Dr Fatima Valdes Mora

Dr Fatima Valdes Mora

Conjoint Senior Lecturer

BSc in Biochemistry, (2000-2004), Autonomous University of Madrid (Spain)

PhD in Biochemistry, Molecular Biology and Biomedicine (09/2004-12/2008), Autonomous University of Madrid (Spain)

Medicine & Health
School of Clinical Medicine

I am a mid-early career researcher arising as an authority in cancer epigenetics, single-cell transcriptomics, and epigenomics. During my career, I have made seminal discoveries in the field of histone variants and cancer epigenetics (Genome Research 2012, Nature Comms 2017, and iScience 2019) where I demonstrated an oncogenic role for acetylation of the histone variant H2A.Z. In the last 5 years, I have also focused on cutting-edge technology implementation, single-cell RNAseq, for the understanding of tumour biology transcriptionally (Cell Reports 2021) and more recently epigenetically, single-cell ATAC-seq. One of the current main foci of my group is the understanding of the epigenetic causes of childhood cancer. https://www.ccia.org.au/about-the-institute/our-research/personalised-medicine/cancer-epigenetic-biology-and-therapeutics

I obtained my PhD in Molecular Biology, Biochemistry, and Biomedicine from CSIC (Autonoma University of Madrid, Spain) in December 2008. I completed my postdoctoral research at Prof Susan Clark’s lab (Garvan Institute, Sydney Australia) in 2013 and obtained a Group Leader appointment at Garvan in 2014 to lead the Histone Variant Group. I have recently joined the Children’s Cancer Institute as Team Leader of the “Cancer Epigenetic Biology and Therapeutics” lab. From 2014, I hold a conjoint Senior Lecturer position at UNSW Sydney that have allowed me to supervise multiple Masters, Honours, and PhD students

I have published 26 peer-reviewed papers since 2004 (15 as corresponding/first author), from which 15 have been published in the last 5 years. During my postdoctoral stage, I have attracted > €2.7 M of competitive funding (as fellowships and research grants) from both public and private Australian funding bodies, including, the highly competitive NHMRC project grants (current success rate is <10%), Cancer Institute NSW, Prostate Cancer Foundation of Australia (PCFA), National Breast Cancer Foundation (NBCF) and Cure Cancer. I currently hold a CINSW Career Development Fellowship which is allowing her to establish my own research niche in epigenomics and cancer.

I have a passion for the development and implementation of novel technology that has allowed her to develop a multidisciplinary profile. I have a strong profile in molecular biology, epigenetics, single-cell transcriptomics, next-generation sequencing and bioinformatics interpretation of genome-wide data. I perform extremely well as a hinge joint between bioinformatics and biology, interpreting and integrating sequencing data into meaningful biological outputs.

