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Archives of Medical Research 54 (2023) 102915
REVIEW ARTICLE
Genomics, Transcriptomics, and Epigenetics of Sporadic Pituitary Tumors
Daniel Marrero-Rodríguez, Sandra Vela-Patiño, Florencia Martinez-Mendoza,
Alejandra Valenzuela-Perez, Eduardo Peña-Martínez, Amayrani Cano-Zaragoza, Jacobo Kerbel,
Sergio Andonegui-Elguera, Shimon S. Glick-Betech, Karla X. Hermoso-Mier,
Sophia Mercado-Medrez, Alberto Moscona-Nissan, Keiko Taniguchi-Ponciano, and Moises Mercado
Endocrine Research Unit, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
Received for publication July 30, 2023; accepted November 7, 2023 (ARCMED-D-23-00617).
Pituitary tumors (PT) are highly heterogeneous neoplasms, comprising functioning and
nonfunctioning lesions. Functioning PT include prolactinomas, causing amenorrhea-
galactorrhea in women and sexual dysfunction in men; GH-secreting adenomas caus-
ing acromegaly-gigantism; ACTH-secreting corticotrophinomas causing Cushing disease
(CD); and the rare TSH-secreting thyrotrophinomas that result in central hyperthy-
roidism. Nonfunctioning PT do not result in a hormonal hypersecretion syndrome and
most of them are of gonadotrope differentiation; other non-functioning PT include null
cell adenomas and silent ACTH-, GH- and PRL-adenomas. Less than 5% of PT occur in
a familial or syndromic context whereby germline mutations of specific genes account
for their molecular pathogenesis. In contrast, the more common sporadic PT do not
result from a single molecular abnormality but rather emerge from several oncogenic
events that culminate in an increased proliferation of pituitary cells, and in the case of
functioning tumors, in a non-regulated hormonal hypersecretion. In recent years, im-
portant advances in the understanding of the molecular pathogenesis of PT have been
made, including the genomic, transcriptomic, epigenetic, and proteomic characterization
of these neoplasms. In this review, we summarize the available molecular informa-
tion pertaining the oncogenesis of PT. © 2023 Instituto Mexicano del Seguro Social
(IMSS). Published by Elsevier Inc. All rights reserved.
Key Wo rd s : Genomics, Transcriptomics, Methylome, Pituitary tumors, scRNAseq.
Introduction
Traditionally, medical therapeutics are based on the patho-
physiology and clinical features of a particular disease.
Although the individualization of treatment based on clin-
ical judgment is obviously a hallmark of good medical
practice, the design and development of a particular drug
is seldom aimed at the individual patient. The emergence
of ever more powerful molecular biology techniques over
the past 30 years has led to unprecedented advances in
the understanding of the etiology and pathophysiology of
a growing number of diseases resulting in efficient, indi-
vidually tailored targeted therapies and precision medicine
Address reprint requests to: Keiko Taniguchi-Ponciano, Unidad de
Investigación Médica en Enfermedades Endocrinas, Hospital de Espe-
cialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del
Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, 06720, Mexico City,
Mexico; E-mail: keiko.taniguchi@hotmail.com
( 1 ). Precision medicine is currently being used to diagnose
and treat a wide variety of conditions, including metabolic,
neurological, immune-mediated, and neoplastic disorders,
among others.
Pituitary tumors (PT) constitute a heterogeneous group
of epithelial neoplasms that include both functioning
and nonfunctioning lesions ( 2 ). Functioning PT in-
clude prolactin (PRL) -secreting prolactinomas, causing
amenorrhea-galactorrhea in women and sexual dysfunction
in men; growth hormone (GH) -secreting adenomas caus-
ing acromegaly-gigantism; adrenocorticotropic hormone
(ACTH) -secreting corticotrophinomas that cause Cush-
ing disease (CD); and the rare TSH (thyrotropin)-secreting
thyrotrophinomas that result in central hyperthyroidism
( 2 ). Besides immunostaining for their cognate hormones,
ACTH-secreting adenomas immunostain for the T-box
transcription factor (TBX19) also known as T-Pit, whereas
GH-, PRL- and TSH-secreting tumors do so for POU
0188-4409/$ - see front matter. Copyright © 2023 Instituto Mexicano del Seguro Social (IMSS). Published by Elsevier Inc. All rights reserved.
https://doi.org/10.1016/j.arcmed.2023.102915
2 Marrero-Rodríguez et al. / Archives of Medical Research 54 (2023) 102915
class 1 homeobox 1 (POU1F1), also known as Pit-1 ( 2 ).
