Patent Application
20190256930
The present invention relates to methods for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia. The present invention also provides methods for the identification of a responding subject to treatment with an LSD1 inhibitor. Also methods of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor are provided. The methods comprise determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control indicates responsiveness to the LSD1 inhibitor. Methods of treatment of patients with the LSD1 inhibitor, wherein the patients are identified in accordance with the present invention to be responders are also subject of the present invention. LSD1 inhibitors for use in the treatment of this patient group are provided.
Aberrant gene expression in affected tissue as compared to normal tissue is a common characteristic of many human diseases. This is true for cancer and many neurological diseases which are characterized by changes in gene expression patterns. Gene expression patterns are controlled at multiple levels in the cell. Control of gene expression can occur through modifications of DNA: DNA promoter methylation is associated with suppression of gene expression. Another class of modifications involve histones, which are proteins, present in the nucleus of eukaryotic cells, that organize DNA strands into nucleosomes by forming molecular complexes around which the DNA winds. Histones play a critical role in modulating chromatin structure and DNA accessibility for replication, repair, and transcription. The covalent modification of histones is closely associated with regulation of gene transcription. Chromatin modifications have been suggested to represent an epigenetic code that is dynamically ‘written’ and ‘erased’ by specialized proteins, and ‘read’ or interpreted by proteins that translate the code into gene expression changes. A number of histone modifications have been discovered including histone acetylation, histone lysine methylation, histone arginine methylation, histone ubiquinylation, and histone sumoylation.
A group of enzymes known as histone lysine methyl transferases and histone lysine demethylases are involved in histone lysine modifications. One particular human histone lysine demethylase enzyme called Lysine Specific Demethylase-1 (LSD1) (Shi et al. (2004) Cell 119:941) has been reported to be involved in this crucial histone modification. LSD1 has a fair degree of structural similarity, and amino acid identity/homology to polyamine oxidases and monoamine oxidases, all of which (i.e., MAO-A, MAO-B and LSD1) are flavin dependent amine oxidases which catalyze the oxidation of nitrogen-hydrogen bonds and/or nitrogen carbon bonds.
LSD1 has been recognized as an interesting target for the development of new drugs to treat cancer, neurological diseases and other conditions, and a number of LSD1 inhibitors are currently under preclinical or clinical development for use in human therapy.
Finding pharmacodynamic (PD) biomarkers which indicate that a drug is active can be valuable for use during clinical trials or in clinical practice. PD biomarkers can be used to monitor target engagement, i.e. to see if the drug is inhibiting the target against which the drug is designed to act in a subject receiving such drug. They can also be used to monitor the response of those patients receiving the drug. If the biomarker indicates that the patient is not responding appropriately to the drug treatment, then the dosage administered can be increased, reduced or treatment can be discontinued. Biomarkers can also be used to identify particular groups of patients that would benefit, or that would benefit the most, from receiving the drug treatment.
The technical problem underlying the present invention is the provision of means and methods to monitor the response to treatment with an LSD1 inhibitor in subjects suffering from leukemia and to identify subjects suffering from leukemia that respond to an LSD1 inhibitor.
The technical problem is solved by provision of the embodiments characterized in the claims.
Accordingly, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to treatment.
In a further aspect, the present invention relates to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responding subject.
In a related aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responsive proliferative diseased cell.
As documented herein below and in the appended examples, levels of biomarkers in subjects suffering from leukemia, especially acute myeloid leukemia (AML), were determined during the course of treatment with an LSD1 inhibitor. The level was correlated to response to the LSD1 inhibitor (increase in blast differentiation and/or a decrease in blast cells). Thereby, a panel of biomarkers was identified whose increased expression level correlated with the response to the LSD1 inhibitor. These biomarkers were therefore demonstrated herein as being useful for monitoring a response to LSD1 inhibitor in leukemia patients. They can also serve to identify responders to LSD1 inhibitors.
It was demonstrated herein that not all potential biomarkers that are differentially regulated during LSD1 inhibitor treatment are useful for monitoring a response to LSD1 inhibitors in leukemia patients. For example, patient 9 showed a response to LSD1 inhibitor treatment (in this patient, blast differentiation and decrease in blasts was observed), and a decrease in the level of CTSG. However, the level of CTSG was increased in patients 1 and 2, that also responded to LSD1 inhibitor treatment. Thus, the level of CTSG is not consistently increased or decreased in responding subjects. Likewise, the level of CAMSAP2 was decreased in responding patient 9 and increased in responding patients 1, and 2, and 4. Therefore, also the level of CAMSAP2 is not consistently increased or decreased in responding subjects. Thus, CTSG and CAMSAP2 were determined not to be useful for monitoring a response to LSD1 inhibitor treatment.
By contrast, levels of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, and VIM were consistently increased in leukemia patients that responded to treatment with an LSD1 inhibitor. This increased expression level of these biomarkers was particularly consistent and pronounced in AML patients of AML subtype M4 and M5 (see patients 1, 2 and 9). Thus, biomarkers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, and/or VIM are useful to monitor a response to treatment with an LSD1 inhibitor and/or to identify responders. Their use may be particularly advantageous in the patient group of AML subtype M4 and M5. The highest increase was seen for biomarkers S100A12, VCAN, and LY96, particularly in samples from responding patients of the AML M4/M5 subtypes.
Additionally, the expression levels of biomarkers of the invention correlate with the variation of blast cells in bone marrow, particularly in M4/M5 subtypes, further supporting the utility of these marker genes in monitoring response to LSD1 inhibitor treatment in easily accessible samples such as peripheral blood. In particular, the expression levels of Ly96 and ITGAM correlate with the variation of blast cells in bone marrow particularly in M4/M5 subtypes.
In the herein provided experiments peripheral blood samples obtained from the patients have been used. While the present invention is not limited to this type of sample, the use of blood samples is particularly advantageous. Blood extractions are easy to perform and can be performed more frequently than biopsies or bone marrow sampling, and leukemia patients are subject to frequent hemogram analysis. Therefore, a monitoring method that can be used to assess the response to (treatment with) an LSD1 inhibitor in blood samples as described herein is highly desirable.
Unexpectedly, the herein provided biomarkers are not only useful to monitor response to an LSD1 inhibitor or identify responders to treatment with an LSD1 inhibitor. It was shown herein that the biomarkers can also be used to predict whether a subject is at risk of developing a differentiation syndrome (DS). The differentiation syndrome (DS) is a relatively common and potentially severe complication seen in AML patients treated with differentiating agents. LSD1 inhibitors have been shown to induce differentiation of leukemic blast cells. The differentiation of a vast number of leukemic blasts may lead to cellular migration, endothelial activation, and release of interleukins and vascular factors responsible for tissue damage, finally developing in a syndrome characterized by unexplained fever, acute respiratory distress with interstitial pulmonary infiltrates, and/or a vascular capillary leak leading to acute renal failure. In fact, patients 1 and 9 herein that responded well to LSD1 inhibitor treatment developed a differentiation syndrome in the course of the treatment. As demonstrated herein, biomarkers S100A12 and VCAN showed an exacerbated (18 to 550-fold) up-regulation in these patients. Importantly, this up-regulation could be observed up to 2 weeks prior to the clinical diagnosis of the differentiation syndrome. Thus, measuring the increase of S100A12 and VCAN is a useful tool to early monitor the risk of developing a differentiation syndrome in leukemia patients receiving treatment with an LSD1 inhibitor (e.g. ORY-1001), particularly in AML M4/M5 subtypes.
As explained above and shown in the appended examples, S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, and VIM are highly useful biomarkers for monitoring a response to an LSD1 inhibitor or for identifiying responders. Therefore, S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, and VIM can be used advantageously in accordance with the present invention. Subsets of these markers may be particularly advantageously used for specific applications, e.g. for discriminating best responders and worse responders and/or for assessing the risk of developing a differentiation syndrome among those subjects receiving treatment with an LSD1 inhibitor. Based on an overall assessment of the experimental data provided herein, S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and/or LYZ, would be preferred biomarkers for use in the present invention. A more limited panel of one or more of biomarkers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86, would be particularly preferred for use in the present invention.
The terms “marker”/“markers” and “biomarker”/“biomarkers” are used interchangeably herein.
As mentioned above, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to treatment.
It is understood that the response of a subject to an LSD1 inhibitor/to treatment with an LSD1 inhibitor is monitored.
The monitoring method of the invention relates therefore in other words to a method for monitoring the response of a subject suffering from leukemia to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response of said subject to treatment. In yet other words, the present invention relates in an aspect to a method for monitoring the response to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response of said subject to treatment.
The term “treatment” as used in the present invention relates in its broadest sense to the administration of an LSD1 inhibitor to a subject suffering from leukemia. In a more simplified form, the terms “response to treatment with an LSD1 inhibitor in a subject suffering from leukemia” or “treatment with an LSD1 inhibitor in a subject suffering from leukemia” and the like can be phrased “response to an LSD1 inhibitor in a subject suffering from leukemia” or “an LSD1 inhibitor in a subject suffering from leukemia” and the like.
