity.
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Affiliation(s)
- Kentaro Nishi
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Wenqiang Fu
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Ryoiti Kiyama
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
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14
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Lin Z, Chen L, Wu T, Zhang Y, Huang X, Chen Y, Chen J, Xu Y. Prognostic Value of SPOCD1 in Esophageal Squamous Cell Carcinoma: A Comprehensive Study Based on Bioinformatics and Validation. Front Genet 2022; 13:872026. [PMID: 35646092 PMCID: PMC9130929 DOI: 10.3389/fgene.2022.872026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Abstract
In the study, we aimed to explore and analyze the potential function of SPOC Domain Containing 1 (SPOCD1) in esophageal squamous cell carcinoma (ESCC). We performed a comprehensive analysis of gene expression of SPOCD1 and its corresponding clinicopathological features in ESCC. In particular, the correlation between SPOCD1 and ESCC was evaluated using a wide range of analysis tools and databases, including TCGA, GTEx, GenePattern, CellMiner, GDSC, and STRING datasets. Different bioinformatics analyses, including differential expression analysis, mutation analysis, drug sensitivity analysis, function analysis, pathway analysis, co-expression network analysis, immune cell infiltration analysis, and survival analysis, were carried out to comprehensively explore the potential molecular mechanisms and functional effects of SPOCD1 on the initiation and progression of ESCC. The expression of SPOCD1 was upregulated in ESCC tissues compared to those in normal tissues. In the high SPOCD1 expression group, we found apparent mutations in TP53, TTN, and MUC16 genes, which were 92, 36, and 18%, respectively. GO and KEGG enrichment analysis of SPOCD1 and its co-expressed genes demonstrated that it may serve as an ESCC oncogene by regulating the genes expression in the essential functions and pathways of tumorigenesis, such as glycosaminoglycan binding, Cytokine-cytokine receptor interaction, and Ras signaling pathway. Besides, the immune cell infiltration results revealed that SPOCD1 expression was positively correlated with Macrophages M0 and Mast cells activated cells, and negatively correlated with plasma cells and T cells follicular helper cell infiltration. Finally, ESCC patients with high expression of SPOCD1 indicated poor overall survival. qRT-PCR demonstrated that the SPOCD1 expression in ESCC tissues was significantly higher than adjacent tissues (p < 0.001). Our study indicated that SPOCD1 was increased in ESCC tissues. The current data support the oncogenic role of SPOCD1 in the occurrence and development of ESCC. Most importantly, SPOCD1 might be an independent prognostic factor for ESCC patients.
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Affiliation(s)
- Zhizhong Lin
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Lin Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Tingting Wu
- The School of Nusing, Fujian Medical University, Fuzhou, China.,Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yiping Zhang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xinyi Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yuanmei Chen
- Department of Thoracic Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Junqiang Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yuanji Xu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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15
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Iqbal MA, Li M, Lin J, Zhang G, Chen M, Moazzam NF, Qian W. Preliminary Study on the Sequencing of Whole Genomic Methylation and Transcriptome-Related Genes in Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14051163. [PMID: 35267472 PMCID: PMC8909391 DOI: 10.3390/cancers14051163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Epigenetic alterations are critical for tumor onset and development. DNA methylation is one of the most studied pathways concerning various types of cancer. A promising and exciting avenue of research is the discovery of biomarkers of early-stage malignancies for disease prevention and prognostic indicators following cancer treatment by examining the DNA methylation modification of relevant genes implicated in cancer development. We have made significant advances in the study of DNA methylation and thyroid cancer. This study is novel in that it distinguished methylation changes that occurred primarily in the gene body region of the aforementioned hypermethylated or hypomethylated thyroid cancer genes. Our findings imply that exposing whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer provides new insight into the carcinogenesis of thyroid cancer, demonstrating that gene expression mediated by DNA methylation modifications may play a significant role in tumor growth. Abstract Thyroid carcinoma is the most prevalent endocrine cancer globally and the primary cause of cancer-related mortality. Epigenetic modifications are progressively being linked to metastasis. This study aimed to examine whole-genome DNA methylation patterns and the gene expression profiles in thyroid cancer tissue samples using a MethylationEPIC BeadChip (850K), RNA sequencing, and a targeted bisulfite sequencing assay. The results of the Illumina Infinium human methylation kit (850K) analyses identified differentially methylated CpG locations (DMPs) and differentially methylated CpG regions (DMRs) encompassing nearly the entire genome with high resolution and depth. Gene ontology and KEGG pathway analyses revealed that the genes associated with DMRs belonged to various domain-specific ontologies, including cell adhesion, molecule binding, and proliferation. The RNA-Seq study found 1627 differentially expressed genes, 1174 of which that were up-regulated and 453 of which that were down-regulated. The targeted bisulfite sequencing assay revealed that CHST2, DPP4, DUSP6, ITGA2, SLC1A5, TIAM1, TNIK, and ABTB2 methylation levels were dramatically lowered in thyroid cancer patients when compared to the controls, but GALNTL6, HTR7, SPOCD1, and GRM5 methylation levels were significantly raised. Our study revealed that the whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer shed new light on the tumorigenesis of thyroid cancer.
