Advanced Diagnostics for Advancing the Cure

UAMS ADVANCED DIAGNOSTICS FOR ADVANCING CURE

advanced diagnostics for advancing cure Multiple myeloma (myeloma) is a complex cancer that can be difficult to diagnose and challenging to treat.

Every case of myeloma is unique in terms of disease characteristics, including genetic mutations.

Over more than 25 years of focusing exclusively on myeloma and related diseases, we have learned that targeting treatment to each individual’s disease holds the most promise for cure.

Advanced diagnostics at the Myeloma Institute enable us to identify the specifics of each person’s disease and personalize a course of treatment for the best possible results.

Not only do we conduct advanced diagnostic testing, but we also have the expertise to interpret test results and understand their scientific basis and significance.

The ability to develop and utilize advanced diagnostic tools and fine-tune treatment accordingly is unique to the Myeloma Institute.

Background Multiple myeloma is a cancer of plasma cells, a type of white blood cell.

Blood cells develop from blood-forming stem cells in the bone marrow. These stem cells mature into different types of blood cells – white blood cells, red blood cells and platelets. Plasma cells are white blood cells that make antibodies to help protect the body from germs and other harmful substances.

DNA Damage

Damaged white blood cell (B-cell) Multiple Myeloma cell

M Proteins

Myeloma begins when a plasma cell in the bone marrow becomes abnormal. Mature myeloma cells secrete immunoglobulins (antibodies) known as M proteins, which can be detected in the blood.

Molecular genetics & diagnostics “Molecular genetics” refers to the study of the molecular processes underlying gene structure and function.

“Molecular diagnostics” refers to the application of molecular biology techniques and knowledge of the molecular mechanisms of disease to determine diagnosis, prognosis and treatment of disease.

Like other cancers, myeloma is characterized by genetic abnormalities, or mutations, that result from damage to normal cells. In particular, the biologic mechanisms that control normal cell growth are affected. This wreaks havoc with the function of the cells through altered patterns of gene activity, known as gene expression.

The unique characteristics of each individual’s genetic make-up and the genetic changes that give rise to cancer result in a truly unique profile of behavior for each person’s disease. Thus, no two cancers are absolutely identical. The same type of cancer (for example, myeloma or leukemia) is different for each individual.

Therefore, in order to determine the most effective treatment for an individual patient, it is very important to identify the unique characteristics of each person’s disease, including mutations and patterns of gene expression.

At the Myeloma Institute we utilize a full array of standard diagnostic tools, such as blood profiling, Magnetic Resonance Imaging (MRI), skeletal survey, bone densitometry, Positron Emission TomographyComputed Tomography (CT/PET), bone marrow biopsy and more.

In addition, we utilize genetic testing at the molecular level to reveal information about gene expression patterns and disease nuances. This helps us predict how myeloma cells are likely to respond to different therapeutic agents and strategies.

Gene Expression Profiling The Myeloma Institute pioneered the routine use of gene expression profiling (GEP) to uncover important information about myeloma biology.

Based on GEP studies of more than 1,300 newly diagnosed patients, our researchers Identified a set of four genes that allows us to predict with high probability which patients are likely to progress from MGUS (monoclonal gammopathy of undetermined significance, a precursor condition) to myeloma.

Developed a 70-gene test (GEP70) that identifies patients with high risk for short progression-free survival.

Identified seven distinct molecular subtypes of myeloma.

Identified mutations that affect response to therapy.

GEP studies are conducted at time of diagnosis and at various points throughout treatment.

Information gleaned from GEP studies is used to fine-tune and direct individualized therapies.

This is particularly important for patients with highrisk disease.

Predicting Response to Therapy Gene expression profiling makes it possible to predict with significant accuracy how a patient will respond to treatment. Myeloma Institute physicians select treatment plans with the best potential for curative outcome, based on the individual’s genetic profile.

GEP studies

GEP Heatmap

Through gene expression profiling (GEP), researchers at the Myeloma Institute have discovered that myeloma is not one disease, but seven different disease subtypes. While being morphologically indistinguishable from case to case, myeloma can be caused by different molecular defects. This discovery helps explain why some patients respond well to current therapies and others do not. The figure above is known as a heatmap.

The heatmap represents the expression level of 700 genes in myeloma cells from 351 newly diagnosed myeloma patients. Red means the gene is expressed at high levels and green means the gene is low.

Of more than 54,000 gene probes tested, we have identified 700 genes (100 for each subtype) with differential expression. Each disease subtype is characterized by a unique over-expression (red) or under-expression (green) of 100 genes, resulting in the “staircase” appearance of the figure. Genes that are over-expressed in one subtype (for example in CD-1 subtype) are not over-expressed in the other six subtypes. A computer algorithm developed by our researchers uses these gene expression levels to provide a molecular diagnosis of each person’s disease, enabling us to develop individual, disease subtype-specific treatments.

Genomics Genomics refers to the study of genes and their functions. While genetics scrutinizes the functioning and composition of the single gene, genomics addresses all genes and their inter-relationships in order to identify their combined influence on the growth and development of cells.

Through advances in genomics, the Myeloma Institute conducts studies that reveal high-level information for fine-tuning diagnosis and developing “precision medicine” treatments.