Thus, the present invention relates in other words in this sense to a method for monitoring the response to an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to said LSD1 inhibitor. Likewise, the monitoring method of the invention relates in one aspect to a method for monitoring the response of a subject suffering from leukemia to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response of said subject to said LSD1 inhibitor. Likewise, the present invention relates in an aspect to a method for monitoring the response to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to said LSD1 inhibitor.
The method can comprise a step of comparing the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM with a control.
The present invention relates in one aspect accordingly to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising
According to said method, an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM determined in a) compared to a control indicates a response to the treatment with an LSD1 inhibitor.
The monitoring method of the invention relates therefore in other words to a method for monitoring the response of a subject suffering from leukemia to treatment with an LSD1 inhibitor, said method comprising
According to said method, an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM determined in a) compared to a control indicates a response of said subject to the treatment of leukemia with an LSD1 inhibitor.
In yet other words, the present invention relates in an aspect to a method for monitoring the response to treatment with an LSD1 inhibitor, said method comprising
According to said method, an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to treatment.
The term “monitoring the response” as used herein can include or can be an assessment of the response.
The monitoring method of the invention relates therefore in other words in one aspect to a method for assessing the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising assessing the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to treatment. In another aspect, the present invention relates to a method for assessing the response of a subject suffering from leukemia to treatment with an LSD1 inhibitor, said method comprising assessing the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response of said subject to treatment. In yet other words, the present invention relates in an aspect to a method for assessing the response to treatment with an LSD1 inhibitor, said method comprising assessing the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, AN , CD86, GPR65, CRISP9, LYZ and VIM, in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response of said subject to treatment.
It is understood that the term “treatment with an LSD1 inhibitor” as used herein can be a “therapy comprising an LSD1 inhibitor”.
The term “response (to treatment with an LSD1 inhibitor”) as used herein can include or can be “efficacy (of treatment with an LSD1 inhibitor)”.
The monitoring method of the invention relates therefore in other words to a method for monitoring the efficacy of treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising monitoring the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for efficacy of the treatment. In yet other words, the present invention relates in an aspect to a method for monitoring the efficacy of treatment with an LSD1 inhibitor, said method comprising monitoring the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for efficacy of said treatment.
As mentioned above, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for response to treatment.
It is understood that the term “indicative” as used herein refers to the fact that an increase in the level of one or more of the biomarkers disclosed herein reflects the response to (treatment with) an LSD1 inhibitor. Accordingly, the methods of the invention can also be phrased in a more assertive way without deferring from the gist of the invention, e.g. by stating that if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is identified as responsive to (treatment with) an LSD1 inhibitor.
For example, the present invention can accordingly relate in one aspect to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is responsive to treatment with an LSD1 inhibitor. The monitoring method of the invention can likewise relate to a method for monitoring the response of a subject suffering from leukemia to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is responsive to treatment with an LSD1 inhibitor. In yet other words, the present invention relates in an aspect to a method for monitoring the response to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from a subject suffering from leukemia, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is responsive to treatment with an LSD1 inhibitor.
The methods of the invention serve to monitor the response to (treatment with) an LSD1 inhibitor. They thus can be used to identify responding subjects and/or to identify a responding proliferative diseased cell.
Thus, the present invention relates in a related aspect to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responding subject.
In other words, the present invention relates in a one aspect to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is responsive to treatment with an LSD1 inhibitor.
In a related aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responsive proliferative diseased cell. In other words, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the proliferative diseased cell is responsive to treatment with an LSD1 inhibitor.]
As mentioned above, the term “treatment” as used herein relates in its broadest sense to the administration of an LSD1 inhibitor (to a subject suffering from leukemia). In a more simplified form, the terms “response to treatment with an LSD1 inhibitor” and the like can be phrased “response to an LSD1 inhibitor” and the like.
Thus, the present invention relates in a related aspect to a method for the identification of a responding subject to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responding subject. In other words, the present invention relates in a related aspect to a method for the identification of a responding subject to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the subject is responsive to the LSD1 inhibitor.
In a further related aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a responsive proliferative diseased cell. In other words, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein if the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is increased compared to a control, the proliferative diseased cell is responsive to the LSD1 inhibitor.
It is understood that the present invention aims at providing a companion diagnostic test using samples from subjects suffering from leukemia wherein the subjects receive a treatment with an LSD1 inhibitor.
Leukemia is a cancer of the body's blood-forming tissues. These tissues include the bone marrow and the lymphatic system. Leukemia often begins in the bone marrow. A normal bone marrow cell undergoes a change and becomes a type of leukemia cell. Once the marrow cell undergoes such a change, the leukemia cells can grow and survive better than normal cells. Thus, the leukemia cells crowd out or suppress the development of normal cells over time.
Different types of leukemia depend on the type of blood cell that becomes a cancer cell. For example, lymphoblastic leukemia is a cancer of the lymphoblasts.
White blood cells are the most common type of blood cell to become leukemic cancer cells. Thereby, leukemia results in high numbers of abnormal white blood cells. These abnormal white blood cells are not fully developed/differentiated and are called blasts. Red blood cells (erythrocytes) and platelets may also become leukemic cancer cells.
Diagnosis is typically made by blood tests or bone marrow biopsy. Symptoms of leukemia can include bleeding and bruising problems, feeling tired, fever, and an increased risk of infections. These symptoms are caused by a lack of normal blood cells.
Leukemia occurs most often in adults older than 55 years, but it is also the most common cancer in children younger than 15 years. Leukemia can be either acute or chronic. Acute leukemia is a fast-growing cancer that usually gets worse quickly. Chronic leukemia is a slower-growing cancer that gets worse slowly over time. The treatment and prognosis for leukemia depend on the type of blood cell affected and whether the leukemia is acute or chronic, among other factors.
For the purpose of the present invention, “leukemia” is preferably “myeloid leukemia”. “Myeloid leukemia” as used herein means any leukemia that has arisen from any cell of the developmental tree of myeloid cells (including multipotential hematopoietic stem cells, common myeloid progenitors, megakaryoblasts, erythroblasts, myeloblasts, mast cell progenitors, monocytes/macrophages, eosinophils, neutrophils, basophils, megakaryocytes/thrombocytes, erythrocytes, and mast cells, as well as cells that have arosen from other hematopoeietic lineages and that have undergone oncogenic transformation providing myeloid characteristics), both acute and chronic, including also mixed lineage/multilineage leukemias. Myeloid leukemia as used herein thus comprises, without being limited thereto, leukemias as classified in classes C92 to C94 of the International Classification of Diseases ICD-10 (online version 2016).
Most preferred herein is acute myeloid leukemia (AML). Acute myeloid leukemia (AML) is a cancer of the myeloid lineage of blood cells, characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. AML can occur in adults and children. It is the most common type of acute leukemia in adults. AML as used herein includes, inter alia, acute myelogenous leukemia, acute myeloblastic leukemia, acute granulocytic leukemia, and acute nonlymphocytic leukemia.
AML as used herein includes any leukemia classified as such according to any of the medically recognized past, current or future classification systems.
For example, “AML” as used herein includes leukemias of French-American-British (FAB) subtypes M0 to M7. The French-American-British (FAB) AML classification of 1976 (Proposals for the classification of the acute leukaemias. French-American-British (FAB) co-operative group. Bennett J M, Catovsky D, Daniel M T, Flandrin G, Galton D A, Gralnick H R, Sultan C. Br J Haematol. 1976 August; 33(4):451-8) and its subsequent revision (Proposed revised criteria for the classification of acute myeloid leukemia. A report of the French-American-British Cooperative Group. Bennett J M, Catovsky D, Daniel M T, Flandrin G, Galton D A, Gralnick H R, Sultan C. Ann Intern Med. 1985 October; 103(4):620-5) divided AMLs into 8 subtypes, based on morphologic and cytochemical features of the bone marrow leukemic blasts, including the type of cell from which the leukemia developed and how mature the cells were, among others.
In particular, M4, M5, and M6 FAB subtypes correspond to C92.5, C93.0, and C94.0 WHO ICD-10 classes (online version 2016):
C94.0Acute Erythroid Leukaemia
Acute myeloid leukaemia M6 (a)(b)
Erythroleukaemia
The morphologic subtypes of AML also include rare types not included in the FAB system, such as acute basophilic leukemia, which was proposed as a ninth subtype, M8.
For example, “AML” as used herein includes the following categories: AML with recurrent genetic abnormalities, AML with myelodysplasia related changes, therapy related myeloid neoplasms, AML not otherwise specified (NOS), myeloid sarcoma, and myeloid proliferations related to Down Syndrome; or any subcategory thereof defined in the WHO Classification of myeloid neoplasms and acute leukemia (Arber D A, Orazi A, Hasserjian R, Thiele J, Borowitz M J, Le Beau M M, Bloomfield C D, Cazzola M, Vardiman J W. Blood 2016 May 19; 127(20):2391-405).
Particularly preferred herein is AML subtype M4 or M5, as assessed/determined according to French-American-British (FAB) classification. French-American-British (FAB) subtype M4 corresponds to C92.5 and FAB subtype M5 corresponds to C93.0 of WHO classification ICD-10 (version 2016), respectively.
Preferably, the AML herein is acute myelomonocytic leukemia, acute monoblastic leukemia or acute monocytic leukemia.
