Transcriptomic and drug repositioning analysis of

Mucopolysaccharidoses data

Cristal Villalba
Advisor: Professor Ursula Matte

AGENDA
1) Who I am?

2) Lysosomes and Glycosaminoglycans (GAGs)

3) A brief overview of Mucopolysaccharidoses (MPS)

4) My projects

5) Other works

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 LYSOSOMES AND GLYCOSAMINOGLYCANS
(GAGS)
The lysosomes are responsible for the
degradation, and participate of several biological
processes

Defects in lysosomal enzymes culminate in the

lysosomal accumulation of metabolites or
macromolecules, like the glycosaminoglycans
(GAGs)

GAGs are present in the Extracellular Matrix and

interact with a wide range of proteins and
receptors (Zhang et al., 2010)

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 MUCOPOLYSACCHARIDOSES (MPS)
Mucopolysaccharidoses (MPS) are a group of rare genetic diseases when
defects of lysosomal enzymes responsible for the degradation of
glycosaminoglycans (GAGs), with progressive multisystemic involvement
(Fecarotta et al., 2020).

There are 11 types of MPS, which

vary according to the enzyme and
type of accumulated GAG. MPS Types, related lysosomal storage genes and glycosaminoglycans (GAGs) storaged.
CS = Chondroitin Sulfate; DS = Dermatan Sulfate; HA = Hyaluronic Acid; HS = Heparan Sulfate; KS =
Keratan Sulfate

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 PATIENTS WITH MPS PRESENT SEVERAL PROGRESSI VE
MULTISYSTEMIC I NVOLVEMEN T IN SEVERAL TISSUES AND
ORGANS.

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 JUSTIFICATIVE

To explore lysosomal genes using omics data

available in public multi-omic databases may
help us understand the mechanisms involved in
the pathophysiology of Lysosomal Storage
Diseases, like Mucopolysaccharidoses, and
neurological tumors.

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 Manuscript 1
Fantastic Databases and where to find them: Web applications
for researchers in a rush

Case study: ACE2

https://pubmed.ncbi.nlm.nih.gov/33821874/

https://kur1sutaru.github.io/fantastic_databases_and_where_to_find_them/ 6/34
 Manuscript 2
Neurological Impairment and Mucopolysaccharidoses: A system
biology approach

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We did not include the GSE34071 -MPS VII (many different CNS tissues)
Manuscript 2-Results

A = GSE111906, MPS I B = GSE95224, MPS II C = GSE23075, MPS IIIB

D = GSE15758, MPS IIIB E = GSE76283, MPS VII
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Manuscript 2- Results

A = GSE111906, MPS I B = GSE95224, MPS II C = GSE23075, MPS IIIB

D = GSE15758, MPS IIIB E = GSE76283, MPS VII

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https://www.ufrgs.br/mpsbase/
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 Manuscript 2 - Discussion
MPS I ontologies: autophagy, axon guidance, and vesicle trafficking - related to
neurodegeneration (Fecarotta et al., 2020); Notch1 - synaptic plasticity (Ables et
al., 2011)
MPS II ontologies: calcium signaling pathway - deranged in many LSD (Feng &
Yang, 2016); neuroactive ligand receptors pathway, calcium and insulin signalling
- cognitive decline in Alzheimer (Gomez-Ravetti et al., 2010).
MPS IIIB ontologies: TLR4 signaling, Innate Immune System, and Complement
activation (GSE23075) - Brain pathology (Parker & Bigger, 2019; Heon-Roberts et
al., 2020). Humoral immune response and B cell activation (GSE15758) -
according to DiRosario et al. (2009)
MPS VII ontologies: pathways common to MPS II; The Fc receptors (FcRs)
signaling - immune system - generates signals to the lysosomes and
proteasomes to initiate degradation of molecules (Molfetta et al., 2014)
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 Manuscript 2 - Conclusion
Receptors

Proteins GAGS

System biology approaches may help us to understand the

mechanisms of neuropathology in the different types of
Mucopolysaccharidoses, and to discover novel biomarkers and
treatments for the neurological symptoms of these diseases

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 Manuscript 3
Lysosomal genes in neurological tumors: What’s that got to do
with lysosomal storage diseases?

The involvement of lysosomes has also been

described in tumors, related to cell
proliferation and signaling processes, microbial
killing, cytotoxic killing, induction of
angiogenesis, cell adhesion and metastatic
processes (Trejo-Solís et al. , 2018).

