Translational Genomics of Blood Cancers

In recent decades, numerous scientific evidences have demonstrated the presence of a genetic component in the etiology of solid tumors and hematological malignancies, as well as in the pretumoral stages of the latter, including monoclonal gammopathy of uncertain significance (MGUS) or monoclonal B-cell lymphocytosis (MBCL).

Although conventional cytogenetic analysis techniques (karyotyping and FISH) and mutational profiling have proven to be very useful in the diagnosis and prognosis of these pathologies, their use has revealed the existence of important limitations. In addition to the study of chromosomal aberrations, the simultaneous analysis of thousands of genetic and epigenetic variations with the new technologies developed in the field of genomics has become of practical value in the diagnosis and classification of hematological malignancies and solid tumors and, recently, it has been suggested that, unlike cytogenetic analysis, this type of approach can also lead to the development of new prognostic tools, the discovery of new therapeutic targets and the implementation of more individualized treatment strategies. However, despite the spectacular technological progress in functional and structural genomics, there are still a few genetic variations that have been unequivocally identified as being associated with susceptibility to these pathologies and, above all, to their progression.

Figure 1. Some of the most relevant mutations involved in determining susceptibility to hematological malignancies.

That is why our research group focuses its efforts on this line and tries to identify genetic variations (SNPs, mutations, ins/del, CNVs, etc…) involved in these processes, as well as in the triggering of some associated clinical complications such as graft-versus-host disease and infections by opportunistic pathogens (in particular, Aspergillus fungi). In parallel, our group is also considering the analysis of the interaction of genetic variations with environmental factors and the study of the role of these genetic variations in the response to drugs with special attention to those used in chemotherapeutic treatments.

Historically, the strategies chosen for our studies have been fundamentally those based on the study of candidate genes selected according to relevant pathways in each pathology, such as autophagy, proliferation, apoptosis, and telomere regulation.

Figure 2. Autophagy pathway. A pathway intensively studied by our group in both malignant blood disorders and solid tumors.

In recent years we are conducting structural genomic studies oriented to the massive analysis of variations in the genome such as GWAS (Genome-wide association studies), next-generation sequencing techniques, the analysis of gene expression and methylation profiles and determination of telomere length.

The use of these molecular techniques together with functional studies is allowing the identification of genes involved in susceptibility and the improvement in the understanding of the biology and etiopathogenesis of many multifactorial diseases, as well as in the management of therapy based on a large amount of available genetic information. Likewise, the use of these new technologies is enabling a deeper analysis of the tumor genome and facilitating the identification of specific mutations in certain types of tumors, which undoubtedly brings the possibility of identifying new therapeutic targets and adapting treatment strategies even closer.

LINES OF RESEARCH

Line 1: Genetics of hematological malignancies.

Most hematological malignancies are very well characterized from the cytogenetic point of view and, although it is well known which chromosomal alterations occur in each of them and what is their prognostic value, it is increasingly evident that these alterations do not fully explain the genetic basis of these diseases and that other genetic and epigenetic alterations are necessary for the appearance of these diseases. Considering these facts and like the research line developed in myeloma, our research group, in collaboration with other researchers at national level, aims to find those genetic polymorphisms that determine the risk of developing hematological malignancies, as well as to determine the influence of the interaction of these genetic alterations with environmental factors. On the other hand, this line of research also aims to characterize the genetic profile associated with the response to the different therapies used in first and successive lines of treatment, as well as to establish the biological consequences of these alterations by means of functional assays.

Line 2: Genetics of monoclonal gammopathy of uncertain significance (MGUS) and monoclonal B-cell lymphocytosis (MCLB)

Multiple myeloma (MM) or chronic lymphocytic leukemia (CLL) are very heterogeneous hematological malignancies that develop from premalignant stages such as monoclonal gammopathy of uncertain significance (MGUS) or monoclonal B-cell lymphocytosis (MBCL). Although in recent years considerable progress has been made in the understanding of the etiopathogenesis of these pretumoral conditions, the molecular mechanisms underlying the process of tumor transformation are still unknown. In the case of MGUS, for example, the most accepted hypothesis is that it may be due to the accumulation of certain genetic alterations such as translocations in the variable regions of the immunoglobulin (IgH) heavy chains (11q13, 4p16, 16q23, 21q12, and 6p21), deletions in chromosome 13 and trisomies of chromosomes 3, 5, 9, 11, 15, 19 and 21, as well as dysregulation of cyclin D gene expression. However, recent studies have shown that, in addition to these chromosomal alterations, the presence of single nucleotide polymorphisms (SNPs) may influence the development of tumor disease, as well as the degree of tumor progression. Based on this hypothesis, the main objective of our group is to identify genetic variations associated with MGUS and CMLB that may help us to understand the mechanisms underlying tumorogenesis.

