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Malla, Sandhya
Publications (9 of 9) Show all publications
Malla, S. (2023). Dissecting gene expression regulation in mouse embryonic stems. (Doctoral dissertation). Umeå: Umeå University
Open this publication in new window or tab >>Dissecting gene expression regulation in mouse embryonic stems
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Every cell within an organism is derived from a single fertilized egg that undergoes cellular differentiation and development to generate mature specialized cells. Mouse embryonic stem cells (ESCs) derived from the inner cell mass (ICM) of the pre-implantation blastocyst have proven to be a model to study gene expression during differentiation and development. In this thesis, we integrate different layers of gene expression programs, from epigenetics to post-translational regulation, to unravel the intricate network of pluripotency and differentiation in ESCs.

We show that Lysine-specific histone demethylase 1 (LSD1), an epigenetic regulator that removes mono- and di-methyl groups from lysine 4 of histone H3 (H3K4), is not essential for ESC self-renewal. However, the enzymatic activity of LSD1 is indispensable for differentiation. We observe a gain of H3K4me1 in the regulatory regions of pluripotency genes in Lsd1 knockout (KO) ESCs that do not alter gene expression programs related to the ESC state. Additionally, we uncover that independently of its catalytic activity, LSD1 stabilizes the DNA maintenance methylation machinery, such as DNMT1 and UHRF1 proteins, through interaction with ubiquitin-specific peptidase 7 (USP7), which ultimately maintains the DNA methylation equilibrium in the ESC state.

Furthermore, we identify chromodomain-helicase-DNA binding protein 7 (CHD7) as a novel interacting partner of LSD1 in ESCs. CHD7 is an ATP-dependent chromatin remodeler that regulates cell type-specific gene expression, specifically during neurogenesis. Herein, we show that Chd7/Lsd1 double KO ESCs showed a severe defect in differentiation, whereas Chd7 KO ESCs differentiated with mild dysregulation of ectodermal markers. This data suggests that there is a crosstalk between epigenetic regulators which mediate a distinct set of gene expression programs during lineage-specific commitment.

Besides the core pluripotency factors OCT4, SOX2, and NANOG, a cascade of co-transcriptional events such as alternative splicing (AS) and regulation by RNA binding proteins (RBP) also play a critical role in self-renewal and cell-fate decisions. Indeed, we identify Zinc Finger Protein 207 (ZFP207) as a novel RBP, essential to maintain ESC identity in vitro. In addition to impaired neuroectodermal differentiation, we also find abnormal AS events that lead to a differentiated cell-like pattern upon depletion of ZFP207 in ESCs.Altogether, the work of this thesis illustrates the complexity of gene expression regulation that modulates pluripotency and differentiation.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2023. p. 87
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 2248
National Category
Cell and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-206718 (URN)978-91-8070-073-3 (ISBN)978-91-8070-074-0 (ISBN)
Public defence
2023-05-12, Major Groove, Department of Molecular Biology, University hospital area, building 6L, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2023-04-21 Created: 2023-04-14 Last updated: 2023-04-21Bibliographically approved
Malla, S., Bhattarai, D. P., Groza, P., Melguizo-Sanchis, D., Atanasoai, I., Martinez Gamero, C., . . . Aguilo, F. (2022). ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export. EMBO Reports, 23(3), Article ID e53191.
Open this publication in new window or tab >>ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export
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2022 (English)In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 23, no 3, article id e53191Article in journal (Refereed) Published
Abstract [en]

The pluripotent state is not solely governed by the action of the core transcription factors OCT4, SOX2, and NANOG, but also by a series of co-transcriptional and post-transcriptional events, including alternative splicing (AS) and the interaction of RNA-binding proteins (RBPs) with defined subpopulations of RNAs. Zinc Finger Protein 207 (ZFP207) is an essential transcription factor for mammalian embryonic development. Here, we employ multiple functional analyses to characterize its role in mouse embryonic stem cells (ESCs). We find that ZFP207 plays a pivotal role in ESC maintenance, and silencing of Zfp207 leads to severe neuroectodermal differentiation defects. In striking contrast to human ESCs, mouse ZFP207 does not transcriptionally regulate neuronal and stem cell-related genes but exerts its effects by controlling AS networks and by acting as an RBP. Our study expands the role of ZFP207 in maintaining ESC identity, and underscores the functional versatility of ZFP207 in regulating neural fate commitment.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-191672 (URN)10.15252/embr.202153191 (DOI)000743102200001 ()35037361 (PubMedID)2-s2.0-85122763926 (Scopus ID)
Available from: 2022-01-21 Created: 2022-01-21 Last updated: 2024-04-08Bibliographically approved
Martinez-Gamero, C., Malla, S. & Aguilo, F. (2021). LSD1: Expanding functions in stem cells and differentiation. Cells, 10(11), Article ID 3252.
Open this publication in new window or tab >>LSD1: Expanding functions in stem cells and differentiation
2021 (English)In: Cells, E-ISSN 2073-4409, Vol. 10, no 11, article id 3252Article, review/survey (Refereed) Published
Abstract [en]

Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSC) provide a powerful model system to uncover fundamental mechanisms that control cellular identity during mammalian development. Histone methylation governs gene expression programs that play a key role in the regulation of the balance between self-renewal and differentiation of ESCs. Lysine-specific deme-thylase 1 (LSD1, also known as KDM1A), the first identified histone lysine demethylase, demethyl-ates H3K4me1/2 and H3K9me1/2 at target loci in a context-dependent manner. Moreover, it has also been shown to demethylate non-histone substrates playing a central role in the regulation of nu-merous cellular processes. In this review, we summarize current knowledge about LSD1 and the molecular mechanism by which LSD1 influences the stem cells state, including the regulatory cir-cuitry underlying self-renewal and pluripotency.

Place, publisher, year, edition, pages
MDPI, 2021
Keywords
Differentiation, Embryonic stem cells, Epigenetics, Histone methylation, Induced pluripotent stem cells, KDM1A, LSD1, Lysine-specific demethylase, Non-his-tone substrate, Pluripotency, Self-renewal
National Category
Cell and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-189925 (URN)10.3390/cells10113252 (DOI)000724414100001 ()34831474 (PubMedID)2-s2.0-85119274398 (Scopus ID)
Available from: 2021-11-29 Created: 2021-11-29 Last updated: 2023-09-05Bibliographically approved
Vikberg, A.-L., Malla, S. & Golovleva, I. (2020). Differential tissue specific expression of Kif23 alternative transcripts in mice with the human mutation causing congenital dyserythropoietic anemia type III. Blood Cells, Molecules & Diseases, 85, Article ID 102483.
Open this publication in new window or tab >>Differential tissue specific expression of Kif23 alternative transcripts in mice with the human mutation causing congenital dyserythropoietic anemia type III
2020 (English)In: Blood Cells, Molecules & Diseases, ISSN 1079-9796, E-ISSN 1096-0961, Vol. 85, article id 102483Article in journal (Refereed) Published
Abstract [en]

Kinesin Family Member 23 (KIF23), a cell cycle regulator, has a key task in cytokinesis. KIF23 over-expression in cancer has been associated with tumor growth, progression, and poor prognosis, indicating a potential to be a cancer biomarker. A mutation in KIF23 (c.2747C > G, p.P916R) was shown to cause congenital dyserythropoietic anemia, type III (CDA III). To-date, fifteen KIF23 transcripts have been annotated, but their expression is poorly investigated. We hypothesized that tissue specific expression of a particular transcript can be critical for CDA III phenotype. In this study, we quantified expression of alternative Kif23 transcripts in a mouse model with human KIF23 mutation and investigated its association with a regulator of alternative splicing, serine/arginine-rich splicing factor 3 (Srsf3). We confirmed presence of an additional exon 8 in both human and mouse KIF23 transcripts. A transcript lacking exons 17 and 18 was ubiquitously expressed in mice while other isoforms were common in human tissues however in bone marrow of knock-in mice a transcript without exon 18 was prevalent as it was in bone marrow of a CDA III patient. We conclude that the possibility that the tissue specific expression of KIF23 alternative transcripts influence the CDA III phenotype cannot be neglected.

Place, publisher, year, edition, pages
Elsevier, 2020
Keywords
KIF23, Srsf3, CDA III, Expression, Alternative splicing, Droplet digital PCR (ddPCR), Knock-in (KI) mice
National Category
Hematology
Identifiers
urn:nbn:se:umu:diva-175847 (URN)10.1016/j.bcmd.2020.102483 (DOI)000571001800002 ()32818800 (PubMedID)2-s2.0-85089430369 (Scopus ID)
Available from: 2020-10-15 Created: 2020-10-15 Last updated: 2023-03-24Bibliographically approved
Nyrén, R., Makoveichuk, E., Malla, S., Kersten, S., Nilsson, S. K., Ericsson, M. & Olivecrona, G. (2019). Lipoprotein lipase in mouse kidney: effects of nutritional status and high-fat diet. American Journal of Physiology - Renal Physiology, 316(3), F558-F571
Open this publication in new window or tab >>Lipoprotein lipase in mouse kidney: effects of nutritional status and high-fat diet
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2019 (English)In: American Journal of Physiology - Renal Physiology, ISSN 1931-857X, E-ISSN 1522-1466, Vol. 316, no 3, p. F558-F571Article in journal (Refereed) Published
Abstract [en]