  • Book Chapters | 2018
    2018, 'Epigenetic Alterations in Primary Prostate Cancer', in Molecular Pathology Library, Springer International Publishing, pp. 193 - 211, http://dx.doi.org/10.1007/978-3-319-64096-9_13
    Book Chapters | 2016
    2016, 'Single-Cell Genomics and Epigenomics', in Tseng FG; Santra TS (ed.), Essentials of Single-Cell Analysis Concepts, Applications and Future Prospects, edn. Series in BioEngineering, SPRINGER-VERLAG BERLIN, pp. 257 - 301, http://dx.doi.org/10.1007/978-3-662-49118-8_10
  • Journal articles | 2023
    2023, 'Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes', Scientific Reports, 13, pp. 3775, http://dx.doi.org/10.1038/s41598-023-30395-4
    Journal articles | 2023
    2023, 'Pleiotrophin drives a prometastatic immune niche in breast cancer.', J Exp Med, 220, http://dx.doi.org/10.1084/jem.20220610
    Journal articles | 2022
    2022, 'ALTEN: A High-Fidelity Primary Tissue-Engineering Platform to Assess Cellular Responses Ex Vivo', Advanced Science, 9, http://dx.doi.org/10.1002/advs.202103332
    Journal articles | 2022
    2022, 'DIPG-07. Preclinical and case study results underpinning the phase II clinical trial testing the combination of ONC201 and paxalisib for the treatment of patients with diffuse midline glioma (NCT05009992)', Neuro-Oncology, 24, pp. i18 - i19, http://dx.doi.org/10.1093/neuonc/noac079.064
    Journal articles | 2022
    2022, 'Disentangling single-cell omics representation with a power spectral density-based feature extraction', Nucleic Acids Research, 50, pp. 5482 - 5492, http://dx.doi.org/10.1093/nar/gkac436
    Journal articles | 2022
    2022, 'EXTH-12. PRECLINICAL AND CASE STUDY EXAMINATION OF THE COMBINATION OF THE CLPP AGONIST ONC201 WITH THE PI3K/AKT INHIBITOR PAXALISIB FOR THE TREATMENT OF DIFFUSE MIDLINE GLIOMA', Neuro-Oncology, 24, pp. vii211 - vii211, http://dx.doi.org/10.1093/neuonc/noac209.811
    Journal articles | 2022
    2022, 'Erratum: Stromal oncostatin M cytokine promotes breast cancer progression by reprogramming the tumor microenvironment (Journal Clinical Investigation (2022) 132:7 (e148667) 10.1172/JCI148667)', Journal of Clinical Investigation, 132, pp. e165107, http://dx.doi.org/10.1172/JCI165107
    Journal articles | 2022
    2022, 'Erratum: The H2A.Z-nucleosome code in mammals: emerging functions (Trends in Genetics (2022) 38(3) (273–289), (S0168952521002870), (10.1016/j.tig.2021.10.003)): (Trends in Genetics, 38:3 p:273–289, 2022)', Trends in Genetics, 38, pp. 516, http://dx.doi.org/10.1016/j.tig.2022.02.004
    Journal articles | 2022
    2022, 'Stromal oncostatin M cytokine promotes breast cancer progression by reprogramming the tumor microenvironment', Journal of Clinical Investigation, 132, http://dx.doi.org/10.1172/JCI148667
    Journal articles | 2022
    2022, 'TMIC-06. ANTAGONISM OF DRD2 USING ONC201 INCREASED EXPRESSION OF ANTIGEN PRESENTATION PATHWAY PROTEINS IN DIFFUSE MIDLINE GLIOMA, RECRUITING TUMOR INFILTRATING LYMPHOCYTES IN VIVO', Neuro-Oncology, 24, pp. vii272 - vii272, http://dx.doi.org/10.1093/neuonc/noac209.1050
    Journal articles | 2022
    2022, 'Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis', Nature Communications, 13, pp. 4587, http://dx.doi.org/10.1038/s41467-022-32255-7
    Journal articles | 2022
    2022, 'The H2A.Z-nuclesome code in mammals: emerging functions', Trends in Genetics, 38, pp. 273 - 289, http://dx.doi.org/10.1016/j.tig.2021.10.003
    Journal articles | 2021
    2021, 'Advancements in 3D Cell Culture Systems for Personalizing Anti-Cancer Therapies', Frontiers in Oncology, 11, pp. 782766, http://dx.doi.org/10.3389/fonc.2021.782766
    Journal articles | 2021
    2021, 'Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype', Cell Reports, 35, http://dx.doi.org/10.1016/j.celrep.2021.108945
    Journal articles | 2021
    2021, 'Tumor dissociation of highly viable cell suspensions for single-cell omic analyses in mouse models of breast cancer', STAR Protocols, 2, pp. 100841, http://dx.doi.org/10.1016/j.xpro.2021.100841
    Journal articles | 2020
    2020, 'Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-13753-7
    Journal articles | 2020
    2020, 'Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-14098-x
    Journal articles | 2020
    2020, 'Genomic Cytometry and New Modalities for Deep Single-Cell Interrogation', Cytometry Part A, 97, pp. 1007 - 1016, http://dx.doi.org/10.1002/cyto.a.24209
    Journal articles | 2020
    2020, 'Myeloid-Derived Suppressor Cells as a Therapeutic Target for Cancer', Cells, 9, http://dx.doi.org/10.3390/cells9030561
    Journal articles | 2020
    2020, 'Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells', EMBO Journal, 39, http://dx.doi.org/10.15252/embj.2019104324