Line 3: Cancer-related infections

Infections play a very relevant role in the management of cancer patients. One of the most prominent examples is Invasive Aspergillosis (IA), a deadly infection caused mainly by fungi of the genus Aspergillus that frequently colonizes the respiratory tract and spreads rapidly to blood vessels and tissues in immunocompromised individuals.

Figure 3. Invasive Pulmonary Aspergillosis, a common clinical complication in cancer patients.

The incidence of this infection has increased in recent years due to the use of potent immunosuppressants and immunomodulatory drugs and currently continues to have a high morbidity and mortality rate worldwide, especially in immunocompromised patients and those undergoing hematopoietic precursor transplantation. Although several risk factors related to the development of IA (defects in phagocyte function, the use of corticosteroids and broad-spectrum antibiotics, prolonged neutropenia induced by chemotherapy, as well as the existence of previous episodes of infection) have been identified in recent decades, it is still extremely difficult to prevent and diagnose this infectious disease at an early stage. Epidemiological studies have shown that onco-hematological patients with the same underlying pathology and similar risk factors and clinical conditions have very different degrees of susceptibility to invasive fungal infections such as IA, suggesting the existence of a genetic predisposition to develop this type of disease. This fact, together with the difficulty of diagnosing invasive fungal diseases in their early stages, shows the enormous usefulness of identifying genetic biomarkers that would allow us to predict which patients are potentially susceptible to infection, as it would give us the opportunity to design an appropriate prophylactic strategy for each patient.

In the context of an international consortium, AspBIOmics, our research group is developing this line of research based on the study of large-scale genetic polymorphisms and the development of functional assays for the identification of genetic biomarkers that, according to our starting hypothesis, condition the degree of susceptibility and response to antifungals. In this consortium the efforts are not only oriented to the search for genetic biomarkers that allow predicting susceptibility or response to drugs but we also try to evaluate a series of assays for the detection of elements of the Aspergillus fungus (RNA, polysaccharides or proteins) or the patient (cytokine profile, chemokines, etc …) in a multiparametric strategy that we hope will allow us to characterize the disease for the subsequent development of reagents and / or commercial kits. More detailed information on the activity we are developing, as well as on the scientific groups that are part of this initiative, can be found on our consortium’s web page (www.aspBIOmics.eu).

Line 4: Genetics of solid tumors: Colorectal, pancreatic and prostate cancers

Colorectal, prostate, and pancreatic cancers are three significant types of cancer affecting different tissues. Colorectal cancer is one of the most common cancers worldwide, with an estimated 152,810 new cases and 53,010 deaths expected in the United States in 2024. It is the second leading cause of cancer death in the U.S., and regular screening, particularly colonoscopy, can detect early-stage cancer and prevent its development by removing precancerous polyps. Symptoms may include changes in bowel habits, blood in stool, abdominal pain, and unexplained weight loss, with risk factors including family history, hereditary conditions, and a personal history of polyps. Prostate cancer, the second most common cancer affecting males after skin cancer, develops in the prostate gland and affects about 13 out of 100 males in their lifetime. Early-stage prostate cancer rarely causes symptoms, and risk factors include age, race, and family history, with treatment options varying by stage and potentially involving surgery, radiation, or hormone therapy. Pancreatic cancer, though less common, is known for its aggressive nature and poor prognosis, and is linked to a family history of pancreatic cancer, which also increases the risk of other cancers like breast, ovarian, colon, prostate, liver, and bile duct cancers.

Research has shown connections between these cancers that share common risk factors, particularly genetic predisposition and family history, making regular screenings and a healthy lifestyle essential for early detection and prevention. Although in the last decades primary surgical strategies for solid tumors have evolutionarily changed and have markedly improved both short and long-term disease outcomes, a high proportion of patients still experience severe disease relapses leading to short periods of overall survival (OS). Moreover, it is important to note that these cancers are characterized by a marked degree of heterogeneity with patients presenting very stable diseases to patients with rapidly progressive diseases who are destined to succumb in a short time. Because of this great heterogeneity, several years of treatment are often required, so that the economic costs of caring for cancer patients are usually extremely high. There are currently no clinical tools that consider the heterogeneity in the clinical course of these cancers, which severely limits opportunities for early intervention and prevention. In this discouraging context, it is urgent to define new approaches to identify new molecular biomarkers for the development of “genetic/genomic scores” for diagnosis and prognosis to predict the development of these diseases and to implement new therapeutic strategies that are more individualized and economically feasible.