The term “subject suffering from leukemia” as used herein refers to an individual suffering from leukemia. The terms “subject” and “individual” and “patient” are used interchangeably herein. Preferably, the subject is a human. A “subject suffering from leukemia” typically shows/has (clinical) symptoms as described above, e.g. bleeding, bruising problems, feeling tired, fever, and/or an increased risk of infections. These symptoms are normally caused by a lack of normal blood cells. In addition/in the alternative, the “subject suffering from leukemia” has been (clinically) diagnosed for leukemia e.g. by a blood test or by a bone marrow test. By looking at a sample of the blood, it can be determined if a subject suspected of suffering from leukemia has abnormal levels of white blood cells or platelets which indicates that the subject suffers from leukemia. The bone marrow sample can e.g. be taken from the hipbone. By looking at a sample of the bone marrow the presence and/or percentage of leukemia cells can be determined which in turn indicates that the subject suffers from leukemia. A subject that has thus been/is thus diagnosed to suffer from leukemia can be termed a “leukemia patient”. Preferably, the leukemia patient is a human leukemia patient.
The methods of the invention comprise determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM. These markers per se are well known in the art and also described herein below.
The following aliases for these markers are known:
S100a12 has the following aliases according to GeneCards:
S100 Calcium Binding Protein A12, Extracellular Newly identified RAGE-Binding Protein, S100 Calcium-Binding Protein A12 (Calgranulin C), Migration Inhibitory Factor-Related Protein 6, Calcium-Binding Protein In Amniotic Fluid 1, Neutrophil S100 Protein, Calgranulin-C, EN-RAGE, CAAF1, MRP-6, CGRP, CAGC, P6, S100 Calcium Binding Protein A12 (Calgranulin C), S100 Calcium-Binding Protein A12, Calgranulin C, Calcitermin, ENRAGE, MRP6
Vcan has the following aliases according to GeneCards:
Versican, Chondroitin Sulfate Proteoglycan 2, Chondroitin Sulfate Proteoglycan Core Protein 2, Glial Hyaluronate-Binding Protein, Large Fibroblast Proteoglycan, Versican Proteoglycan, CSPG2, GHAP, PG-M, ERVR, WGN1, WGN Itgam has the following aliases according to GeneCards:
CD11b, Integrin Subunit Alpha M, Integrin, Alpha M (Complement Component 3 Receptor 3 Subunit), Cell Surface Glycoprotein MAC-1 Subunit Alpha, Complement Component 3 Receptor 3 Subunit, CD11 Antigen-Like Family Member B, Leukocyte Adhesion Receptor MO1, CR-3 Alpha Chain, CR3A, Integrin, Alpha M (Complement Component Receptor 3, Alpha; Also Known As CD11b (P170), Macrophage Antigen Alpha Polypeptide), Neutrophil Adherence Receptor Alpha-M Subunit, Macrophage Antigen Alpha Polypeptide, Neutrophil Adherence Receptor, Antigen CD11b (P170), CD11b Antigen, MAC-1, MAC1A, SLEB6, MO1A
Ly96 has the following aliases according to GeneCards:
Lymphocyte Antigen 96, Protein MD-2, ESOP-1, Ly-96, MD2, Myeloid Differentiation Protein-2, ESOP1, MD-2
Anxa2 has the following aliases according to GeneCards:
Annexin A2, Annexin II Placental Anticoagulant Protein IV, Calpactin I Heavy Chain, Calpactin-1 Heavy Chain, Chromobindin-8, Lipocortin II, Protein I, Annexin-2, ANX2L4, PAP-IV, CAL1H, LPC2D, ANX2, P36 Epididymis Secretory Protein Li 270, Calpactin I Heavy Polypeptide, Chromobindin 8, HEL-S-270, L IP2, LPC2
Cd86 has the following aliases according to GeneCards:
CD86 Molecule, CD86 Antigen (CD28 Antigen Ligand 2, B7-2 Antigen), CTLA-4 Counter-Receptor B7.2, CD28LG2, FUN-1, BU63, B70, B-Lymphocyte Activation Antigen B7-2, B-Lymphocyte Antigen B7-2, Activation B7-2 Antigen, CD86 Antigen, LAB72, B7-2, B7.2
Gpr65 has the following aliases according to GeneCards:
G Protein-Coupled Receptor 65, T-Cell Death-Associated Gene 8 Protein, G-Protein Coupled Receptor 65, TDAG8, HTDAG8
Crisp9 has the following aliases according to GeneCards:
PI16, Peptidase Inhibitor 16, Cysteine-Rich Secretory Protein 9, Protease Inhibitor 16, PSP94-Binding Protein, PSPBP, Microseminoprotein, Beta-Binding Protein, Beta-Binding Protein, Microseminoprotein, MSMBBP, CD364
LYZ has the following aliases according to GeneCards:
Lysozyme, 1, 4-Beta-N-Acetylmuramidase C, EC 3.2.1.17, LZM, Lysozyme (Renal Amyloidosis), Renal Amyloidosis, C-Type Lysozyme, Lysozyme F1, LYZF1
Vim has the following aliases according to GeneCards:
Vimentin, Epididymis Luminal Protein 113, CTRCT30, HEL113
Further, also Camsap2 and Ctsg are known.
Camsap2has the following aliases according to GeneCards:
Calmodulin Regulated Spectrin Associated Protein Family Member 2, Calmodulin Regulated Spectrin-Associated Protein Family, Member 2, Calmodulin-Regulated Spectrin-Associated Protein 1-Like Protein 1, CAMSAP1L1, Calmodulin Regulated Spectrin-Associated Protein 1-Like 1, KIAA1078
Ctsg has the following aliases according to GeneCards:
Cathepsin G, CG, EC 3.4.21.20, EC 3.4.21,CATG
Aliases for each of the 2 endogenous control markers as employed herein are as follows:
Gapdh has the following aliases according to GeneCards:
Glyceraldehyde-3-Phosphate Dehydrogenase, Peptidyl-Cysteine S-Nitrosylase GAPDH, EC 1.2.1.12,
GAPD, Epididymis Secretory Sperm Binding Protein Li 162eP, Aging-Associated Gene 9 Protein, HEL-S-162eP, EC 2.6.99.-, EC 1.2.1, G3PD
Hprt has the following aliases according to GeneCards:
Hypoxanthine Phosphoribosyltransferase 1, EC 2.4.2.8, HGPRTase, HGPRT, HPRT1, Hypoxanthine-Guanine Phosphoribosyltransferase 1, Testicular Tissue Protein Li 89, Lesch-Nyhan Syndrome
As used herein, the names of the markers can interchangeably be written in capital letters or small case letters. Therefore, VCAN is equivalent to Vcan, S100A12 is equivalent to S100a12, LY96 is equivalent to Ly96 etc
Public data base entries:
DNA and protein sequences of human S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, as well as of Camsap2, Ctsg, Gapdh, and Hprt1 have been previously reported, see GenBank Numbers (NCBI-GenBank Flat File Release 216.0, Oct. 15, 2016) and UniProtKB/Swiss-Prot Numbers (Knowledgebase Release 2016_09) listed below, each of which is incorporated herein by reference in its entirety for all purposes. Such sequences can be used to design procedures for determining and analysis of the level of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, as well as of Camsap2, Ctsg, Gapdh, and Hprt1 by ways known to one skilled in the art.
Exemplary amino acid sequences and nucleotide sequences of human S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, VIM, CAMSAP2, CTSG, Gapdh, and Hprt1 are shown in SEQ ID NO: 1 to 28 herein. The following table allocates the markers and the respective sequences:
The methods of the invention can comprise determining the level of 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, or 9, or 10 of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM. In a more preferred aspect, the methods of the invention comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM).
Preferably, the methods of the invention comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM), wherein a subject/diseased cell is identified as responsive to (treatment with) an LSD1 inhibitor if at least 6 (e.g. 6, 7, 8, 9 or all) of said markers are increased compared to a control, and preferably if at least 7 (e.g. 7, 8, 9 or all) of said markers are increased compared to a control.
The methods of the invention can comprise determining the level of one or more, of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ. The methods of the invention can comprise determining the level of one or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or 9, of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ. In a more preferred aspect the methods of the invention comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ).
In one aspect, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ compared to a control is indicative for response to treatment.
In one aspect, the present invention relates to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ compared to a control is indicative for a responding subject.
In one aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ compared to a control is indicative for a responsive proliferative diseased cell.
Preferably, the methods of the invention comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, and LYZ), wherein a subject/diseased cell is identified as responsive to (treatment with) an LSD1 inhibitor if at least 6 (e.g. 6, 7, 8, 9 or all) of said markers are increased compared to a control, and preferably if at least 7 (e.g. 7, 8, 9 or all) of said markers are increased compared to a control.
In a preferred aspect, the methods of the invention comprise determining the level of one or more, 2 or more, 3 or more, 4 or more, 5 or 6 of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86. In a particularly preferred aspect, the methods of the invention comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 (i.e. a combination of markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 is used).
In one preferred aspect, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 compared to a control is indicative for response to treatment.
In one preferred aspect, the present invention relates to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 compared to a control is indicative for a responding subject.
In one preferred aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, and CD86 compared to a control is indicative for a responsive proliferative diseased cell.