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Affiliation(s)
- Muhammad Asad Iqbal
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
| | - Mingyang Li
- Department of Basic Medical Sciences, Affiliated to School of Medicine, Jiangsu University, Zhenjiang 212002, China;
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Guoliang Zhang
- Department of General Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Miao Chen
- Department of Pathology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | | | - Wei Qian
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
- Correspondence: ; Tel.: +86-0511-88917833 or +86-1535-8586188
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Zheng T, Zhang X, Wang Y, Wang A. SPOCD1 regulated by miR-133a-3p promotes hepatocellular carcinoma invasion and metastasis. J Int Med Res 2022. [PMCID: PMC8733378 DOI: 10.1177/03000605211053717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Objective To investigate the tumorigenic role of spen paralogue and orthologue C-terminal domain-containing 1 (SPOCD1) in hepatocellular carcinoma (HCC) and identify the upstream regulatory mechanism. Methods We analyzed SPOCD1 and miR-133-3p expression in normal and HCC tissues from the Cancer Genome Atlas and UALCAN databases, and in normal hepatocytes and HCC cell lines by real-time quantitative polymerase chain reaction and western blot. We identified the miR-133a-3p-binding site on the SPOCD1 3ʹ-untranslated region using TargetScan. Hierarchical regulation was confirmed by luciferase assay and miR-133a-3p overexpression/silencing. Cell proliferation, migration, invasion, and colony formation were assessed by MTT, scratch, transwell, and clonogenic assays, respectively. Results SPOCD1 was highly expressed in HCC tissues and cell lines, while miR-133a-3p expression was significantly downregulated. Kaplan–Meier analysis indicated that high SPOCD1 expression was significantly associated with poor survival. TargetScan and luciferase reporter assay revealed that SPOCD1 was the downstream target of miR-133a-3p. Overexpression of miR-133a-3p significantly inhibited the expression of SPOCD1, while miR-133a-3p knockdown significantly increased SPOCD1 expression. Conclusion SPOCD1, regulated by miR-133a-3p, promotes HCC cell proliferation, migration, invasion, and colony formation. This study provides the first evidence for the role of the miR-133a-3p/SPOCD1 axis in HCC tumorigenesis.
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Affiliation(s)
- Tianying Zheng
- Department of Medical Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xin Zhang
- Department of Medical Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yonggang Wang
- Department of Medical Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Aijun Wang
- Department of Medical Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
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17
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Radio FC, Pang K, Ciolfi A, Levy MA, Hernández-García A, Pedace L, Pantaleoni F, Liu Z, de Boer E, Jackson A, Bruselles A, McConkey H, Stellacci E, Lo Cicero S, Motta M, Carrozzo R, Dentici ML, McWalter K, Desai M, Monaghan KG, Telegrafi A, Philippe C, Vitobello A, Au M, Grand K, Sanchez-Lara PA, Baez J, Lindstrom K, Kulch P, Sebastian J, Madan-Khetarpal S, Roadhouse C, MacKenzie JJ, Monteleone B, Saunders CJ, Jean Cuevas JK, Cross L, Zhou D, Hartley T, Sawyer SL, Monteiro FP, Secches TV, Kok F, Schultz-Rogers LE, Macke EL, Morava E, Klee EW, Kemppainen J, Iascone M, Selicorni A, Tenconi R, Amor DJ, Pais L, Gallacher L, Turnpenny PD, Stals K, Ellard S, Cabet S, Lesca G, Pascal J, Steindl K, Ravid S, Weiss K, Castle AMR, Carter MT, Kalsner L, de Vries BBA, van Bon BW, Wevers MR, Pfundt R, Stegmann APA, Kerr B, Kingston HM, Chandler KE, Sheehan W, Elias AF, Shinde DN, Towne MC, Robin NH, Goodloe D, Vanderver A, Sherbini O, Bluske K, Hagelstrom RT, Zanus C, Faletra F, Musante L, Kurtz-Nelson EC, Earl RK, Anderlid BM, Morin G, van Slegtenhorst M, Diderich KEM, Brooks AS, Gribnau J, Boers RG, Finestra TR, Carter LB, Rauch A, Gasparini P, Boycott KM, Barakat TS, Graham JM, Faivre L, Banka S, Wang T, Eichler EE, Priolo M, Dallapiccola B, Vissers LELM, Sadikovic B, Scott DA, Holder JL, Tartaglia M. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 2021; 108:502-516. [PMID: 33596411 PMCID: PMC8008487 DOI: 10.1016/j.ajhg.2021.01.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
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Affiliation(s)
| | - Kaifang Pang
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ciolfi
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucia Pedace
- Oncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Zhandong Liu
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Adam Jackson
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rosalba Carrozzo
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | | | - Christophe Philippe
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Joanne Baez
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | | | - Peggy Kulch
- Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | | | | | - Berrin Monteleone
- Clinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - July K Jean Cuevas
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Laura Cross
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | | | | | - Fernando Kok
- Mendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil
| | | | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eva Morava
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35137 Padua, Italy
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Lynn Pais
- Medical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | | | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sian Ellard
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sara Cabet