Nonfunctioning PT do not result in a hormonal hyper-
secretion syndrome and most of them are of gonadotrope
differentiation, as they immunostain for the common α-
subunit, luteinizing hormone ( β-LH) or follicle-stimulating
hormone ( β-FSH), as well as for the transcription factor
nuclear receptor subfamily 5 group A member 1 (NR5A1)
also known as steroidogenic factor 1, or SF1 . Other non-
functioning PTs include null cell adenomas and silent
ACTH-, GH-, and PRL-adenomas ( 3 ). Less than 5% of PT
occur in a familial or syndromic context, where germline
mutations of specific genes are responsible for their molec-
ular pathogenesis ( 4–6 ). In contrast, the more common
sporadic PTs do not result from a single molecular ab-
normality, but rather from multiple oncogenic events that
culminate in an increased pituitary cell proliferation and,
in the case of functioning tumors, in a non-regulated hor-
monal hypersecretion ( 2 ). In a way, before the terms “pre-
cision” or “personalized” medicine were coined, pituitary
specialists had been approaching patients with PT in an in-
dividualized manner by immunophenotyping these lesions
according to their expression of hormones, transcription
factors and more recently, somatostatin and dopamine re-
ceptors. Although the immunohistochemical evaluation of
PT has allowed us to better classify and diagnose these
lesions and has contributed to more rational therapeutic
decisions, it remains a methodology that is limited by the
subjective interpretation of a pathologist ( 7 ). Over the past
10 years, there have been important advances in the un-
derstanding of the genomics, transcriptomics, proteomics,
and epigenetics of PT. In this review, we summarize and
critically analyze the molecular landscapes of sporadic
PT, focusing on those findings that are likely to con-
tribute to a better diagnosis and treatment of these patients
( Figure 1 ).
The Genomics of Pituitary Tumor s
The genomic characterization of sporadic PT has gen-
erated information on the mutational burden (single nu-
cleotide variants, or SNVs), and the presence of chromoso-
mal gains and losses in specific cytogenetic regions (copy
number variation, or CNVs). Genetic variations in the hu-
man genome include SNVs, but also large chromosomal
aberrations such as unbalanced deletions, duplications and
amplifications of DNA segments ranging from a few to
several hundred base pairs ( 8 , 9 ). Whereas whole genome
sequencing (WGS) comprises the entire genome, including
exons and introns, whole exome sequencing (WES) only
evaluates coding exons and in some cases, the intron-exon
boundaries ( 10 ). The frequency of chromosomal alterations
in PT varies according to the type of secretion: 7% for non-
functioning gonadotrophinomas and null cell adenomas,
1% for silent ACTH-adenomas, 50% for PRL-adenomas
and TSH-adenomas, 30% for corticotrophinomas causing
CD, and 20% for somatotrophinomas and plurihormonal
tumors ( 11 ).
Corticotrope Tumo rs
Activating mutations of the gene encoding the ubiquitin
specific peptidase 8 ( USP8 ) are found in 20–40% of spo-
radic ACTH-secreting PT causing CD ( 12 , 13 ). Patients har-
boring these genetic variants are characteristically younger,
more frequently women and in some, but not all, studies
have been found to develop long-term recurrences more
frequently ( 14 , 15 ). USP8 mediates the deubiquitination of
the epidermal growth factor receptor ( EGFR ) by inhibiting
its interaction with the protein 14-3-3, which in turn pre-
vents its proteosomal degradation, leading to an increased
signaling by the deubiquitinated EGFR , which ultimately
results in increased cellular proliferation and transcription
of the proopiomelanocortin ( POMC ) gene ( 16 ). The gene
encoding another ubiquitin specific peptidase, USP48 , has
also been found to be somatically mutated in up to 23% of
ACTH tumors, which also results in an increased ACTH
synthesis ( 17 ).