As explained above and shown in the appended examples, the level of markers Ly96 and ITGAM in blood has been confirmed herein to correlate with the effect of treatment with an LSD1 inhibitor on blast number in bone marrow, particularly in samples from patients of the AML M4/M5 subtype. Thus, if it is desired to monitor the levels of blast cells in the bone marrow, determining the level of markers Ly96 and/or ITGAM (preferably the level in a blood sample from said subject, particularly a peripheral blood sample from said subject) is particularly envisaged.
In one aspect, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of the markers Ly96 and/or ITGAM, in a sample from said subject, wherein an increased level of the markers Ly96 and/or ITGAM compared to a control is indicative for response to treatment.
In one aspect, the present invention relates to a method for the identification of a responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of the markers Ly96 and/or ITGAM in a sample from a subject suffering from leukemia, wherein an increased level of the markers Ly96 and/or ITGAM compared to a control is indicative for a responding subject.
In one aspect, the present invention relates to a method of determining whether a proliferative diseased cell is responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of the markers Ly96 and/or ITGAM in a sample from a subject suffering from leukemia, wherein an increased level of the markers Ly96 and/or ITGAM compared to a control is indicative for a responsive proliferative diseased cell.
It is preferred in this context that the level of Ly96 and ITGAM is determined.
As demonstrated herein, the herein provided markers are not only useful to monitor response to an LSD1 inhibitor or identify responders to treatment with an LSD1 inhibitor, but are also useful for predicting/assessing whether a subject is at risk of developing/suffering from a differentiation syndrome (DS). The subject is suffering from leukemia and is treated with an LSD1 inhibitor. In this context the term “monitoring response” or “identifying a responding subject” can include or be predicting/assessing whether a subject is at risk of developing a differentiation syndrome (DS). As demonstrated herein, biomarkers S100A12 and VCAN showed an exacerbated (18 to 550-fold) up-regulation in patients that developed differentiation syndrome. Importantly, this up-regulation could be observed up to 2 weeks prior to the clinical diagnosis of the differentiation syndrome. Thus, S100A12 and VCAN are a useful tool to early monitor the risk of developing a differentiation syndrome in leukemia patients receiving treatment with an LSD1 inhibitor (e.g. ORY-1001), particularly in AML M4/M5 subtypes.
In accordance with the above, the present invention relates in one aspect to a method for predicting/assessing whether a subject is at risk of developing/suffering from a differentiation syndrome (DS), said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for an increased risk of developing/suffering from a differentiation syndrome (DS). The subject is suffering from leukemia and is treated with an LSD1 inhibitor. In a preferred aspect, the present invention relates to a method for predicting/assessing whether a subject is at risk of developing/suffering from a differentiation syndrome (DS), said method comprising determining the level of one or more of the markers S100A12 and VCAN in a sample from said subject, wherein an increased level of one or more of the markers S100A12 and VCAN compared to a control is indicative for a(n) (increased) risk of developing/suffering from a differentiation syndrome (DS). The subject is suffering from leukemia and is treated with an LSD1 inhibitor.
In one aspect, the present invention relates to a method for the identification of a subject that is at risk of developing/suffering from a differentiation syndrome (DS), said method comprising determining the level of one or more of the markers S100A12, VCAN, 1TGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a(n) (increased) risk of developing/suffering from a differentiation syndrome (DS). The subject is suffering from leukemia and is treated with an LSD1 inhibitor (i.e. is undergoing treatment with an LSD1 inhibitor). In a preferred aspect, the present invention relates to a method for the identification of a subject that is at risk of developing/suffering from a differentiation syndrome (DS), said method comprising determining the level of one or more of the markers S100A12 and VCAN in a sample from a subject suffering from leukemia, wherein an increased level of one or more of the markers S100A12 and VCAN compared to a control is indicative for a(n) (increased) risk of developing/suffering from a differentiation syndrome (DS).
In a further aspect, the present invention relates to a method for monitoring the risk of developing/suffering from a differentiation syndrome in a subject with/suffering leukemia receiving treatment/being treated with an LSD1 inhibitor, which comprises determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for an increased risk of developing/suffering from a differentiation syndrome (DS). In a preferred aspect the present invention relates to a method for monitoring the risk of developing/suffering from a differentiation syndrome in a subject with/suffering leukemia receiving treatment/being treated with an LSD1 inhibitor, which comprises determining the level of one or more of the markers S100A12 and VCAN, in a sample from said subject, wherein an increased level of one or more of the markers S100A12 and VCAN compared to a control is indicative for an increased risk of developing/suffering from a differentiation syndrome (DS).
In the context of the methods for assessing the risk for developing/suffering from a differentiation syndrome, a risk of developing DS is identified if the level of one or more of the markers to be used herein, particularly of S100A12 and/or VCAN, is increased at least 8-fold in comparison to a control, and the risk is even higher if the level of said markers is increased by at least 16-fold in comparison to a control.
In this context, the treatment of said subject with said LSD1 inhibitor can be adapted if the level of one or more of the markers to be used herein, particularly of S100A12 and/or VCAN, is increased in comparison to a control. For example, the adaption of the treatment may comprise administering a decreased amount of the LSD1 inhibitor for a certain period of the treatment, a treatment stop of the LSD1 inhibitor, or the administration of an additional therapy (e.g. a therapy treating, preventing or ameliorating (the side-effects of) the differentiation syndrome).
The type of sample to be used herein is not limited as long as leukemic cells/leukemic cancer cells are present in the sample. For example, tissues invaded by leukemic tumor cells may be used. Also a bone marrow sample from a subject can be used. Yet, the use of blood samples is generally preferred herein, and peripheral blood samples are particularly preferred.
It is understood that the cancer cell(s)/proliferative diseases cell(s) to be evaluated/assessed/scrutinized may be part of a sample (like a blood sample or a bone marrow sample). In relation to leukemia, the term “cancer cell(s)” can refer to (a) “proliferative diseased cell(s)”. In this context, also the level of (a) marker(s) of the invention in cells other than “proliferative diseased cell(s)” from a given sample (like a bone marrow sample or a blood sample) may be determined without deferring from the gist of this invention. In this context, it can be contemplated that a prior isolation (by sorting, MACS, etc.) of myeloid cells (e.g. from blood) is performed to enrich for myeloid cells and, hence, also for “proliferative diseased cell(s)” in the sample. “prior isolation” means “isolation” prior to determining the level of one or more of the markers of the invention.
The sample (e.g. the sample comprising the at least one “proliferative diseased cell”) can be obtained from a subject. In one aspect, the methods of the invention can comprise a step of obtaining a sample from a subject. The obtaining step is prior to the “determining the level of one or more of the markers of the invention” and prior to a potential step of isolation (by sorting, MACS, etc.) of myeloid cells from said obtained sample, if applicable.
The term “proliferative diseased cell(s)” as used herein refers to a leukemic cell/leukemic cancer cell, for example (an) immature white blood cell(s)/immature leukocye(s)/blast(s).
The term “responsiveness” (and likewise “respond” and grammatical variants thereof) as used herein means that (a) proliferative diseased cell/cancer cell and/or a patient as defined herein responds to or has an increased likelihood of responding to an LSD1 inhbitor. The term “response” as used in the context of the present invention (e.g. in the context of response to (treatment with) an LSD1 inhibitor or in the context of response of a subject or diseased cell to (treatment with) an LSD1 inhibitor) means: (i) blast differentiation in bone marrow and/or peripheral blood, and/or (ii) a decrease in blast counts in bone marrow and/or peripheral blood; preferentially, “response” includes a decrease in blast counts in bone marrow and/or peripheral blood, most preferably “response” means: (i) blast differentiation in bone marrow and/or peripheral blood, and (ii) a decrease in blast counts in bone marrow and/or peripheral blood. Ideally, a “response” translates into a complete remission (CR), morphologic complete remission with incomplete blood count recovery (CRi), morphologic leukemia-free state, cytogenetic complete remission (CRc), molecular complete remission (CRm), or partial remission (PR) of said subject, which can be assessed as known in the art (see e.g. H. Döhner et al, Blood. 2010 Jan. 21; 115(3):453-74. doi: 10.1182/blood-2009-07-235358. Epub 2009 Oct. 30; B D Cheson et al, J Clin Oncol. 2003 Dec. 15; 21(24):4642-9).
The herein provided methods can be useful in a therapeutic setting, i.e. if a patient suffers from leukemia and is treated with an LSD1 inhibitor. In other words, if leukemia has already been diagnosed and the subject is undergoing anti-leukemia therapy is, the methods of the present invention can allow stratification of subjects which can benefit from therapy with an LSD1 inhbitor. If, for example, one or more of the markers of the invention is increased in a sample, the patient can be eligible for (ongoing) therapy with an LSD1 inhibitor. For such patients the LSD1 inhibitor might be the sole anti-cancer therapy or LSD1 inhibitor might be administered as co-therapy (e.g. in combination with a second (or yet further) LSD1 inhibitor or in combination with conventional therapy). The methods of the present invention may also be useful in order to stratify patients which cannot benefit from therapy with an LSD1 inhibitor.