    Journal articles | 2019
    2019, 'A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation', iScience, 21, pp. 773 - 788, http://dx.doi.org/10.1016/j.isci.2019.10.053
    Journal articles | 2019
    2019, 'A novel microRNA-based strategy to expand the differentiation potency of stem cells', , http://dx.doi.org/10.1101/826446
    Journal articles | 2019
    2019, 'Characterisation of developmental pathways that drive metastatic progression of breast cancer at single cell resolution', Oncology Abstracts, http://dx.doi.org/10.1530/oncolabs.1.p022
    Journal articles | 2019
    2019, 'Droplet-based single cell RNAseq tools: A practical guide', Lab on a Chip, 19, pp. 1706 - 1727, http://dx.doi.org/10.1039/c8lc01239c
    Journal articles | 2019
    2019, 'Single cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype', , http://dx.doi.org/10.1101/624890
    Journal articles | 2018
    2018, 'Single-cell transcriptomics in cancer immunobiology: The future of precision oncology', Frontiers in Immunology, 9, http://dx.doi.org/10.3389/fimmu.2018.02582
    Journal articles | 2017
    Valdés-Mora F; Gould CM; Colino-Sanguino Y; Qu W; Song JZ; Taylor KM; Buske FA; Statham AL; Nair SS; Armstrong NJ; Kench JG; Lee KM L; Horvath LG; Qiu M; Ilinykh A; Yeo-Teh NS; Gallego-Ortega D; Stirzaker C; Clark SJ, 2017, 'Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer', Nature Communications, 8, http://dx.doi.org/10.1038/s41467-017-01393-8
    Journal articles | 2017
    Valdés-Mora F; Locke WJ; Bandrés E; Gallego-Ortega D; Cejas P; García-Cabezas MA; Colino-Sanguino Y; Feliú J; del Pulgar TG; Lacal JC, 2017, 'Clinical relevance of the transcriptional signature regulated by CDC42 in colorectal cancer', Oncotarget, 8, pp. 26755 - 26770, http://dx.doi.org/10.18632/oncotarget.15815
    Journal articles | 2017
    2017, 'Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer', Oncogene, 36, pp. 1328 - 1338, http://dx.doi.org/10.1038/onc.2016.297
    Journal articles | 2016
    Colino-Sanguino Y; Clark SJ; Valdes-Mora F, 2016, 'H2A.Z acetylation and transcription: Ready, steady, go!', Epigenomics, 8, pp. 583 - 586, http://dx.doi.org/10.2217/epi-2016-0016
    Journal articles | 2015
    Gallego-Ortega D; Ledger A; Roden DL; Law AM K; Magenau A; Kikhtyak Z; Cho C; Allerdice SL; Lee HJ; Valdes-Mora F; Herrmann D; Salomon R; Young AI J; Lee BY; Sergio CM; Kaplan W; Piggin C; Conway JR W; Rabinovich B; Millar EK A; Oakes SR; Chtanova T; Swarbrick A; Naylor MJ; O’Toole S; Green AR; Timpson P; Gee JM W; Ellis IO; Clark SJ; Ormandy CJ, 2015, 'ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells', PLoS Biology, 13, http://dx.doi.org/10.1371/journal.pbio.1002330
    Journal articles | 2015
    Valdés-Mora F; Clark SJ, 2015, 'Prostate cancer epigenetic biomarkers: next-generation technologies', Oncogene, 34, pp. 1609 - 1618, http://dx.doi.org/10.1038/onc.2014.111
    Journal articles | 2013
    Stone A; Cowley MJ; Valdes-Mora F; McCloy RA; Sergio CM; Gallego-Ortega D; Caldon CE; Ormandy CJ; Biankin AV; Gee JM W; Nicholson RI; Print CG; Clark SJ; Musgrove EA, 2013, 'BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer', Molecular Cancer Therapeutics, 12, pp. 1874 - 1885, http://dx.doi.org/10.1158/1535-7163.MCT-13-0012
    Journal articles | 2013
    Stone A; Valdes-Mora F; Clark SJ, 2013, 'Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer', Epigenomics, 5, pp. 595 - 598, http://dx.doi.org/10.2217/epi.13.70
    Journal articles | 2012
    2012, 'Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer', Genome Research, 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110
    Journal articles | 2012
    2012, 'ELF5 Suppresses Estrogen Sensitivity and Underpins the Acquisition of Antiestrogen Resistance in Luminal Breast Cancer', PLoS Biology, 10, pp. e1001461, http://dx.doi.org/10.1371/journal.pbio.1001461
    Journal articles | 2012
    2012, 'Tamoxifen-induced epigenetic silencing of oestrogen-regulated genes in anti-hormone resistant breast cancer', PLoS One, 7, pp. e40466, http://dx.doi.org/10.1371/journal.pone.0040466
    Journal articles | 2011
    Gallego-Ortega D; Gómez del Pulgar T; Valdés-Mora F; Cebrián A; Lacal JC, 2011, 'Involvement of human choline kinase alpha and beta in carcinogenesis: A different role in lipid metabolism and biological functions', Advances in Enzyme Regulation, 51, pp. 183 - 194, http://dx.doi.org/10.1016/j.advenzreg.2010.09.010
    Journal articles | 2011
    2011, 'CDC42 (cell division cycle 42 (GTP binding protein, 25kDa))', Atlas of Genetics and Cytogenetics in Oncology and Haematology, http://dx.doi.org/10.4267/2042/44606
    Journal articles | 2011