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Joset Pascal
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Sarit Ravid
- Pediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel
| | - Alison M R Castle
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Melissa T Carter
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Louisa Kalsner
- Connecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marijke R Wevers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Helen M Kingston
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Willow Sheehan
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | | | | | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar Sherbini
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Krista Bluske
- Illumina Clinical Services Laboratory, San Diego, CA 92122, USA
| | | | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | | | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gilles Morin
- CA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Teresa Robert Finestra
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Laurence Faivre
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Manuela Priolo
- UOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimmy Lloyd Holder
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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Kulasekaran G, Chaineau M, Piscopo VEC, Verginelli F, Fotouhi M, Girard M, Tang Y, Dali R, Lo R, Stifani S, McPherson PS. An Arf/Rab cascade controls the growth and invasiveness of glioblastoma. J Cell Biol 2021; 220:e202004229. [PMID: 33443570 PMCID: PMC7812876 DOI: 10.1083/jcb.202004229] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/27/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma is the most common and deadly malignant brain cancer. We now demonstrate that loss of function of the endosomal GTPase Rab35 in human brain tumor initiating cells (BTICs) increases glioblastoma growth and decreases animal survival following BTIC implantation in mouse brains. Mechanistically, we identify that the GTPase Arf5 interacts with the guanine nucleotide exchange factor (GEF) for Rab35, DENND1/connecdenn, and allosterically enhances its GEF activity toward Rab35. Knockdown of either Rab35 or Arf5 increases cell migration, invasiveness, and self-renewal in culture and enhances the growth and invasiveness of BTIC-initiated brain tumors in mice. RNAseq of the tumors reveals up-regulation of the tumor-promoting transcription factor SPOCD1, and disruption of the Arf5/Rab35 axis in glioblastoma cells leads to strong activation of the epidermal growth factor receptor, with resulting enhancement of SPOCD1 levels. These discoveries reveal an unexpected cascade between an Arf and a Rab and indicate a role for the cascade, and thus endosomal trafficking, in brain tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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Li Y, Lv Y, Cheng C, Huang Y, Yang L, He J, Tao X, Hu Y, Ma Y, Su Y, Wu L, Yu G, Jiang Q, Liu S, Liu X, Liu Z. SPEN induces miR-4652-3p to target HIPK2 in nasopharyngeal carcinoma. Cell Death Dis 2020; 11:509. [PMID: 32641685 PMCID: PMC7343777 DOI: 10.1038/s41419-020-2699-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023]
Abstract
SPEN family transcriptional repressor (SPEN), also known as the SMART/HDAC1-associated repressor protein (SHARP), has been reported to modulate the malignant phenotypes of breast cancer, colon cancer, and ovarian cancer. However, its role and the detail molecular basis in nasopharyngeal carcinoma (NPC) remain elusive. In this study, the SPEN mRNA and protein expression was found to be increased in NPC cells and tissues compared with nonmalignant nasopharyngeal epithelial cells and tissues. Elevated SPEN protein expression was found to promote the pathogenesis of NPC and lead to poor prognosis. Knockdown of SPEN expression resulted in inactivation ofPI3K/AKT and c-JUN signaling, thereby suppressing NPC migration and invasion. In addition, miR-4652-3p was found to be a downstream inducer of SPEN by targeting the homeodomain interacting protein kinase 2 (HIPK2) gene, a potential tumor suppressor that reduces the activation of epithelial-mesenchymal transition (EMT) signaling, thereby reducing its expression and leading to increased NPC migration, invasion, and metastasis. In addition, SPEN was found to induce miR-4652-3p expression by activating PI3K/AKT/c-JUN signaling to target HIPK2. Our data provided a new molecular mechanism for SPEN as a metastasis promoter through activation of PI3K/AKT signaling, thereby stimulating the c-JUN/miR-4652-3p axis to target HIPK2 in NPC.
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Affiliation(s)
- Yang Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Yumin Lv
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Chao Cheng
- Department of Pediatric Otorhinolaryngology, Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liu Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Jingjing He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Xingyu Tao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Yingying Hu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Yuting Ma
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Yun Su
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Liyang Wu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Guifang Yu
- Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingping Jiang
- Department of Pathology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shu Liu
- Department of Breast Surgery, Guiyang Maternal and Child Healthcare Hospital, Guiyang, 550003, Guizhou, China
| | - Xiong Liu
- E.N.T. Department of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Zhen Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 510095, Guangdong, China.
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