OTHER AREAS OF INTEREST

Genetic basis of rheumatoid arthritis and ankylosing spondylitis

Rheumatoid arthritis (RA) and ankylosing spondylitis (AS) are chronic inflammatory diseases that affect the joints, but they differ in various aspects such as age of onset, gender prevalence, and genetic associations. AS typically begins earlier, around 28 years, compared to RA, which usually starts between 40-50 years, and AS predominantly affects males, while RA is more common in females. The genetic associations of these diseases are significant, as 95% of AS patients are HLA-B27 positive, whereas 60% of RA patients are HLA DR4 or DR1 positive, highlighting the importance of genetic analysis in diagnosis and treatment. RA primarily affects peripheral joints like the hands and feet, while AS mainly impacts the spine and sacroiliac joints, with potential involvement of larger joints. RA shows bone resorption with erosive changes in radiographs, whereas AS is characterized by bone formation with vertebral syndesmophytes. Both diseases present different symptoms, with RA causing joint pain, swelling, stiffness, and fatigue, and AS causing lower back and hip pain that improves with exercise. Genetic testing plays a crucial role in confirming diagnoses, as it helps differentiate between these conditions and guides treatment. While NSAIDs and TNF-alpha blocking drugs are effective for both conditions, DMARDs are important in RA but have limited use in AS. To date, several genetic markers have been identified as associated with response to DMARDS and anti-TNF drugs, which confirms the importance of genetic testing in the management of patients.

The co-occurrence of both diseases is rare but has been observed, and patients with both often display more severe symptoms and radiological changes. Even though RA and AS share some characteristics as chronic inflammatory diseases, they have distinct genetic links, clinical presentations, and responses to treatment, which underscores the need for precise genetic testing to ensure effective management.

The genetic factors involved in the triggering of RA and AS have been the subject of intense research but, to date, only a few studies have investigated the relationship between the presence of genetic alterations and gender-associated differences in susceptibility to these diseases. With these facts in mind, our research group is focused on identifying gender-associated genetic variations in immune system genes that are associated with an increased risk of developing RA and AS. In addition, our group is studying overlapping genetic factors and whether the interaction of genetic alterations and environmental factors modulates the risk of developing both diseases.

TECHNOLOGICAL PLATFORMS

Large-scale genotyping techniques

Massive Genotyping – Infinium® HD Beadchips, Illumina® Technology

iSelect HD Custom Genotyping, Illumina® Technology

Small Scale Genotyping – 7500 Technology Real Time PCR System (TaqMan® Applied Biosystems, KASPar® KBiosciences)

ImmunoChip (Illumina® Technology).

Bulk Sequencing

Sequencing

Illumina® Sequencing Technology

Gene Expression

CodeLink Platform (Applied Microarrays)

CodeLink Human Whole Genome Arrays

CodeLink Mouse Whole Genome Arrays

Functional Assays

FUNDING AGENCIES OF THE GROUP’S PROJECTS

– ERA-NET Pathogenomics

– Carlos III Institute of Health (ISCIII).

– Ministry of Economy and Business.

– Ministry of Science and Innovation.

– Ministry of University, Research and Innovation.

– Ministry of Health and Consumer Affairs.

– Regional Ministry of Health and Families.

– Regional Ministry of Innovation, Science and Enterprise. Regional Government of Andalusia

– Office for the Transfer of Research Results (OTRI) – UGR.

– Celgene

– Roche-Pharma

– Andalusian Rheumatology Foundation

INTERNATIONALIZATION

Coordination and participation in national and international consortia.

– CIBER (Center for Biomedical Research Network)

– InterLymph (Malignant Hemopathies)

– IMMEnSE (Multiple Myeloma)

– CRuCIAL (Chronic Lymphocytic Leukemia)

– NuCLEAR (Acute Myeloid Leukemia)

– aspBIOmics (Invasive Fungal Infections)

– IMPULSE (Myelodysplastic Syndrome)

– MIRACLE (Myeloproliferative Syndromes)

– GECCO (Colorectal Cancer)

– PRACTICAL (Prostate Cancer)

– REPAIR (Rheumatoid Arthritis and Ankylosing Spondylitis)