Up to 16% of ACTH-secreting PT harbor the BRAF
(B-Raf Proto-Oncogene, Serine/Threonine Kinase) V600E
variant which is considered a driver mutation that induces
MAP2K1 (mitogen-activated protein kinase kinase 1) and
MAPK1/2 (mitogen-activated protein kinase 1/2) phospho-
rylation and thus, activates the transcription factor NR4A1
(nuclear receptor subfamily 4, group A, member 1) which
in turn promotes the transcription of POMC ( 17 ). The
gene encoding ATRX ( ATRX chromatin remodeler) has
been found to be mutated in one-third of corticotrophi-
nomas, particularly in tumors with an aggressive behav-
ior and in carcinomas ( 18 ). ATRX interacts with DAXX
(death domain associated protein) and histone H3.3 in het-
erochromatin remodeling and telomere maintenance and
function, therefore inactivation of ATRX leads to telomere
destabilization ( 18 ). Phosphatidylinositol-4,5-bisphosphate
3-kinase catalytic subunit α(PIK3CA ) gene mutations have
been found in 4% of ACTH-secreting tumors and are asso-
ciated with invasiveness ( 19 ). Finally, up to 33% of ACTH-
secreting tumors harbor tumor protein p53 ( TP53 ) muta-
tions, which appear to correlate with a more aggressive
behavior ( 13 , 20 ).
We recently evaluated through whole exome sequenc-
ing 10 PTs, representing the whole pathological spec-
trum of the corticotrope, and including 4 CD-causing
ACTH adenomas, three silent corticotrope tumors, one
ACTH-secreting macroadenoma in a patient with Nelson’s
syndrome, a Crooke cell macroadenoma and an ACTH-
secreting carcinoma that developed from a microadenoma
over a 15-year period ( 13 ). We found, previously re-
ported recurrent somatic mutations in 6 pathogenically rel-
evant genes: hydroxy- δ-5-steroid dehydrogenase, 3 β- and
steroid delta-isomerase 1 ( HSD3B1 ) in all 10 tumors, TP53
Molecular Biology of Pituitary Tumors 3
Figure 1. Advances in precision medicine for pituitary tumors. Multiomics (genomic, transcriptomic, proteomic, epigenomic, immunomic, and clinical
data) networks can provide knowledge for better sample classification, disease subtyping, biomarker discovery and prognosis prediction in pituitary
tumors. These insights will contribute to a better diagnosis and treatment of these patients.
in all, except one silent ACTH adenoma, cyclin depen-
dent kinase inhibitor 1A (CDKN1A ) in six tumors, EGFR
in six tumors, Aurora kinase A ( AURKA) in four tumors,
and USP8 in two tumors ( 13 ). The ACTH-secreting carci-
noma was the tumor with the highest number of genomic
abnormalities, including SNV and CNV ( 13 ). A phylo-
genetic inference analysis was carried out to establish a
hypothetical sequential transformation from a silent cor-
ticotrope adenoma to a functional tumor and finally, to
an ACTH-secreting carcinoma ( 13 ). We found two dis-
tinct clades, the first one was characterized by expressing
a SNV of the gene encoding the activating transcription
factor 7-interacting protein (rs.3213764) and includes two
of the three silent adenomas and two of the five corti-
cotrophinomas causing CD ( 13 ). These four tumors have
the same SNV profile, so we can assume that they harbor
all the genes that must be altered to allow the transition
from a silent adenoma to a clinically evident tumor ( 13 ).
The second and largest clade includes the Crooke cell ade-
noma, two ACTH-adenomas causing CD, one of the silent
ACTH-adenomas and the ACTH-secreting carcinoma ( 13 ).
All the tumors in this clade harbor the necessary molecular
alterations to evolve from a functioning ACTH adenoma
to a malignant corticotrophinoma and are characterized by
expressing a polymorphism of the gene encoding the DNA
mismatch repair protein (rs.1650697) ( 13 ).
Clinically non-functioning Pituitary Tumor s
Clinically non-functioning PT harbor very few mutations,
in particular, none of the previously mentioned vari-
ants reported in tumors of other lineages are present in
these neoplasms of gonadotrope differentiation ( 21 ). This
is consistent with their low proliferative index, which
4 Marrero-Rodríguez et al. / Archives of Medical Research 54 (2023) 102915
means that mechanisms other than somatic mutations are
likely to be involved in their oncogenesis ( 21 ). Never-
theless, a few genes, including platelet-derived growth
factor D ( PDGFD ), NDRG family member 4 ( NDRG4 ),
and Mitogen-Activated Protein Kinase Kinase Kinase 20
( MAP3K20 ) ( 21 ), as well as isoleucyl-tRNA synthetase
1 ( IARS1 ) and thyroid hormone receptor interactor 12
( TRIP12 ) ( 22 ) have been described to harbor isolated, non-
recurrent mutations. Some silent corticotrope tumors have
been found to harbor the same USP8 somatic mutation,
previously described in ACTH-secreting adenomas causing
CD ( 23 , 24 ). However, neither Perez-Rivas L, et al. ( 25 ),
nor our group ( 13 ) have found such molecular abnormality
in these clinically silent ACTH-producing lesions. Isolated
inactivating mutations of the gene encoding the aryl hydro-
carbon receptor-interacting protein ( AIP ) have been found
in some clinically silent somatotroph tumors ( 26 ).