    2011, 'Lineage specific methylation of the Elf5 promoter in mammary epithelial cells', Stem Cells, 29, pp. 1611 - 1619, http://dx.doi.org/10.1002/stem.706
    Journal articles | 2011
    2011, 'TWIST1 (twist homolog 1 (Drosophila))', Atlas of Genetics and Cytogenetics in Oncology and Haematology, http://dx.doi.org/10.4267/2042/44846
    Journal articles | 2009
    Gallego-Ortega D; de Molina AR; Ramos MA; Valdes-Mora F; Barderas MG; Sarmentero-Estrada J; Lacal JC, 2009, 'Differential role of human choline kinase α and β enzymes in lipid metabolism: Implications in cancer onset and treatment', PLoS ONE, 4, http://dx.doi.org/10.1371/journal.pone.0007819
    Journal articles | 2009
    Valdés-Mora F; Gómez Del Pulgar T; Bandrés E; Cejas P; Ramírez De Molina A; Pérez-Palacios R; Gallego-Ortega D; García-Cabezas MA; Casado E; Larrauri J; Nistal M; González-Barón M; García-Foncillas J; Lacal JC, 2009, 'TWIST1 overexpression is associated with nodal invasion and male sex in primary colorectal cancer', Annals of Surgical Oncology, 16, pp. 78 - 87, http://dx.doi.org/10.1245/s10434-008-0166-x
    Journal articles | 2008
    Gómez Del Pulgar T; Valdés-Mora F; Bandrés E; Pérez-Palacios R; Espina C; Cejas P; García-Cabezas MA; Nistal M; Casado E; González-Barón M; García-Foncillas J; Lacal JC, 2008, 'Cdc42 highly expressed in colorectal adecarcinoma and downregulates ID4 through an epigenetic mechanism', International Journal of Oncology, 33, pp. 185 - 193
    Journal articles | 2008
    2008, 'Differential role of choline kinase alpha and beta isoforms in human carcinogenesis', European Journal of Cancer Supplements, 6, pp. 26 - 26, http://dx.doi.org/10.1016/s1359-6349(08)71275-8
    Journal articles | 2007
    Gómez del Pulgar T; Bandrés E; Espina C; Valdés-Mora F; Pérez-Palacios R; García-Amigot F; García-Foncillas J; Lacal JC, 2007, 'Differential expression of Rac1 identifies its target genes and its contribution to progression of colorectal cancer', International Journal of Biochemistry and Cell Biology, 39, pp. 2289 - 2302, http://dx.doi.org/10.1016/j.biocel.2007.06.014
  • Working Papers | 2021
    2021, Disentangling single-cell omics representation with a power spectral density-based feature extraction, http://dx.doi.org10.1101/2021.10.25.465657
  • Preprints | 2023
    2023, Systematic comparison of high throughput Single-Cell RNA-Seq platforms in complex tissues, , http://dx.doi.org/10.1101/2023.04.04.535585
    Conference Papers | 2022
    2022, 'ANTAGONISM OF DRD2 USING ONC201 INCREASED EXPRESSION OF ANTIGEN PRESENTATION PATHWAY PROTEINS IN DIFFUSE MIDLINE GLIOMA, RECRUITING TUMOR INFILTRATING LYMPHOCYTES IN VIVO', in NEURO-ONCOLOGY, OXFORD UNIV PRESS INC, FL, Tampa, pp. 272 - 272, presented at 27th Annual Scientific Meeting and Education Day of the Society-for-Neuro-Oncology (SNO), FL, Tampa, 16 November 2022 - 20 November 2022, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000888571001365&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Preprints | 2020
    2020, Stromal Oncostatin M axis promotes breast cancer progression, , http://dx.doi.org/10.1101/2020.10.30.356774
    Conference Abstracts | 2015
    2015, 'The ETS transcription factor ELF5 drives metastasis via angiogenesis and recruitment of Gr-1+ CD11b+ myeloid derived suppressor cells in luminal breast cancer', in Clinical and Experimental Metastasis, Springer Verlag (Germany), Vol. 32, pp. 203 - 203, presented at MRS 15th International biennial congress of the metastasis research society, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000351601900067&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
    Conference Papers | 2014
    Ortega DG; Ledger A; Roden D; Cho C; Allerdice S; Lee H; Valdes-Mora F; Salomon R; Oakes S; Ormandy C, 2014, 'THE ETS TRANSCRIPTION FACTOR ELF5 IS A KEY DETERMINANT OF THE LETHAL PHENOTYPE IN LUMINAL BREAST CANCER, DRIVING THE ACQUISITION OF ANTIESTROGEN RESISTANCE AND METASTATIC ACTIVITY', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 16 - 17, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000344745100030&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 2008
    2008, 'TWIST1 overexpression is associated with nodal invasion and male gender in primary colorectal cancer', in EJC SUPPLEMENTS, PERGAMON-ELSEVIER SCIENCE LTD, FRANCE, Lyon, pp. 154 - 154, presented at 20th Meeting of the European-Association-for-Cancer-Research, FRANCE, Lyon, 05 July 2008 - 08 July 2008, http://dx.doi.org/10.1016/S1359-6349(08)71767-1
    Preprints |
    Single Cell Transcriptomics Reveals Involution Mimicry During the Specification of the Basal Breast Cancer Subtype, , http://dx.doi.org/10.2139/ssrn.3634808