Activity of lipoprotein lipase (LPL) is high in mouse kidney, but the reason is poorly understood. The aim was to characterize localization, regulation, and function of LPL in kidney of C57BL/6J mice. We found LPL mainly in proximal tubules, localized inside the tubular epithelial cells, under all conditions studied. In fed mice, some LPL, colocalized with the endothelial markers CD31 and GPIHBP1 and could be removed by perfusion with heparin, indicating a vascular location. The role of angiopoietin-like protein 4 (ANGPTL4) for nutritional modulation of LPL activity was studied in wild-type and Angptl4-/- mice. In Angptl4-/- mice, kidney LPL activity remained high in fasted animals, indicating that ANGPTL4 is involved in suppression of LPL activity on fasting, like in adipose tissue. The amount of ANGPTL4 protein in kidney was low, and the protein appeared smaller in size, compared with ANGPTL4 in heart and adipose tissue. To study the influence of obesity, mice were challenged with high-fat diet for 22 wk, and LPL was studied after an overnight fast compared with fasted mice given food for 3 h. High-fat diet caused blunting of the normal adaptation of LPL activity to feeding/fasting in adipose tissue, but in kidneys this adaptation was lost only in male mice. LPL activity increases to high levels in mouse kidney after feeding, but as no difference in uptake of chylomicron triglycerides in kidneys is found between fasted and fed states, our data confirm that LPL appears to have a minor role for lipid uptake in this organ.

Place, publisher, year, edition, pages
American Physiological Society, 2019
Keywords
angiopoietin-like protein 4, high-fat diet, lipoprotein lipase, mouse, triglyceride uptake
National Category
Physiology
Identifiers
urn:nbn:se:umu:diva-158108 (URN)10.1152/ajprenal.00474.2018 (DOI)000462008700015 ()30698048 (PubMedID)2-s2.0-85062588398 (Scopus ID)
Funder
Swedish Research Council, 2015-02942Swedish Heart Lung Foundation, 2016-245-32M
Available from: 2019-04-12 Created: 2019-04-12 Last updated: 2020-05-18Bibliographically approved
Malla, S., Melguizo-Sanchis, D. & Aguilo, F. (2019). Steering pluripotency and differentiation with N6-methyladenosine RNA modification. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, 1862(3), 394-402
Open this publication in new window or tab >>Steering pluripotency and differentiation with N6-methyladenosine RNA modification
2019 (English)In: Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, ISSN 1874-9399, E-ISSN 1876-4320, Vol. 1862, no 3, p. 394-402Article in journal (Refereed) Published
Abstract [en]

Chemical modifications of RNA provide a direct and rapid way to modulate the existing transcriptome, allowing the cells to adapt rapidly to the changing environment. Among these modifications, N6-methyladenosine (m6A) has recently emerged as a widely prevalent mark of messenger RNA in eukaryotes, linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. m6A modification modulates a broad spectrum of biochemical processes, including mRNA decay, translation and splicing. Both m6A modification and the enzymes that control m6A metabolism are essential for normal development. In this review, we summarized the most recent findings on the role of m6A modification in maintenance of the pluripotency of embryonic stem cells (ESCs), cell fate specification, the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), and differentiation of stem and progenitor cells.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
Adipogenesis, Cellular differentiation, Embryonic stem cell, Epitranscriptomics, Hematopoietic stem cell, Induced pluripotent stem cell, METTL3, Myogenesis, N(6)-methyladenosine, Neurogenesis, RNA methylation, Spermatogenesis
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-153977 (URN)10.1016/j.bbagrm.2018.10.013 (DOI)000462104500017 ()30412796 (PubMedID)2-s2.0-85056392321 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationVästerbotten County CouncilThe Kempe Foundations, JCK-1723.1Swedish Research Council, 2017-01636
Note

This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert

Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2023-03-24Bibliographically approved
Malla, S., Kumari, K., Martinez Gamero, C., Achour, C., Mermelekas, G., Coege, A., . . . Aguilo, F.LSD1 interacts with CHD7 to regulate the chromatin landscape in mouse embryonic stem cells.
Open this publication in new window or tab >>LSD1 interacts with CHD7 to regulate the chromatin landscape in mouse embryonic stem cells
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

 

 

 

National Category
Cell and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-206717 (URN)
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2023-04-14
Achour, C., Bhattarai, D. P., Esteva-Socias, M., Rodriguez-Barrueco, R., Malla, S., Seier, K., . . . Aguilo, F.Reshaping the role of METTL3 in breast tumorigenesis.
Open this publication in new window or tab >>Reshaping the role of METTL3 in breast tumorigenesis
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(English)Manuscript (preprint) (Other academic)
National Category
Cell Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-201048 (URN)
Available from: 2022-11-16 Created: 2022-11-16 Last updated: 2024-03-22
Malla, S., Kumari, K., Martinez Gamero, C., García-Prieto, c. A., Álvarez-Errico3, D., Stransky, S., . . . Aguilo, F.The catalytic-independent function of LSD1 modulates the epigenetic landscape of mouse embryonic stem cells.
Open this publication in new window or tab >>The catalytic-independent function of LSD1 modulates the epigenetic landscape of mouse embryonic stem cells
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(English)Manuscript (preprint) (Other academic)
Keywords
LSD1, DNA methylation, DNMT1, UHRF1 and USP7
National Category
Cell and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-206715 (URN)
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2023-04-14
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