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Luo H, Cortés-López M, Tam CL, Xiao M, Wakiro I, Chu KL, Pierson A, Chan M, Chang K, Yang X, Fecko D, Han G, Ahn EYE, Morris QD, Landau DA, Kharas MG. SON is an essential m 6A target for hematopoietic stem cell fate. Cell Stem Cell 2023; 30:1658-1673.e10. [PMID: 38065069 PMCID: PMC10752439 DOI: 10.1016/j.stem.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/23/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Stem cells regulate their self-renewal and differentiation fate outcomes through both symmetric and asymmetric divisions. m6A RNA methylation controls symmetric commitment and inflammation of hematopoietic stem cells (HSCs) through unknown mechanisms. Here, we demonstrate that the nuclear speckle protein SON is an essential m6A target required for murine HSC self-renewal, symmetric commitment, and inflammation control. Global profiling of m6A identified that m6A mRNA methylation of Son increases during HSC commitment. Upon m6A depletion, Son mRNA increases, but its protein is depleted. Reintroduction of SON rescues defects in HSC symmetric commitment divisions and engraftment. Conversely, Son deletion results in a loss of HSC fitness, while overexpression of SON improves mouse and human HSC engraftment potential by increasing quiescence. Mechanistically, we found that SON rescues MYC and suppresses the METTL3-HSC inflammatory gene expression program, including CCL5, through transcriptional regulation. Thus, our findings define a m6A-SON-CCL5 axis that controls inflammation and HSC fate.
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Affiliation(s)
- Hanzhi Luo
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariela Cortés-López
- New York Genome Center, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Cyrus L Tam
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael Xiao
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isaac Wakiro
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Aspen Pierson
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Fecko
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Han
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Quaid D Morris
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep 2023; 13:5238. [PMID: 37002329 PMCID: PMC10066285 DOI: 10.1038/s41598-023-32245-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)-proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.
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Affiliation(s)
- Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kaitlin U Laverty
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kate Nie
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Reuben Samson
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sara E Pour
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cyrus L Tam
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Niklas von Krosigk
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Benjamin Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Tam CL, Yuen MH, Nim YS, Xu YF, Au SWN, Ngo JCK, Huang P, Wong KB. Structure-based discovery of inhibitors of Helicobacter pylori urease: abridged secondary publication. Hong Kong Med J 2020; 26 Suppl 4:29-31. [PMID: 32690816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Affiliation(s)
- C L Tam
- School of Life Sciences, The Chinese University of Hong Kong
| | - M H Yuen
- School of Life Sciences, The Chinese University of Hong Kong
| | - Y S Nim
- School of Life Sciences, The Chinese University of Hong Kong
| | - Y F Xu
- College of Chinese Medicine, Guangzhou University of Chinese Medicine
| | - S W N Au
- School of Life Sciences, The Chinese University of Hong Kong
| | - J C K Ngo
- School of Life Sciences, The Chinese University of Hong Kong
| | - P Huang
- College of Chinese Medicine, Guangzhou University of Chinese Medicine
| | - K B Wong
- School of Life Sciences, The Chinese University of Hong Kong
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Tam CL, Foo YC, Lee TH. The association between perceived social support, socio-economic status and mental health in young Malaysian adults. East Asian Arch Psychiatry 2011; 21:73-78. [PMID: 21838210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVES To examine gender differences in mental health and perceived social support, relationship between parents' income and mental health, and differences in mental health across education levels. METHODS A total of 303 students aged 16 to 26 years were recruited from Selangor, Malaysia. The Multidimensional Scale of Perceived Social Support and General Health Questionnaire were used to measure the level of perceived social support and the mental health status. Demographic data, including education level and parents' income, were also obtained. RESULTS Females perceived significantly higher levels of overall social support than males (t = -2.7; p < 0.05). However, there were no significant differences in mental health status between males and females (t = -1.8; p > 0.05), as well as mental health status among different parental income groups (chi2 = 5.0; p > 0.05) and the education levels of the subjects (chi2 = 0.7; p > 0.05). A more favourable mental health status of the subjects was associated with higher parental incomes (r = -0.1; p < 0.05). CONCLUSIONS There were gender differences for perceived social support, but not for mental health status in older adolescents and young adults. There was also a relationship between parental income and an individual's mental health status, but mental health was not related to their education level.
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Affiliation(s)
- C L Tam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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Teoh HJ, Tam CL. A comparison of headache and non-headache sufferers on measures of social support and mental health problems. Malays Fam Physician 2008; 3:82-6. [PMID: 25606122 PMCID: PMC4170315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
138 headaches sufferers and 138 subjects without headaches were studied to investigate if there were differences between headache and non-headache sufferers in terms of their mental health and social support levels. The overall results of this study indicated that headache sufferers, as compared with non-headache sufferers had slightly more mental health problems, and more social support from their family members. When the results were scrutinised in more detail, it was observed that headache sufferers reported that they felt less capable of making decisions about things, were not always able to face up to their problems, and sometimes thought about themselves as a worthless. Given that the study was based on a community, rather than clinic sample, further research would be required to examine the differing the types of headaches that people are suffering from, and the intensity of the headaches, in relation to mental health problems.