Somatotrophinomas
Activating somatic mutations of the gene encoding the
GNAS complex locus ( GNAS ) have been reported in up
to 40–50% of GH-secreting tumors in Caucasian ( 27 ) and
Japanese ( 28 ) patients, although the prevalence of this
molecular abnormality is much lower in Mexican (18%)
( 29 ) and Korean ( 30 ) subjects. This mutation disrupts the
GTPase activity of the Gs protein α-subunit leading to con-
stitutive activation of the growth hormone releasing hor-
mone receptor ( TRH-R ) that results in a constant activa-
tion of adenylate cyclase and thus, an increased generation
of intracellular cyclic adenosine monophosphate (cAMP)
which through cAMP response element binding protein
( CREB ) increases the transcription of the genes encoding
GH and POU1F1 and also results in an increased cellular
proliferation ( 31 ). Tumors bearing GNAS mutations char-
acteristically have a densely granulated pattern by elec-
tron microscopy or CAM5.2 immunostaining, are usually
smaller and less invasive and appear to respond favorably
to somatostatin analogs ( 27 , 29 ).
No other consistently recurrent somatic mutations have
been found upon WGS and WES in patients with GH-
secreting tumors. However, several somatic variants of
genes involved in the cAMP pathway such as protein ki-
nase AMP-activated catalytic subunit alpha 2 ( PRKAA2 ),
calcium signaling such as calcium voltage-gated channel
subunit alpha 1H ( CACNA1H ), as well as AT P signaling
such as suv3 like RNA helicase ( SUPV3L1 ) have been ob-
served in some of these patients ( 32 , 33 ).
Thyrotrophinomas and Prolactinomas
TSH-secreting tumors or thyrotrophinomas are extremely
rare and present clinically with central hyperthyroidism.
Whole exome sequencing studies have identified candi-
date driver mutations in genes such as spermine oxidase
( SMOX) and synaptotagmin like 3 ( SYTL3 ) which are in-
volved in oxidative damage and the Rab signaling pathway,
respectively. No other altered genes were found in these
tumors ( 34 ).
The molecular evaluation of prolactinomas is hampered
by the fact that most of these neoplasms are pharmaco-
logically treated with dopamine agonists and therefore,
tissue availability is very limited. Recently, Li C, et al.
carried out whole genome sequencing of 21 macropro-
lactinomas and found a recurrent somatic missense mu-
tation in the gene encoding splicing factor 3B subunit 1
( SF3B1 ), that changes Arginine for Histidine at position
625 ( SF3B1 R625H ) in two of these tumors ( 35 ). These
authors validated this finding in 206 prolactinomas by dig-
ital PCR analysis and found that 43 of them (20.8%) har-
bored the SF3B1 R625H mutant ( 35 ). None of the 120 non-
prolactinoma PTs harbored this molecular abnormality, and
no germline mutation was found in 13 blood DNA sam-
ples ( 35 ). Primary cell cultures of mutant tumors showed
higher PRL secretion than wild-type tumors, and further-
more, adenoviral expression of SF3B1 R625H into GH3
and MMQ cell lines resulted in an increased cellular pro-
liferation and reduced apoptosis ( 35 ). SF3B1 R625H re-
sults in aberrant splicing of the estrogen-related receptor
gamma ( ESRRG ) gene, resulting in the generation of an
abnormal, cryptic mRNA ( 35 ). Patients carrying this so-
matic missense mutation appear to have higher PRL levels
and a decreased progression-free survival ( 35 ). POU class
6 homeobox 2 ( POU6F2 ) acts as a tumor suppressor and is
involved in the predisposition to Wilms tumor ( 36 ). Miao
Y, et al. reported the case of a male patient with an ag-
gressive macroprolactinoma resistant to dopamine agonist
therapy, who underwent debulking surgery and the excised
tumor was subjected to whole genome sequencing and was
found to have two biallelic POU6F2 mutations (p.P280L
and p.N292S) ( 37 ). In vitro expression studies revealed
that this biallelic mutation resulted in an increased PRL
secretion and cell viability ( 37 ). Thus far, the presence of
this molecular abnormality has not been reported by other
investigators ( Table 1 ).