A person skilled in the art will appreciate that a positive test that the level of one or more of the markers of the invention is increased does not necessarily translate 1:1 into a successful treatment of leukemia. However, by these methods sub-groups of patients/subjects are identified that have a higher chance of a positive clinical response (=show a better response rate) to a treatment with an LSD1 inhibitor, as compared to the sub-group of patients not showing these positive test results. In other words, a positive result indicates that the subject/patient has a higher chance to respond to treatment with an LSD1 inhibitor as compared to a subject/patient with no increased level of one or more of the markers of the invention.
In accordance with the present invention, the sample is obtained (or is to be obtained) from the subject after the initiation of the treatment with the LSD1 inhibitor. In other words, the sample is obtained (or is to be obtained) from the subject during the treatment with the LSD1 inhibitor and, optionally, after the treatment with the LSD1 inhibitor (after the treatment is terminated). For example, the sample is obtained (or is to be obtained) from the subject at day 3 or at a subsequent day after the initiation of the treatment with the LSD1 inhibitor (i.e. at any one day during the treatment with an LSD1 inhibitor, preferably starting at day 3 of the treatment). The sample can also be obtained earlier, e.g. at day 1 or day 2. As non-limiting examples, the sample is (to be) obtained at day 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 etc. days after the initiation of the treatment with said LSD1 inhibitor. The sample can also be obtained earlier, e.g. at day 1 or day 2 after the initiation of the treatment with said LSD1 inhibitor. The “initation of the treatment” would be at “day 1”.
It is contemplated herein that several samples from said same subject can be obtained, e.g. samples at different days after the initiation of the treatment (e.g. the first sample is obtained not earlier than at day 3, and (an) additional sample(s) is optionally obtained at (a) later day(s) during the treatment). Generally, the methods of the invention can comprise in accordance with the above determining the level of one or more of the markers of the invention in a second, third, fourth, fifth, sixth, seventh, eighth, ninth, tenth, eleventh, twelfth, thirteenth, fourteenth, fifteenth, sixteenth, seventeenth, eighteenth, nineteenth, twentieth, twenty-first, twenty-second, twenty-third, twenty-fourth, twenty-fifth, twenty-sixth etc. sample.
It is also envisaged herein that several samples can be obtained from the subject on the same day at different time points (hours). For example, two, 3, 4, 5, or more sample(s) can be obtained from the subject on the same day. As a further non-limiting example, the multiple sample are (to be) obtained at day 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, and/or 26 etc. days after the initiation of the treatment with said LSD1 inhibitor.
As mentioned, an increased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, indicates a response. Whether there is an increase is determined in comparison to a control, preferably a control for said marker.
As used in context of the methods of the present invention, a non-limiting example of a “control” (for a specific marker) can be a “non-responder” control, for example the level of a specific marker to be used herein in a sample/cell/tissue obtained from one or more healthy subjects or obtained from one or more subjects suffering from leukemia but already known to be not responsive to an LSD1 inhibitor. Another example for a “non-responder” control is the level of specific marker to be used herein in a cell line/sample/cell/tissue that shows no response to an LSD1 inhibitor in an ex-vivo/in vitro test. Another non-limiting example of a “control” is an “internal standard”, for example purified or synthetically produced RNA, proteins and/or peptides or a mixture thereof, where the amount of each RNA/protein/peptide is gauged by using the “non-responder” control described above. The control may also be the level of a specific marker to be used herein in a sample/cell/tissue obtained from said same subject suffering from leukemia, provided that the sample/cell/tissue does not contain proliferative diseased cells as defined herein. The control may also be the level of a specific marker to be used herein in a sample/cell/tissue obtained from an subject suffering from leukemia that has been obtained prior to the development or diagnosis of said leukemia.
Preferably, a “control” for a specific marker to be used herein (i.e. S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ or VIM), is the level of said specific marker (i.e. S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ or VIM, respectively), determined in a sample of said same subject prior to the initiation of treatment with the LSD1 inhibitor. In other words, the control is the “base line” level of said marker in a sample from a subject suffering from leukemia before the subject has received treatment with an LSD1 inhibitor. For example, if the level of the marker S100A12 is determined in a sample from a subject suffering from leukemia after the inititation of treatment with the LSD1 inhibitor, the control for said marker S100A12 is the level of said marker S100A12 determined in a sample of said same subject prior to the initiation of treatment with said LSD1 inhibitor. This explanation and definition applies mutatis mutandis to marker(s) VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, respectively.
It is contemplated herein that the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, is at least 1.3-fold, preferably at least 2-fold increased in comparison to a control.
Particular in relation to assessing the risk for developing a differentiation syndrome the level of one or more of the markers to be used herein, particularly of S100A12 and/or VCAN, is at least 8-fold (e.g. at least 16-fold) increased in comparison to a control.
The fold change herein is defined as the ratio of the level of the biomarker in the sample relative to the control. A fold change of 2, or 2-fold increase in the sample over the control means that the level of the biomarker in the sample was twice as high as the level in the control, a fold change of 0.5, or 2-fold decrease in the sample over the control means that the level of the biomarker in the sample was half as the level in the control. In a preferred embodiment of the method, the control is a sample obtained from the patient at baseline, i.e. prior to the administration of the first dose of LSD1 inhibitor.
The fold change can be calculated as the ratio of the biomarker's gene expression level in the sample relative to the biomarker's gene expression level in the control. Different methods have been described to assess relative levels of biomarker's gene expression. For example, the level of the biomarker in the sample relative to the control can be assessed by qRT-PCR. In the exponential phase of the amplification reaction, the intensity of the fluorescence is directly proportional to the quantity of PCR product formed. In qRT-PCR analysis, the fold change is calculated as 2̂(−ΔCp) or preferably as 2̂(−ΔΔCp)), where Cp is calculated applying the Second Derivative Maximum (SDM) cycle values; or as 2̂(−ΔCT) or preferably as 2̂(−ΔΔCT), where CT is the threshold cycle value, or as 2̂(−ΔCq) 2̂(−ΔΔCq), where CT is is the quantification cycle values.
For example, the LightCycler® 480 Software determines the “crossing point” (Cp), i.e. the point where the reaction's fluorescence reaches the maximum of the second derivative of the amplification curve, which corresponds to the point where the acceleration of the fluorescence signal is at its maximum. The Cp values reflect the target mRNA concentration in the original RNA sample. Differences in Cp values (ΔCp) for a gene X of interest in a given sample relative to a control sample reflect changes in mRNA concentration of the gene X in a given amount of total RNA in the respective sample, and are calculated as:
ΔCp, gene X=Cp(sample, gene X)−Cp(control, gene X)
To compensate for errors in the determination of RNA concentration or efficiency of 1st strand synthesis or amplification, an endogenous reference gene is usually assessed in parallel to the gene X of interest for normalization, and the ΔΔCp is then calculated as:
ΔΔCp, gene X=[Cp(sample, gene X)−Cp(sample, reference gene)]−[Cp(control, gene X)−Cp(control, reference gene)]
The fold change in mRNA concentration is calculated as 2−ΔΔCp, a negative ΔΔCp representing an increase in the expression level, and vice versa.
Microarray hybridization using chips or slides covered with probes to interrogate biomarkers can also be used to assess gene expression levels. In two-colour microarray analysis the fold change is calculated as the ratio between the signal intensities generated by the amplified and/or labeled nucleic acid derived from the RNA of the sample, labeled with one fluorophore; and the amplified and/or labeled nucleic acid derived from the RNA of the control, labeled with a second fluorophore, at the position of the biomarker probe. The ratio is frequently calculated after data processing of the raw signal intensities, including global normalization, compensation of spatial deviation and background subtraction. Microarray data are also frequently expressed as log2(ratio of the signal intensity of the marker in the sample/relative to the control). Microarray analysis can also be performed by using independent single colour hybridizations of the amplified and/or labeled RNAs derived from the sample and from the control, and by calculating the ratio between the ratio of the signal intensities in silico. Levels can also be calculated from the signals of multiple probes interrogating the biomarkers, and the raw signal intensities can be corrected by subtraction of the background or signal for a mismatch probe. Other techniques used to assess differential gene expression include RNA sequencing; in this case the expression level of a biomarker in a sample is determined by counting the amount of sequence reads corresponding to the biomarker relative to the total amount of sequence reads in the sample, and the fold change is calculated as the ratio of the relative level of the biomarker in the sample and the control. Other methods that can be used to measure RNA levels include digital PCR and nanopore sequencing.
The fold change can also be calculated from the ratio of the biomarker's protein level in the sample and of the biomarker's protein level in the control. Biomarker protein levels can be measured using immune based protein detection techniques including protein microarrays, colorimetric or chemoluminescent ELISA; or proximity assays including the Förster/Resonance Energy Transfer (FRET), AlphaLISA, DELFIA, and proximity ligation assays (protein PCR), or fluorescence activated cell sorting (FACS). Immune agents used to detect the protein can include biomarker specific antibodies, antibody fragments, or can be substituted by aptamers, chemoprobes or other molecules binding the biomarker protein with appropriate specificity and affinity. Biomarker protein levels can further be quantified by iTRAQ or SILAC; by spectral counting or by targeted biomarker protein quantitation using multiple-reaction monitoring (MRM) mass spectrometry.
In the methods of the present invention, the level of said one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is the expression level.