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Affiliation(s)
- HJ Teoh
- Assoc Prof Dr Teoh Hsien-Jin () and Dr Tam Cai Lian () are from the Dept of Psychology, School of Health and Natural Sciences, Sunway University College, Malaysia
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England A, Tam CL, Thacker DE, Walker AL, Parkinson AS, Demello W, Bradley AJ, Tuck JS, Laasch HU, Butterfield JS, Ashleigh RJ, England RE, Martin DF. Patterns, incidence and predictive factors for pain after interventional radiology. Clin Radiol 2005; 60:1188-94. [PMID: 16223615 DOI: 10.1016/j.crad.2005.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 05/04/2005] [Accepted: 05/05/2005] [Indexed: 11/28/2022]
Abstract
AIM To evaluate prospectively the pattern, severity and predictive factors of pain after interventional radiological procedures. MATERIALS AND METHODS All patients undergoing non-arterial radiological interventional procedures were assessed using a visual-analogue scale (VAS) for pain before and at regular intervals for 24 h after their procedure. RESULTS One hundred and fifty patients (87 men, mean age 62 years, range 18-92 years) were entered into the study. Significant increases in VAS score occurred 8 h after percutaneous biliary procedures (+47.7 mm, SD 14.9 mm; p=0.001), 6 h after central venous access and gastrostomy insertion (+23.7 mm, SD 19.5 mm; p=0.001 and +28.4 mm, SD 9.7 mm; p=0.007, respectively) and 4h after oesophageal stenting (+27.8 mm, SD 20.2 mm, p=0.001). Non-significant increases in VAS pain score were observed after duodenal and colonic stenting (duodenal: +5.13 mm, SD 7.47 mm; p=0.055, colonic: +23.3 mm, SD 13.10 mm, p=0.250) at a mean of 5h (range 4-6h). Patients reported a significant reduction in pain score for nephrostomy insertion (-28.4mm, SD 7.11 mm, p=0.001). Post-procedural analgesia was required in 99 patients (69.2%), 40 (28.0%) requiring opiates. Maximum post-procedural VAS pain score was significantly higher in patients who had no pre-procedural analgesia (p=0.003). CONCLUSION Post-procedural pain is common and the pattern and severity of pain between procedures is variable. Pain control after interventional procedures is often inadequate, and improvements in pain management are required.
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Affiliation(s)
- A England
- Department of Radiology, South Manchester University Hospitals NHS Trust, Southmoor Road, Manchester, UK.
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Murakami TK, Benenson W, Chen Y, Clayton J, Kashy E, Stevenson J, Tam CL, Hanold K, Mohar M. High-energy gamma rays from reactions induced by E/A=15 MeV heavy-ion beams. Phys Rev C Nucl Phys 1989; 40:2079-2083. [PMID: 9966205 DOI: 10.1103/physrevc.40.2079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Clayton J, Stevenson J, Benenson W, Chen Y, Kashy E, Lampis AR, Samuel M, Tam CL, Mohar MF, Morrissey DJ, Murakami TK, Sherrill B, Winfield JS. High-energy gamma-ray production in the heavy-ion reaction 136Xe + Sn at E/A=89 and 124 MeV. Phys Rev C Nucl Phys 1989; 40:1207-1212. [PMID: 9966094 DOI: 10.1103/physrevc.40.1207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Tam CL, Stevenson J, Benenson W, Clayton J, Chen Y, Kashy E, Lampis AR, Morrissey DJ, Samuel M, Murakami TK, Winfield JS. Mass dependence of high-energy gamma-ray production in heavy-ion reactions. Phys Rev C Nucl Phys 1989; 39:1371-1376. [PMID: 9955344 DOI: 10.1103/physrevc.39.1371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Tam CL, Stevenson J, Benenson W, Clayton J, Chen Y, Kashy E, Lampis AR, Morrissey DJ, Samuel M, Murakami TK, Winfield JS. High-energy gamma-ray production in light-ion induced reactions. Phys Rev C Nucl Phys 1988; 38:2526-2530. [PMID: 9955095 DOI: 10.1103/physrevc.38.2526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Lampis AR, Stevenson J, Benenson W, Clayton J, Cebra D, Chen Y, Fox D, Kashy E, Morrissey DJ, Samuel M, Smith R, Tam CL, Westfall GD, Wilson K, Winfield JS. Correlations between high energy gamma rays and light fragments in heavy ion collisions. Phys Rev C Nucl Phys 1988; 38:1961-1964. [PMID: 9955013 DOI: 10.1103/physrevc.38.1961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Stevenson J, Beard KB, Benenson W, Clayton J, Kashy E, Lampis A, Morrissey DJ, Samuel M, Smith RJ, Tam CL, Winfield JS. High-energy gamma-ray emission in heavy-ion collisions. Phys Rev Lett 1986; 57:555-558. [PMID: 10034092 DOI: 10.1103/physrevlett.57.555] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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