Specifically, we use DNA and RNA sequencing methods to look for a range of mutations that can help us target treatment. The data can inform us of treatment strategies and can help us identify approaches for cure. We also use Methylation Analysis to guide treatments that target tumor suppressor genes.

DNA Sequencing DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.

It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine and thymine – in a strand of DNA. The development of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

The first DNA sequences were obtained in the early 1970s through laborious methods based on two-dimensional chromatography. Following the development of fluorescence-based sequencing methods with automated analysis, DNA sequencing has become much easier and faster.

Next-generation sequencing, via high-throughput technology, enables sequencing of multiple genes and samples at one time. The technologies parallelize the sequencing process, producing thousands or millions of sequences concurrently.

RNA Sequencing RNA Sequencing is a technology that uses the capabilities of next-generation sequencing to reveal the mutations causing myeloma that can be targeted with specific therapies. It can also be used to understand the level at which a gene is turned into a protein.

Genomic-based Sequencing Studies at the Myeloma Institute include Targeted Sequencing Whole Exome Sequencing RNA Sequencing Whole Genome Sequencing BRAF/MEK inhibitors

NRAS

CCND1 BRAF FAM46C

MYC 3

RB1

HIST1H1E EGR14 IRF

DIS

TP53

RAS Pathway Mutations

CYLD

MMSET

RPS18

BRAF FAM46C

MYC 3

KRAS

PRAMEF2 FGFR3 RB1

MAX

HIST1H1E EGR1 IRF4

DIS

Gene Expression Changes

LTB

CCAC3

MAF

MMSET

RPS18

LTB

TP53

CYLD

Copy Number Abnormalities

MYC inhibitors

Acquired Mutations

MYC Copy NumberSecondary Epigenetic inhibitors TranslocationsModiďŹ cations Abnormalities

CCAC3

MAF

Secondary Translocations

BRAF/MEK

inhibitors Gene Expression Changes

NRAS KRAS CCND1 MAX

PRAMEF2 FGFR3

Acquired Mutations

RAS Pathway Mutations

Epigenetic ModiďŹ cations

HDAC & DNMT3 inhibitors

HDAC & DNMT3

Primary inhibitors MMSET/CCND Translocations/ Primary Hyperdiploidy MMSET/CCND inhibitors Translocations/ Hyperdiploidy

inhibitors

Numerous genetic alterations, or mutations, affect myeloma cells, making them complex and difficult to eradicate. A primary mutation, as depicted on the tree trunk, can evolve into many mutations over time, as depicted on the tree branches. All of these mutations are then present in the myeloma cell, as depicted in gray.

It is important to target each alteration with specific inhibitors in order to fully destroy the myeloma cell. Advanced understanding of myeloma genetics and precision medicine enable identification of each genetic alteration and development of targeted therapies.

Methylation Analysis DNA methylation is a chemical reaction that places a methyl group (combination of carbon and hydrogen atoms) at a particular spot on DNA. It can cause tumor suppressor genes that keep cell behavior normal to be switched off during myeloma progression.

Methylation Analysis provides insight for switching the tumor suppressor genes back on through the use of epigenetic treatments in order to normalize DNA packing and cell behavior.

Epigenetics refers to the way DNA is packed and wound into chromosomes and modifications to the genome that influence when and how often a gene is active.

Benefits of Advanced Diagnostics Information obtained from advanced diagnostic testing, including Gene Expression Profiling and DNA and RNA sequencing, allows us to develop precision medicine approaches based on incorporating targeted therapies that are individualized for each patient.

The information supports development of prevention and early intervention strategies.

Understanding this information enables us to: Design methods for normalizing cell biology that has gone astray and preventing disease progression.

Design treatment regimens based on altering the cell’s behavior to prevent resistance to therapy and disease relapse.

Design treatment strategies aimed at switching off the genetic signals that lead to myeloma development.

Identify additional mutations that could initiate cancerous activity in cells.

Cure more patients with less toxic treatments.

Advanced diagnostics make it possible to predict which patients will benefit from a given drug. For example, Myeloma Institute researchers recently demonstrated the effectiveness of trametinib for patients with refractory and relapsed myeloma who had unique genetic alterations. Says Dr. Gareth Morgan, director of the Myeloma Institute: “Despite diagnostic and therapeutic advances for patients with multiple myeloma, finding effective treatment options for patients who progress after initial therapies remains a key challenge…The majority of patients treated with trametinib experienced stabilization of their disease or disease regression…These data support the application of personalized treatment strategies and an individualized approach to the management of highrisk multiple myeloma patients.”

Prognosis: Cure is Achievable With our robust diagnostic capabilities and a state-ofthe-art laboratory dedicated to molecular diagnostics discovery, we are well equipped to define the nuances of each patient’s disease. This, in turn, allows us to develop individualized treatment regimens for optimal effectiveness and, ultimately, cure for patients with myeloma and related diseases.

The Myeloma Institute conducts comprehensive diagnostic testing, utilizing advanced genomic technology, to ensure that each patient receives a personalized treatment plan for the most promising outcome.

cure is achievable

Myeloma.uams.edu

4301 West Markham Street, #816 Little Rock, AR 72205 www.myeloma.uams.edu 501-526-2873 E-mail: mirt@uams.edu facebook.com/uamsmyelomainstitute