2021-2023. Co-Investigator 2. Investigator initiated Research Scheme. National Breast Cancer Foundation. (3 years, $393,078). Ranked Top 1 nationally.

2021-2022. CIA. The Cure Starts Now. (1 year, $150, 379)

2020-2021. Co-Investigator Seed Funding Award UNSW Cellular Genomics Futures Institute. (1 year, $100,000). CIA Dr Fatemeh Vafaee.

2020. Co-Investigator 3R project UNSW. (1 year, $65,000). CIA Dr David Gallego Ortega

2019-2021. Cancer Institute NSW Career Development Fellowship (CDF181218, 3 years $ 600,000). Sole CIA

2018-2020. Co-Investigator B in NHMRC project grant (APP1144574, 3 years $ 859,350). CIA Prof Susan Clark.

2014-2016. Co-Investigator B in NHMRC project grant (APP1063560, 3 years $591,599). CIA Prof Susan Clark.

2011-2013. Co-Investigator of Prostate Cancer Foundation of Australia Project Grant. (PG4310. 3 years, $ 375K). CIA Prof Susan Clark.

2013-2018. National Breast Cancer Foundation/ Cure Cancer Australia Foundation Postdoctoral Training Fellowship (PF-13-11. 4 years excluding career disruption, $400K). Sole CIA

My Research Supervision

2020-2021. Supervisor of SOMS Honours Student (UNSW), Ms Dana Kisswani

2020-2025. PhD Co-Supervisor of Robert Salomon (UNSW-UTS).

2019-2023. Joint Supervisor of International student Ms Laura Rodriguez de la Fuente Faculty of Medicine. St Vincent’s Clinical School (UNSW)