Preferably, the expression level is the mRNA expression level. Methods for detecting mRNA expression level can preferably include but are not limited to PCR, gene expression analyses, microarray analyses, gene expression chip analyses, Whole Transcriptome Sequencing (RNAseq), nanopore sequencing, digital gene expression, hybridization techniques and chromatography as well as any other techniques known in the art, e.g. those described in Ralph Rapley, “The Nucleic Acid Protocols Handbook”, published 2000, ISBN: 978-0-89603-459-4.
The PCR may be quantitative PCR or RealTime PCR, preferably quantitative RealTime PCR (qPCR).
The protein expression level can be detected preferably by immune assays which include the recognition of the protein or protein complex by anti antibody or antibody fragment, comprising but not limited to enzyme linked immunosorbent assays (ELISA), “sandwich” immunoassays, immunoradiometric assays, in situ immunoassays, alphaLISA immunoassays, protein proximity assays, proximity ligation assay technology (e.g. protein qPCR), western blot analysis, immunoprecipitation assays, immunofluorescent assays, flow cytometry, immunohistochemistry (IHC), immuneeletrophoresis, protein immunestaining, confocal microscopy; or by similar methods in which the antibody or antibody fragment is substituted by a chemical probe, aptamer, receptor, interacting protein or other by another biomolecule recognizing the biomarker protein in a specific manner; or by Förster/fluorescence resonance energy transfer (FRET), differential scanning fluorimetry (DSF), microfluidics, spectrophotometry, mass spectrometry, enzymatic assays, surface plasmon resonance, or combinations thereof. Immunoassays may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves the specific antibody, a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof can be carried out in a homogeneous solution. Immunochemical labels which may be employed include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, or coenzymes. In a heterogeneous assay approach, the reagents are usually the sample, the antibody, and means for producing a detectable signal. The antibody can be immobilized on a support, such as a bead, plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the sample. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, or enzyme labels.
In the methods according to the invention, an antibody to the biomarker of interest can be used. In the methods according to the present invention, a kit for detection can be used. Such antibodies and kits are available from commercial sources such as EMD Millipore, R&D Systems for biochemical assays, Thermo Scientific Pierce Antibodies, Novus Biologicals, Aviva Systems Biology, Abnova Corporation, AbD Serotec or others. Alternatively, antibodies can also be synthesized by any known method. The term “antibody” as used herein is intended to include monoclonal antibodies, polyclonal antibodies, and chimeric antibodies. Antibodies can be conjugated to a suitable solid support (e.g., beads such as protein A or protein G agarose, microspheres, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as passive binding. Antibodies as described herein may likewise be conjugated to detectable labels or groups such as radiolabels (e.g., 35S), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), fluorescent labels (e.g., fluorescein, Alexa, green fluorescent protein, rhodamine), can generated by release of singlet oxygen by phthalocyanine containing beads after irradiation at 680 nM and subsequent absorption and emission of light by acceptor beads containing Europium or Therbium, and oligonucleotide labels. Labels can generate signal directly or indirectly. Signal generated can include fluorescence, radioactivity, luminescence, in accordance with known techniques.
The expression level can be normalized to the expression level of an endogenous gene. An endogenous gene must meet a series of criteria, as known by those skilled in the art, e.g. its expression level must be unaffected by experimental factors, show minimal variability in its expression between tissues and physiological states, etc. Examples of suitable endogenous genes are, e.g, GADPH or HPRT1.
In the methods of the present invention, the evaluation of the morphological blast differentiation and blast counts can be performed in accordance with methods known in the art, for example in accordance to ICSH guidelines (ICSH guidelines for the standardization of bone marrow specimens and reports, Lee S H, Ether W N, Porwit A, Tomonaga M, Peterson L C; International Council for Standardization In Hematology, International journal of laboratory hematology 2008 October; 30(5):349-64) by microscopic examination of smears of bone marrow aspirate and/or peripheral blood stained with the May-Grünwald-Giemsa method or similar Romanofsky staining methods. (Immuno)histochemistry and functional techniques (e.g. chemotaxis/phagocytic test) can be also used for blast identification.
The term “treatment with an LSD1 inhbitor” can comprise or be administration of the LSD1 inhibitor to a subject suffering from leukemia. A non-limiting treatment with an LSD1 inhbitor” can comprise or be administering the LSD1 inhibitor (e.g. ORY-1001) according to the following schedule: 140 microgram/m2/day on a dosing scheme 5 days on, 2 days off, up to 4 cycles.
If the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM is not increased in a sample of the subject compared to a control, the treatment with said LSD1 inhibitor can be adapted (e.g. the exemplary treatment specified above can be adapted).
For example, said adaption of the treatment with said LSD1 inhibitor can comprise or be termination of the treatment with said LSD1 inhibitor.
For example, said adaption of the treatment with said LSD1 inhibitor comprises increasing the dose of said LSD1 inhibitor. The dose can, for example, be increased until a response to said LSD1 inhibitor can be determined (e.g.
either by determining an increase level of one of the markers to be used herein and/or by determining a (clinical) reponse, such as a decreased number/percentage of blasts and/or an increased number/percentage of differentiated blasts). The dose can be further (continuously) increased until a plateau is reached, e.g. until the level of one of the markers to be used herein does not further increase and/or until the number/percentage of blasts does not further decrease and/or an number/percentage of differentiated blasts does not further increase; or until a maximum desirable level of marker induction is reached.
If the level of only one marker in a sample from a subject is not increased and the level of all remaining markers is increased, this would not be necessarily interpreted as meaning that the dose given was too low and needs to be adapted/increased. Thus, if none of the markers is increased compared to the control (or if only 1 marker, or if only 2 markers are above said cutoff), then this might suggest there is not enough LSD1 inhibition (target engagement) to lead to a clinical response in said subject. In such a situation the adaption of the treatment can be contemplated, particularly an increase of the dose of the LSD1 inhibitor to be administered to said subject.
It is preferred herein that the method(s) herein above is an in vitro method. “In vitro”, as used herein, means that the method(s) of the invention is (are) are not performed in vivo, i.e. directly on a subject, but on a sample obtained from and separated/isolated from said subject (i.e. removed from its in vivo location).
The LSD1 inhibitor to be used in the methods of the invention can be any LSD1 inhibitor known in the art. As used herein, an LSD1 inhibitor (LSD1i) is a compound which inhibits LSD1. Both irreversible and reversible LSD1i have been reported. Irreversible LSD1 inhibitors exert their inhibitory activity by becoming covalently bound to the FAD cofactor within the LSD1 active site and are generally based on a 2-cyclyl-cyclopropylamino moiety such as a 2-(hetero)arylcyclopropylamino moiety. Reversible inhibitors of LSD1 have also been reported.
LSD1 inhibitors are for example disclosed in: WO2010/043721, WO2010/084160, WO2011/035941, WO2011/042217, WO2011/131697, WO2012/013727, WO2012/013728, WO2012/045883, WO2013/057320, WO2013/057322, WO2010/143582, US2010-0324147, WO2011/022489, WO2011/131576, WO2012/034116, WO2012/135113, WO2013/022047, WO2013/025805, WO2014/058071, WO2014/084298, WO2014/086790, WO2014/164867, WO2014/205213, WO2015/021128, WO2015/031564, US2015-0065434, WO2007/021839, WO2008/127734, WO2015/089192, CN104119280, CN103961340, CN103893163, CN103319466, CN103054869, WO2014/194280, WO2015/089192, WO2015/120281, WO2015/123465, WO2015/123437, WO2015/123424, WO2015/123408, WO2015/134973, WO2015/156417, WO2015/168466, WO2015/181380, WO2015/200843, WO2016/003917, WO2016/004105, WO2016/007722, WO2016/007727, WO2016/007731, WO2016/007736, WO2016/034946, WO2016/037005, WO2016/123387, WO2016/130952, WO2016/161282, WO2016/172496, as well as in K Taeko et al, Bioorg Med Chem Lett. 2015, 25(9):1925-8. doi: 10.1016/j.bmc1.2015.03.030. Epub 2015 Mar 20, PMID: 25827526; S Valente et al, Eur J Med Chem. 2015, 94:163-74. doi: 10.1016/j.ejmech.2015.02.060. Epub 2015 Mar. 3, PMID:25768700; MN Ahmed Khan et al Med. Chem. Commun., 2015, 6, 407-412, DOI: 10.1039/C4MD00330F epub 29 Sep. 2014; M Pieroni et al, Eur J Med Chem. 2015; 92:377-386. doi: 10.1016/j.ejmech.2014.12.032. Epub 2015 Jan. 7. PMID:25585008; V Rodriguez et al, Med. Chem. Commun., 2015, 6, 665-670 DOI: 10.1039/C4MD00507D, Epub 23 Dec. 2014; P Vianello et al, Eur J Med Chem. 2014, 86:352-63. doi: 10.1016/j.ejmech.2014.08.068. Epub 2014 Aug. 27; D P Mould et al, Med. Res. Rev., 2015, 35:586-618. doi:10.1002/med.21334, epub 24 Nov. 2014; L Y Ma et al, 2015, 58(4):1705-16. doi: 10.1021/acs.jmedchem.5b00037. Epub 2015 Feb. 6; S L Nowotarski et al, 2015, 23(7):1601-12. doi: 10.1016/j.bmc.2015.01.049. Epub 2015 Feb. 7. PMID:25725609; C J Kutz et al Med chem comm. 2014, 5(12):1863-1870 PMID: 25580204; C Zhou et al, Chemical Biology & Drug Design,2015, 85(6):659-671. doi:10.1111/cbdd.12461, epub 22 Dec. 2014; P Prusevich et al, ACS Chem Biol. 2014, 9(6):1284-93. doi: 10.1021/0500018s. Epub 2014 Apr. 7; B Dulla et al, Org Biomol Chem 2013, 11, 3103-3107, doi: 10.1039/c3ob40217g; J R Hitchin et al, Med Chem Commun, 2013, 4, 1513-1522 DOI: 10.1039/c3md00226h; and Y Zhou et al, Biorg Med Chem Lett, 2015, online publication 20 Jun. 2015, doi:10.1016/j.bmcl.2015.06.054. LSD1 inhibitors are further disclosed e.g. in WO2017/027678, CN106045862, WO2017/004519, WO2014/164867, WO2017/079476, WO2017/079670, WO2017/090756, WO2017/109061, WO2017/116558, WO2017/114497, CN106432248, CN106478639, CN106831489, CN106928235, CN107033148, WO2017149463, CN107174584, CN107176927, WO2017157322, US20170283397, and JP2017178811.