Submitted to Journal of Neuro-Oncology

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 Manuscript 3 - Aims

To investigate the differential expression and variants in

lysosomal storage disease genes in samples of brain tumors,
with focus on Lower Grade Glioma – LGG, and Glioblastoma
Multiforme – GBM and the correlation between expression
and survival status of these patients .

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Manuscript 3 - Results

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GBM

LGG

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LGG

GBM

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 Manuscript 3 - Discussion

In neurological tumors, lysosomal membrane destabilization leads to

vulnerability of invasive glioblastoma cells (Le Jouncur et al., 2019)

CD68 are upregulated in GBM and IDH wt gliomas, and were correlated
with tumor-associated macrophages (Wang et al., 2018)

V-ATPase are related with IDHwt lower-grade gliomas and are associated
with glioma growth and serve as biomarker (Halcrow et al., 2019)

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 Manuscript 3 - Conclusion
We represented a comprehensive annotation of genomic alterations
status of a set of lysosomal related genes in neurological tumors,
specially in LGG and GBM.

Differentially expressed genes may serve as prognostic biomarkers

and therapeutic targets.

More importantly, studying the lysosomal gene signature in tumors

may help understand the mechanisms by which neurological
dysfunction occurs both in patients with neurological tumors and in
patients with lysosomal storage diseases.
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 Oncogenic pathways deranged in Mucopolysaccharidoses

In MPS, secondary cell disturbance affects pathways common to cancer

To identify oncogenic signaling pathways in the different MPS datasets

available in Arrayxpress and GEO

To compare the ontologies across the different types of MPS

This work was published in the Lecture Notes in Bioinformatics Journal

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 METHODS

1 3 8

DATASETS
FROM MPS I, MPS II, MPS IIIA, MPS
IIIB, MPS VI and MPS VII
DATA ANALYSIS
We use EdgeR for RNA-seq data, and
limma, oligo and affy for Microarray
data, according with the used
platform
Cluego Cluepedia
ENRICHMENT ANALYSIS
For this work, we use the Cytoscape plugins
Bingo and Cluego/Cluepedia. To reduce the
GO terms redundant, we use QuickGO.

For more informations about the datasets, please visit our tool MPSBase:
https://www.ufrgs.br/mpsbase/
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 RESULTS
12 DATASETS
ONTOLOGIES THAT APPEARS
We found 680 oncogenic ontologies:
392 KEGG pathways IN ALL THE DATASETS
221 GO BP Hippo signaling pathway (hsa04390)
50 GO MF MAPK signaling pathway (hsa04010)
17 GO CC

ONTOLOGIES THAT APPEARS ONTOLOGIES THAT APPEARS

IN 11 OF 12 DATASETS IN ALL THE MPS TYPES
Axon guidance
Proteoglycans in cancer (hsa05205) Pathways in Cancer
Focal adhesion
Rap 1 signaling pathway (hsa04015) Proteoglycans in Cancer
Hippo signaling pathway
Cytokine-mediated signaling pathway PI3K-Akt signaling pathway
MAPK signaling pathway
(GO:0019221- Biological Process) Rap-1 signaling pathway
Metabolic pathways
Ras signaling pathway
Wnt signaling pathway

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 DISCUSSION

Oncogenic pathways deranged in MPS

Adaptation of the KEGG: Proteoglycans in Cancer. 24/34
 DISCUSSION

Glycosaminoglycans play an essential role in the composition

of the extracellular matrix, helping to regulate processes
such as metabolic signaling, apoptosis, cell migration,
adhesion, and antigen presentation (Walker et al., 2018).

These processes are altered in both cancer and in the MPS.

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 CONCLUDING REMARKS

Studying the tumor ontology signature in lysosomal

disorders may help understand lysosomal storage diseases
and cancer's common underlying mechanisms. This may
help amplify therapeutic approaches for both types of
diseases.

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 Manuscript 5
Repetitive Elements, Neurological damage and MPS

Cancer

Metabolic Diseases

Parkinson Disease

Alzheimer Disease

And how about MPS?