Transcriptomics of Pituitary Tumors
In 2020, two independent groups of investigators reported
that transcriptomically, PT segregate into three distinct
clusters according to the expression of the transcription
factor that drives the terminal differentiation of the pitu-
itary cell type from which they originate ( 11 , 38 ). Accord-
ing to this paradigm, clinically nonfunctioning adenomas
of gonadotrope differentiation which are driven by NR5A1
constitute the first cluster; ACTH-secreting adenomas caus-
ing CD, which are driven by TBX19 , represent the second
cluster; and PRL-, GH- and TSH-secreting adenomas con-
form the third cluster and are driven by POU1F1 ( 11 , 38 ).
Silent corticotroph adenomas, which express TBX19 seem
Molecular Biology of Pituitary Tumors 5
Tab l e 1. Most common genomic mutation in PT
Gene Pituitary Tum o r
BRAF
USP48
CDKN1A
AURKA ACTH- secreting tumors
EGFR
PIK3CA
USP8
ATRX ACTH-secreting tumor and ACT H carcinoma
HSD3B1 CD-causing ACTH-adenomas, ACTH-secreting macroadenoma in a patient with Nelson’s syndrome, Crooke cell
macroadenoma, ACTH carcinoma and silent ACTH
TP53 CD-causing ACTH-adenomas, ACTH-secreting macroadenoma in a patient with Nelson’s syndrome, Crooke cell
macroadenoma and ACTH carcinoma
PDGFD
NDRG4
MAP3K20 FSH/LH-secreting tumor
IARS1
TRIP12
GNAS
PRKAA2
CACNA1H GH-secreting tumors
SUPV3L1
AIP
SMOX TSH-secreting tumors
SYTL3
SF3B1
POU6F2 PRL-secreting tumors
to share some transcriptomic features with the more fre-
quent clinically nonfunctioning adenoma of gonadotrope
differentiation ( 38 ). Interestingly, these two groups ar-
rived at the same conclusion using different methodolo-
gies which underscores the biological significance of their
findings. While Taniguchi-Ponciano K, et al. carried out a
whole coding transcriptome analysis at the gene and exon
level using a microarray that identified over 540 thousand
transcripts, including also long non-coding RNA (LIN-
CRNA), microRNA (miRNA) and circular RNA (circRNA)
( 38 ), while Neou M, et al. used direct RNA sequencing
( 11 ).
While there is an overexpression of the mRNA of
the anterior pituitary hormone specific for each tumor
type (i.e., PRL in prolactinomas, POMC in corticotrophi-
nomas, GH in somatotrophinomas, TSH in thyrotrophi-
nomas, LH/FSH in gonadotrophinomas), the mRNAs of
their corresponding cognate receptors are expressed in a
non-specific manner. Interestingly, the mRNA expression
of the receptors for the different hypothalamic releas-
ing hormones was variable ( 38 ). The thyrotropin releas-
ing hormone receptor ( TRH-R ) mRNA was clearly over-
expressed in thyrotrophinomas, gonadotrophinomas and to
a lesser extent somatotrophinomas (this explains the para-
doxical rise of GH upon thyrotropin releasing hormone
(TRH) stimulation in some patients with acromegaly),
while it was underexpressed in ACTH-secreting tumors.
The corticotropin releasing hormone receptor 1 ( CRH-R1 )
mRNA was distinctly overexpressed in corticotroph tu-
mors compared to other tumor types. The GHRH-R mRNA
was expressed in all tumor types with perhaps a slight
predominance in GH- and TSH-secreting tumors. The
gonadotropin-releasing hormone receptor ( GnRH-R ) was
also distinctly overexpressed in gonadotrophinomas com-
pared to other tumor types. TSH- and GH-secreting tumors
had the highest somatostatin receptor 2 ( SSTR2 ) mRNA ex-
pression, which are the tumor types that respond to first-
generation somatostatin analogs ( 38 ). In contrast, the so-
matostatin receptor 5 ( SSTR5 ) mRNA was overexpressed
in PRL-, TSH- and to a lesser extent in GH- and ACTH-
secreting tumors, which explains the favorable response
of corticotrophinomas to pasireotide, a second-generation
somatostatin analog ( 38 ). The expression of dopamine re-
ceptor mRNA was highest in prolactinomas, followed by
thyrotrophinomas, gonadotrophinomas, and somatotrophi-
nomas. Some genes, such as solute carrier family 25 mem-
ber 2 ( SLC25A2 ), miR590 , and LINC00412 were clearly
overexpressed in all PT types, compared to non-tumoral
gland ( 38 ).