The LSD1 inhibitor to be used herein is preferably a 2-(hetero)arylcyclopropylamino compound. As used herein, a “2-(hetero)arylcyclopropylamino LSD1i” or a “2-(hetero)arylcyclopropylamino compound” means a LSD1i whose chemical structure comprises a cyclopropyl ring substituted at position 1 with an amino group, which can be optionally substituted, and substituted at position 2 with an aryl or heteroaryl group (wherein the aryl or heteroaryl group can be optionally substituted). Such 2-(hetero)arylcyclopropylamino-based LSD1i are for example disclosed in WO2010/043721, WO2010/084160, WO2011/035941, WO2011/042217, WO2011/131697, WO2012/013727, WO2012/013728, WO2012/045883, WO2013/057320, WO2013/057322, WO2012/135113, WO2013/022047, WO2014/058071, WO2010/143582, US2010-0324147, WO2011/131576, WO2014/084298, WO2014/086790, WO2014/164867, WO2014/194280, WO2015/021128, WO2015/123465, WO2015/123437, WO2015/123424, WO2015/123408, WO2015/156417, WO2015/181380, WO2016/123387 and WO2016/130952. The following compounds are examples of 2-(hetero)arylcyclopropylamino-based LSD1 inhibitors:
4-((4-((((1R,2S)-2-phenylcyclopropyl)amino)methyl)piperidin-1-yl)methyl)benzoic acid;
1-((4-(methoxymethyl)-4-(((1R,2S)-2-phenylcyclopropylamino)methyl)piperidin-1-yl)methyl)cyclobutanecarboxylic acid;
N-[4-[2-[(cyclopropylmethylamino)methyl]cyclopropyl]phenyl]-1-methyl-pyrazole-4-carboxamide;
N-[(2S)-5-{[(1R,2S)-2-(4-fluorophenyl)cyclopropyl]amino}-1-(4-methylpiperazin-1-yl)-1-oxopentan-2-yl]-4-(1H-1, 2,3-triazol-1-yl)benzamide;
4-[2-(4-amino-piperidin-1-yl)-5-(3-fluoro-4-methoxy-phenyl)-1-methyl-6-oxo-1,6-dihydro-pyrimidin-4-yl]-2-fluorobenzonitrile;
and pharmaceutically acceptable salts or solvates thereof.
More preferably, the LSD1 inhibitor is (trans)-N1-((1R,2S)-2-phenylcyclopropyl)cyclohexane-1,4-diamine or a pharmaceutically acceptable salt or solvate thereof. Even more preferably, the LSD1 inhibitor is (trans)-N1-((1R,2S)-2-phenylcyclopropyl)cyclohexane-1,4-diamine bis-hydrochloride. The compound (trans)-N1-((1R,2S)-2-phenylcyclopropyl)cyclohexane-1,4-diamine is also known as ORY-1001 and has been disclosed for example in WO2013/057322, see example 5. Pharmaceutical formulations comprising ORY-1001 for administration to subjects can be prepared following methods known to those skilled in the art, for example as described in WO2013/057322.
Furthermore, therapeutic uses are contemplated, i.e. treatment of the herein identified responders/responding subjects with an LSD1 inhibitor.
For example, the present invention relates to a method of treating a subject suffering from leukemia with an LSD1 inhibitor, wherein the subject is identified as a responder to treatment with an LSD1 inhibitor in accordance with this invention.
The present invention also relates to to an LSD1 inhibitor for use in treating a subject suffering from leukemia, wherein the subject is identified as a responder to treatment with an LSD1 inhibitor in accordance with this invention.
Moreover, kits for use in the invention are provided. For example, a kit for use in carrying out the method in accordance with this invention is provided, comprising means for determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM.
In a further aspect, the present invention relates to a method for monitoring the response to treatment with an LSD1 inhibitor in a subject suffering from leukemia, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM, in a sample from said subject, wherein a decreased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a non-response to treatment.
In one aspect, the present invention relates to a method for the identification of a non-responding subject to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein a decreased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a non-responding subject.
In one aspect, the present invention relates to a method of determining whether a proliferative diseased cell is non-responsive to treatment with an LSD1 inhibitor, said method comprising determining the level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM in a sample from a subject suffering from leukemia, wherein a decreased level of one or more of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM compared to a control is indicative for a non-responsive proliferative diseased cell.
For example, if there is no response to treatment with the LSD1 inhibitor, the decision may be taken to discontinue treatment or increase the dose of the LSD1 inhibitor.
The above methods to identify non-responding subjects/diseased cells can comprise determining the level of 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, or 9, or 10 of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM. In a more preferred aspect, said methods comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM). Preferably, said methods comprise determining the level of all of the markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM (i.e. of a combination of S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ and VIM), wherein a subject/diseased cell is identified as non-responsive to treatment if at least 3 of said markers are decreased compared to a control.
As used herein, the terms “comprising” and “including” or grammatical variants thereof are to be taken as specifying the stated features, integers, steps or components but do not preclude the addition of one or more additional features, integers, steps, components or groups thereof. This term encompasses the terms “consisting of” and “consisting essentially of.”
Thus, the terms “comprising”/“including”/“having” mean that any further component (or likewise features, integers, steps and the like) can be present.
The term “consisting of” means that no further component (or likewise features, integers, steps and the like) can be present.
The term “consisting essentially of” or grammatical variants thereof when used herein are to be taken as specifying the stated features, integers, steps or components but do not preclude the addition of one or more additional features, integers, steps, components or groups thereof but only if the additional features, integers, steps, components or groups thereof do not materially alter the basic and novel characteristics of the claimed composition, device or method.
Thus, the term “consisting essentially of” means that specific further components (or likewise features, integers, steps and the like) can be present, namely those not materially affecting the essential characteristics of the composition, device or method. In other words, the term “consisting essentially of” (which can be interchangeably used herein with the term “comprising substantially”), allows the presence of other components in the composition, device or method in addition to the mandatory components (or likewise features, integers, steps and the like), provided that the essential characteristics of the device or method are not materially affected by the presence of other components.
The term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, biological and biophysical arts.
The present invention is further described by reference to the following non-limiting figures and examples. The Figures show:
The Example illustrates the invention.
As part of a Phase I clinical study assessing the human pharmacokinetics and safety of ORY-1001 in acute leukemia patients, an extension cohort of 14 patients (mean age 57; range 30-78, gender 8M/6F) was opened in order to provide a preliminary assessment of efficacy. A summary of the patients recruited in this extension cohort can be found in Table 1.
Preliminary clinical efficacy endpoints included (a) morphological blast differentiation and (b) decrease in blast %. In addition, gene expression determinations of selected markers were performed.
1.2: Treatment
Drug: ORY-1001, which is the compound with the following chemical name and structure: (trans)-N1-((1R,2S)-2-phenylcyclopropyl)cyclohexane-1,4-diamine [CAS Reg. No. 1431304-21-0].
ORY-1001 was administered to patients as the dihydrochloride salt, i.e. (trans)-N1-((1R,2S)-2-phenylcyclopropyl)cyclohexane-1,4-diamine bis-hydrochloride.
Each patient received ORY-1001 for oral intake as a solution at a dose of 140 microgram/m2/day (as free base) q.d., during 5 consecutive days with 2 days of rest, for 4 cycles (total of 28 days), or until disease progression or unacceptable toxicity was observed.
1.3: Clinical Response Determinations
For the evaluation of the morphological blast differentiation and blast counts, smears of bone marrow aspirate and/or peripheral blood were prepared, stained by the May-Grünwald-Giemsa method, and microscopically examined in accordance with ICSH guidelines (ICSH guidelines for the standardization of bone marrow specimens and reports, Lee S H, Erber W N, Porwit A, Tomonaga M, Peterson L C; International Council for Standardization In Hematology, International journal of laboratory hematology 2008 October; 30(5):349-64).