Billingsley et al., 2019 27/34
 Manuscript 5 - Methods
.FASTA genes

REMP

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Manuscript 5 - Results

ARSB - MPS VI
Size: 208,879 bases
GC level: 41.00 %
Bases masked: 121464 bp ( 57.82 %)

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 Manuscript 5 - Results

ARSB - MPS VI

SNP found in RE: 73

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 Manuscript 5 - Ongoing work

To compare the presence of the RE in other species

To analyze the methylation pattern of the RE (active / or not)

To develop a R package for analysis of RE elements (all the steps)

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 Manuscript 5 - Summary
We analyzed 56 lysosomal storage related genes, with a total of 6627 RE

The most abundant RE are the Alu family, according to Larsen et al. (2018)

We revised the literature about LSD and RE - 17 about LSD and 8 about MPS

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 References
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adaptive immune activation in the brain of MPS IIIB mouse model. Journal of neuroscience research, 87(4), 978–990.
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Fecarotta, S., Tarallo, A., Damiano, C., Minopoli, N., & Parenti, G. (2020). Pathogenesis of Mucopolysaccharidoses, an Update. International
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Feng, X., & Yang, J. (2016). Lysosomal Calcium in Neurodegeneration. Messenger (Los Angeles, Calif. : Print), 5(1-2), 56–66.
https://doi.org/10.1166/msr.2016.1055
Gómez Ravetti, M., Rosso, O. A., Berretta, R., & Moscato, P. (2010). Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the
Changes of Hippocampus’ Gene Expression Profiles in Alzheimer’s Disease. PLoS ONE, 5(4), e10153. doi:10.1371/journal.pone.0010153
Heon-Roberts, R., Nguyen, A., & Pshezhetsky, A. V. (2020). Molecular Bases of Neurodegeneration and Cognitive Decline, the Major Burden of
Sanfilippo Disease. Journal of clinical medicine, 9(2), 344. https://doi.org/10.3390/jcm9020344
Le Joncour V, Filppu P, Hyvönen M, et al. (2019). Vulnerability of invasive glioblastoma cells to lysosomal membrane destabilization. EMBO Mol
Med 11(6):e9034. doi:10.15252/emmm.201809034
Parker, H., & Bigger, B. W. (2019). The role of innate immunity in mucopolysaccharide diseases. Journal of neurochemistry, 148(5), 639–651.
https://doi.org/10.1111/jnc.14632
Tomatsu, S., Alméciga-Díaz, C. J., Montaño, A. M., Yabe, H., Tanaka, A., Dung, V. C., Giugliani, R., Kubaski, F., Mason, R. W., Yasuda, E.,
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Trejo-Solís, C; Serrano-Garcia, N; Escamilla-Ramírez, Á; Castillo-Rodríguez, RA; Jimenez-Farfan, D; Palencia, G; … Sotelo, J (2018). Autophagic and
Apoptotic Pathways as Targets for Chemotherapy in Glioblastoma. Intern J Mol Sci , 19(12), 3773. doi:10.3390/ijms19123773
Walker, C., Mojares, E., & Del Río Hernández, A. (2018). Role of Extracellular Matrix in Development and Cancer Progression. International journal
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 Other works
Summary published in proceedings of conferences
SILVA, G. C. V.; MATTE, U. S. DOENÇAS LISOSSÔMICAS E GLIOMAS: O QUE ELES TÊM EM COMUM? 40a Semana Científica HCPA 2020.
https://postersc.hcpa.edu.br/;
SILVA, G. C. V.; MATTE, U. S. Cancer pathways are deranged in Mucopolysaccharidosis. 28th International Conference On Intelligent Systems for Molecular
Biology. 2020. <https://doi.org/10.7490/f1000research.1118053.1 >(Congress);
SILVA, G. C. V.; MATTE, U. S. Differential expression analysis of lysosomal storage-related genes in gliomas. Advances in Computational Biology
Conference 2019. <https://doi.org/10.7490/f1000research.1117674.1 >(Congress);
SANTOS, H. S. ; SILVA, G. C. V. ; BALDO, G. ; MATTE, U. S. . C HARACTERIZATION OF REPETITIVE ELEMENTS IN GENES ENCODING DIFFERENT
MUCOPOLYSACCHARIDOSES. In: XXXI Congresso Brasileiro de Genética Médica, 2019, Salvador. ANAIS CBGM 2019, 2019;
SILVA, G. C. V.; MATTE, U. S. Latin American School of Human and Medical Genetics.Autophagy and lysosomal regulation in Neurological tumors: What’s
that got to do with lysosomal storage diseases? 2019.

Awards
SILVA, G. C. V. Award of virtual ECCB2020 - New trends in Bioinformatics, European Student Council Symposium – 19th European Conference on
Computational Biology.

https://aime-registry.org/
Martiela,Cristal, and more people :P

Transcriptome analysis of HPP Development of In silico biomarkers of

stem cells / gene candidate Ovarian Response[...]
analysis using systems biology Fertility and sterility Journal
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