Corticotrope Tumo rs
ACTH-secreting tumors causing CD and silent corti-
cotrophinomas, both express POMC and the transcription
factor TBX19 ; however, their transcriptomic profiles are
otherwise different. CD-causing ACTH-secreting adeno-
6 Marrero-Rodríguez et al. / Archives of Medical Research 54 (2023) 102915
mas are characterized by expressing arginine vasopressin
receptor 1B ( AVPR1B ), androgen receptor ( AR ), CRH-
R1, nuclear receptor subfamily 1, group F, member 2
( NR1F2 ), PLAG1 zinc finger ( PLAG1 ), and EPH receptor
A4 ( EPHA4 ) mRNA ( 38 ). Silent corticotrope adenomas
specifically overexpress calcium voltage-gated channel
auxiliary subunit alpha2delta 4 ( CACNA2D4 ), paired like
homeodomain 2 ( PITX2 ), retinoid X receptor gamma
( RxRG ), and EPH receptor B6 ( EPHB6 ) ( 38 ). Pathways
involved in ACTH-secreting tumors include enzymes in-
volved in drug metabolism, metabolism of xenobiotics by
cytochrome P450, and the renin-angiotensin-aldosterone
system, as well as tryptophan and pyrimidine metabolism
( 38 ). ACTH-secreting tumors bearing USP8 somatic
mutations overexpress SSTR5 mRNA, which seems to
correlate with the therapeutic response to pasireotide, as
mentioned above ( 11 , 38 ).
Clinically Non-functioning Pituitary Tumor s
Clinically nonfunctioning adenomas of gonadotrope differ-
entiation and null cell tumors share an important num-
ber of expressed genes, including neuronal differentiation
1 ( NEUROD1 ), zinc finger protein 804A ( ZNF804A ), zinc
finger BED-type containing 2 ( ZBED2 ), retina and anterior
neural fold homeobox 2 ( RAX2 ), ISL LIM homeobox 1
( ISL1 ) and high mobility group AT-hook 2 ( HMGA2 ) ( 11 ).
Genes such as CACNA2D4 and EPHB6 are upregulated
in gonadotrophinomas, silent ACTH tumors and null cell
adenomas ( 38 ). Pathways altered in gonadotrophinomas in-
clude WNT , estrogen and calcium signaling pathways, as
well as immune- related events such as Th17 cell differen-
tiation ( 38 ). Other investigators have found upregulation of
genes involved in the regulation of epithelial-mesenchymal
transition, particularly in fast-growing gonadotrope tumors
( 39 ).
GH-, TSH- and PRL-tumors
The cluster comprising GH-, PRL- and TSH-PT is char-
acterized by upregulation of genes encoding proteins such
as slit guidance ligand 1 ( SLIT1 ), PRL receptor ( PRLR )
and solute carrier family 6 member 6 ( SLC16A6 ) ( 38 ).
The GH-, TSH-tumors and POU1F1 -plurihormonal tumors
share the expression of SRY-box transcription factor 5
( SOX5 ), regulatory factor X4 ( RFX4 ), zinc finger protein
536 ( ZNF536 ), among others ( 11 ). Prolactinomas express
neuronal differentiation 4 ( NEUROD4 ) , estrogen receptor 1
( ESR1 ) and LIM homeobox 3 ( LHX3 ) ( 11 ). GH-secreting
tumors harboring GNAS mutations express higher amounts
of dopamine receptor D2 ( D2R ), which could be related to
a more favorable response to dopamine agonists ( 11 ).
Cell Populations Define Aggressiveness, Recurrence, and
Functionality
Recently, Zhang Q, et al. found that pituitary tumors
also may cluster according to their degree of differenti-
ation ( 40 ). The poorly differentiated cluster is character-
ized by an abnormal expression of genes involved in the
metabolism of lipids, as well as in cholesterol and long
chain fatty acid synthesis ( 40 ).