Preliminary evidence of early clinical response was observed in peripheral blood and/or bone marrow, i.e. morphologic blast differentiation and decrease in blast cells, respectively in 5/14 and 6/14 patients throughout all the four FAB subtypes, as shown in Table 2.
aDiagnosed with a differentiation syndrome on day 26
b Diagnosed with a differentiation syndrome on day 6
c Cutaneous leukemia
d % variation of blast % between pre- and post-treatment (day 7 to 29, depending on patient); “=” indicates no or no clinically relevant variation
e Between day 5 and 12 of treatment
fBetween day 15 and 29 of treatment
1.4: Blood Sampling
All patients underwent serial collection of whole blood at pre-established time points up to 768 h (day 33) after the first dose, i.e. pre-dose, and 2, 4, 6, 8, 12, 18, 24, 48, 72, 96, 98, 100, 102, 104, 120, 144, 168, 264, 336, 432, 504, 600, 602, 604, 606, 608, 612, 618, 624, 672, and 768 h post-dose. Five ml of blood were collected using an S-Monovette K3 EDTA tube.
1.5: Sample Processing for RNA Extraction
Plasma for pharmacokinetic determinations was separated by centrifugation. The remaining cell volume was resuspended in 2 mL PBS and an aliquot of 2.5 mL was stabilized in a PAXgene® Blood RNA tube as described by the vendor and kept frozen for subsequent RNA extraction and qRT-PCR.
1.6: RNA Extraction
RNA extraction was performed using PAXgene® Blood RNA Kit (PreAnalytix) as described by the vendor. RNA quality was assessed using an Agilent 2100 Bioanalyzer™ and quantity was measured using a NanoDrop™ spectrophotometer.
1.7: Reverse Transcription
An amount of 0.5 micrograms of total RNA was reverse transcribed to obtain 1st strand cDNA (iScript® Reverse Transcription Supermix for RTqPCR; Bio-Rad).
1.8: Gene Expression Analysis by qRT-PCR
Gene expression was analyzed by qRT-PCR, a variant of the PCR (Polymerase Chain Reaction) method that permits the simultaneous exponential amplification and detection of specific cDNA fragments. Taqman gene expression assays were used, which employ the principle of doubly labeled hydrolysis probes marked with a fluorescent moiety at their 5′ end and with a quencher moiety at the 3′ end, which prevents the generation of fluorescence according to the Förster energy transfer principle.
During the amplification process, the hydrolysis probe hybridizes to its complementary sequence in the target amplicon. During each cycle, the Taq polymerase initiates the production of a copy of the target sequence starting from the primer. When the Taq polymerase reaches the hydrolysis probe, its 5′-3′ exonuclease activity fragments the hydrolysis probe, and liberates the fluorescent group from the quencher moiety, resulting in the emission of a fluorescent signal.
In the exponential phase of the amplification reaction, the intensity of the fluorescence is directly proportional to the quantity of PCR product formed. The LightCycler® 480 Software determines the “crossing point” (Cp), i.e. the point where the reaction's fluorescence reaches the maximum of the second derivative of the amplification curve, which corresponds to the point where the acceleration of the fluorescence signal is at its maximum. The Cp values reflect the target mRNA concentration in the original RNA sample. Differences in Cp values (ΔCp) for a gene X of interest in a given sample relative to a control sample reflect changes in mRNA concentration of the gene X in a given amount of total RNA in the respective sample, and are calculated as:
ΔCp, gene X=Cp(sample, gene X)−Cp(control, gene X)
To compensate for errors in the determination of RNA concentration or efficiency of 1st strand synthesis or amplification, an endogenous reference gene is usually assessed in parallel to the gene X of interest for normalization, and the ΔΔCp is then calculated as:
ΔΔCp, gene X=[Cp(sample, gene X)−Cp(sample, reference gene)]−[Cp(control, gene X)−Cp(control, reference gene)]
The fold change in mRNA concentration is calculated as 2−ΔΔCp, a negative ΔΔCp representing an increase in the expression level, and vice versa.
For a gene to be regarded as a reliable reference, it must meet a series of criteria, as known by those skilled in the art, e.g. its expression level being unaffected by experimental factors, showing minimal variability in its expression between tissues and physiological states, etc. Examples of suitable endogenous genes are GAPDH and HPRT1, among others.
An amount of 0.5 micrograms of the 1st strand product was used to perform qRT-PCR reactions in triplicate (Taqman® gene expression assay, Life technologies, see Table 3) in a Roche LightCycler®480. In order to analyze the changes in the expression levels of ANXA2, CAMSAP2, CD86, CRISP9, CTSG, GPR65, ITGAM, LY96, LYZ, S100A12, VCAN, and VIM, ΔΔCp values for a given patient and time point were calculated as described above, relative to the endogenous reference gene HPRT1 and to a control sample obtained from the same patient at pre-dose (i.e. prior to administration of the first dose of ORY-1001 to said patient).
For the analysis of the gene expression data, the time point (or time interval) showing the maximum response is typically selected. This time point/interval may change depending on the specific dose, administration scheme, etc. In the present study, all the gene expression and correlation analysis was performed by using the data obtained after administration of day 5, i.e. within the time interval between 98 and 168 h after the first dose. The maximum response observed within this time interval is referred to in the tables herein as “Maximum response (ΔΔCp) on day 5”. This time interval was selected based on the fact that gene expression levels were overall qualitatively comparable to the maximum response achieved at the end of treatment (i.e. after administration on day 26) (see Table 4 as an example, a comparison of maximum response on days 1, 5, and 26 for 2 patients and genes).
a Maximum response (in ΔΔCp) within first 24 h after the first administration.
b Maximum response (in ΔΔCp) within 98 and 168 h after the first administration.
c Maximum response (in ΔΔCp) within 602 and 768 h after the first administration.
In total, expression changes in 12 potential PD marker genes associated to blast differentiation (mostly to monocyte/macrophage) were monitored in peripheral blood of all 14 patients. Results of maximum response on day 5 are shown in Table 5.
1.9: Correlations Between Gene Expression and Response to Treatment with an LSD1 Inhibitor
Possible correlations between expression changes in marker genes described in table 5 and response to ORY-1001 treatment (see Table 2) were investigated.
A 1.3 to 550-fold (corresponding to −0.4 to −9.1 ΔΔCp) up-regulation of the gene markers S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, and VIM was observed in patients showing both blast morphological differentiation and a decrease in blast cells, particularly in M4/M5 subtypes (see Table 6). In contrast, some of the genes were down-regulated (0.6 to 0.05-fold change, corresponding to 0.8 to 4.4 ΔΔCp) in patients showing no morphological differentiation and/or no effect or increase in blast cells (see Table 7). LYZ, GPR65, ANXA2, S100A12, CRISP9, and VIM were clearly differentially regulated in M4/M5 patients showing blast count decrease (markers up-regulated) compared to those showing blast differentiation with no decrease in blast count (markers down-regulated). The expression levels of Ly96 and ITGAM did additionally correlate with the variation of blast cells in bone marrow (see
1.10: Correlation between S100A12 and VCAN Gene Expression and Differentiation Syndrome
The differentiation syndrome (DS), also known as retinoic acid syndrome, is a relatively common and potentially severe complication seen in AML patients treated with differentiating agents, such as all-trans retinoic acid and/or arsenic trioxide. The differentiation of vast numbers of leukemic blasts may lead to cellular migration, endothelial activation, and release of interleukins and vascular factors responsible for tissue damage, finally developing in a syndrome characterized by unexplained fever, acute respiratory distress with interstitial pulmonary infiltrates, and/or a vascular capillary leak leading to acute renal failure.
S100A12 and VCAN showed an exacerbated (18 to 550-fold, corresponding to −4.2 to −9.1 ΔΔCp) up-regulation pattern in patients developing a differentiation syndrome (Patients 01 and 09, see Table 5) within 98 and 168 h after the first dose, and this could be already observed up to 2 weeks prior to its clinical diagnosis (see
The present invention refers to the following nucleotide and amino acid sequences:
The sequences provided herein are available in the NCBI database and can be retrieved from www.ncbi.nlm.nih.qov/sites/entrez?db=gene; Theses sequences also relate to annotated and modified sequences. The present invention also provides techniques and methods wherein homologous sequences, and variants of the concise sequences provided herein are used. Preferably, such “variants” are genetic variants, e.g. splice variants.
Exemplary amino acid sequences and nucleotide sequences of human S100A12, VCAN, ITGAM, LY96, ANXA2, CD86, GPR65, CRISP9, LYZ, VIM, CAMSAP2, CTSG, Gapdh, and Hprt1 are shown in SEQ ID NO: 1 to 28 herein below.
All references cited herein are fully incorporated by reference. Having now fully described the invention, it will be understood by a person skilled in the art that the invention may be practiced within a wide and equivalent range of conditions, parameters and the like, without affecting the spirit or scope of the invention or any embodiment thereof.
| Number | Date | Country | Kind |
|---|---|---|---|
| 16382506.0 | Nov 2016 | EP | regional |
| 16382588.8 | Dec 2016 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2017/078084 | 11/2/2017 | WO | 00 |