Single-cell RNA sequencing (scRNAseq) studies have
revealed that silent ACTH-tumors exhibit increased expres-
sion of epithelial-mesenchymal transition related genes,
along with the loss of transcripts related to hormonal bio-
genesis and secretion ( 41 ). In contrast, CD-causing cor-
ticotrophinomas show marked overexpression of secre-
togranin V ( SCG5 ) , g alanin and GMAP prepropeptide
( GAL ) , TIMP metallopeptidase inhibitor 1 ( TIMP1 ), and
adipocyte plasma membrane-associated protein ( APMAP )
which are related to secretory vesicles, ( 41 ) ( Table 2 ).
The Epigenetic Landscape of PT
Epigenetically, PT also cluster according to the tran-
scription factor that determines their terminal differenti-
ation ( 38 ). Approximately 649 genes have been found to
be potentially regulated by DNA methylation in ACTH-
secreting tumors causing CD. In these tumors, genes such
as AVPR1B, EPHA4 , and glutamate ionotropic receptor
NMDA type subunit 2B ( GRIN2B ) are upregulated due
to promoter demethylation ( 38 ). Silent corticotrope tumors
have a different methylation profile and are epigenetically
closer to nonfunctioning gonadotrophinomas than to clini-
cally eloquent ACTH-secreting adenomas ( 11 ). USP8 mu-
tation status does not appear to correlate with methyla-
tion profiles ( 11 ). CD-causing and silent ACTH tumors
also differ in their miRNA expression profile ( 42 ). Elo-
quent ACTH tumors overexpress miR-129-2-3p, miR-129-
5p, miR-124-3p, miR-132-5p, miR-129-1-3p, miR-135b-5p,
miR-27a-3p, miR-10b-5p, miR-9-3p, miR-6506-3p, miR-
6864-5p, let-7b-5p, miR-670-3p, miR-22-5p, miR-346 and
miR-9-5p, whereas miR-1909-3p, miR-4319, miR-181b-3p,
and miR4501 ( 38 , 42 ). These miRNAs are involved in the
regulation of steroid hormone receptor, nuclear receptor,
and ligand-activated transcription factor activity, as well as
steroid hormone-mediated signaling pathway. The differen-
tially expressed miRNAs in tumors causing CD to play a
role in the regulation of glucocorticoid receptor levels and
probably in reducing the effect of the negative feedback
mediated by corticosteroids ( 42 ).
Approximately 1066 genes have been found to be po-
tentially controlled by methylation in nonfunctioning ade-
nomas. Genes such as CACNA2D4, glutamate ionotropic
receptor AMPA type subunit 2 ( GRIA2 ), miR4774,
miR1179 and LINC01351 appear to be upregulated due
to lower methylation rates ( 38 ). Clinically nonfunction-
Molecular Biology of Pituitary Tumors 7
Tab l e 2. Differentially expressed genes in PT
Gene Regulation Pituitary Tum o r
SLC25A2 Upregulated All tumors
miR590
LINC00412
GHRH-R Upregulated All tumor with predominance in GH- and TSH- secreting tumors.
GnRH-R Upregulated FSH/LH secreting tumors
NR5A1
NEUROD1
ZNF804A
ZBED2
RAX2
ISL1
HMGA2
CACNA2DA Upregulated FSH/LH-, silent ACTH secreting tumor and null cell adenomas
EPHB6
SSTR2 Upregulated GH- and TSH-secreting tumors
POU1F1 Upregulated GH-, PRL- and TSH-secreting tumors
SLIT1
PRLR
SLC16A6
SOX5 Upregulated GH-, TSH- and POU1F1-plurihormonal tumor
RFX4
ZNF536
NEUROD4 Upregulated PRL-secreting tumors
ESR1
LHX3
D2R Downregulated GNAS mutation GH-secreting tumors
SSTR5 Upregulated PRL-, TSH- and to a lesser extent in GH- and ACTH-secreting tumors
USP8 somatic mutation ACTH-tumor
TRH-R Upregulated USP8 somatic mutation ACTH-tumor
SCG5 Upregulated CD-causing ACTH secreting tumors
GAL
TIMP1
APMAP
POMC Upregulated ACTH-secreting tumors and silent ACTH tumors
TBX19
AVPR1B Upregulated ACTH-secreting tumors
CRHR1
AR
NR1F2
PLAG1
EPHA4
PITX2 Upregulated Silent ACTH tumor
RxRG
ing adenomas of gonadotroph differentiation, null cell ade-
nomas and silent ACTH tumors share the overexpression
of miR-582, miR-1468-5p, miR-28, miR-532 and miR-137
( 11 ). Interestingly, the miRNA signature could potentially
discriminate patients with invasive from those with non-
invasive gonadotrope tumors. A gene set of six miRNAs
( miR184, miR181a-2-3p, miR93-3p, miR574-5p, miR185-
5p, and miR3200-5p ) may represent potential biomarkers
of invasiveness of clinically nonfunctioning gonadotrope
tumors, although this is still controversial and requires fur-
ther research ( 43 ).
GH-, PRL- and TSH-secreting adenomas have 184, 204,
and 68 distinct genes, respectively that could be poten-
tially regulated by methylation ( 38 ). In thyrotrophinomas,
these genes include SSTR2, GRIA2 and LINC01173 ; in so-
matotrophinomas, transmembrane protein 233 ( TMEM233 )
and glutamate ionotropic receptor AMPA type subunit
4 ( GRIA4 ); and in prolactinomas, glutamate ionotropic
receptor NMDA type subunit 3A ( GRIN3A ). All three
POU1F1 -derived tumors overexpress miR377 and miR136
( 38 ). GH-secreting tumors overexpress miR21-5p, miR34a,
miR145, miR23b and miR107 which in turn regulate
genes such as insulin-like growth factor 1 ( IGF1 ), SRY-
box transcription factor 7 ( SOX7 ), and MYCN proto-
oncogene, bHLH transcription factor ( MYCN ) involved
in cell proliferation and apoptosis ( 43 ). PRL-secreting
tumors characteristically overexpress miR72a, miR93,
miR1299 and miR130a-3p, which in turn regulate pro-
lactin production and resistance to dopamine agonists
(DA) ( 43 ).
8 Marrero-Rodríguez et al. / Archives of Medical Research 54 (2023) 102915
Chromatin Remodeling Proteins in Pituitary Tum ors
Chromatin remodeling refers to the post-translational mod-
ification of histones, including methylation, lysine addition,
acetylation and citrullination, which are crucial for DNA
packaging in the formation of nucleosomes ( 44 ). Chro-
matin remodeling complexes (CRCs) can be described as
specialized multiprotein machinery that allow access to
DNA by temporarily modifying the structure or compo-
sition of nucleosomes ( 44 ). Ikaros ( IK ) is a protein ex-
pressed in normal pituitaries that plays a critical role in
the development and expansion of corticotrophs and so-
matotrophs, putatively acting through the fibroblast growth
factor receptor 4 ( FGFR4 ). The IK1 and IK2/3 alterna-
tively spliced isoforms, as well as the dominant-negative
IK6 isoform are expressed in nearly 50% of human pitu-
itary adenomas ( 45 ). IK selectively deacetylates histone 3
residues on the proximal transfected or endogenous GH
promoter and limits access to the POU1F1 activator ( 45 ).
In contrast, IK acetylates histone 3 on the proximal PRL
promoter and facilitates POU1F1 binding to this region
in the same cells. These data provide evidence for IK-
mediated histone acetylation and chromatin remodeling in
the selective regulation of pituitary GH and PRL hormone
gene expression ( 45 ). MAGE family member A3 ( MAGE-
A3 ) transcripts are abundant in PT and have been impli-
cated in the transcriptional silencing of p53 through histone
deacetylation. Furthermore, MAGE-A3 downregulation re-
sults in p53 and p21 accumulation ( 45 ).
Concluding Remarks
The advent of genomics, transcriptomics, epigenetics, im-
munomics, metabolomics, proteomics, and their correlation
with clinical data, has provided researchers with an integral
perspective of the underlying complexity of PT, highlight-
ing their architecture, their molecular changes, and cellular
responses. Additionally, it has furthered our understanding
of the interactions between the tumor and its microenvi-
ronment and has broaden the therapeutic horizon with po-
tential, personalized molecular strategies that may be par-
ticularly useful in aggressive and recurrent neoplasms, as
well as in the rare cases of pituitary carcinoma. It is worth
mentioning that the main limitation of this review is the
significant heterogeneity of the data, which stems from the
different experimental approaches used in each of the re-
viewed studies. In our opinion, this data heterogeneity pre-
cludes us from drawing an integrative scenario encompass-
ing all the potential molecular alterations that contribute to
pituitary tumorigenesis.
Conflicts of Interest
There is no conflict of interest that could be perceived to
affect the impartiality of the reported research.
Acknowledgments
SVP and SAE are recipients of a grant from the Na-
tional Council for Humanities, Science and Technol-
ogy (CONAHCyT). All images were created in BioRen-
der.com.
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