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WO 2013/064702 A2 10 May 2013 (10.05.2013) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2013/064702 A2 10 May 2013 (10.05.2013) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12Q 1/68 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, PCT/EP2012/071868 KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (22) International Filing Date: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 5 November 20 12 (05 .11.20 12) NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, (25) Filing Language: English TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, (26) Publication Language: English ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 1118985.9 3 November 201 1 (03. 11.201 1) GB kind of regional protection available): ARIPO (BW, GH, 13/339,63 1 29 December 201 1 (29. 12.201 1) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (71) Applicant: DIAGENIC ASA [NO/NO]; Grenseveien 92, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, N-0663 Oslo (NO). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (72) Inventors: SHARMA, Praveen; Lille Borgen vei 1A, N- TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, 0370 Oslo (NO). LINDAHL, Torbjorn; G0teborggata ML, MR, NE, SN, TD, TG). 31b, N-0566 Oslo (NO). Published (74) Agent: JONES, Elizabeth, Louise; St. Bride's House, 10 Salisbury Squre, London, Greater London EC4Y 8JD — without international search report and to be republished (GB). upon receipt of that report (Rule 48.2(g)) (81) Designated States (unless otherwise indicated, for every with sequence listing part of description (Rule 5.2(a)) kind of national protection available): AE, AG, AL, AM, < o © o (54) Title: PROBES FOR DIAGNOSIS AND MONITORING OF NEURODEGENERATIVE DISEASE (57) Abstract: The present invention relates to oligonucleotide probes and their use in assessing gene transcript levels in a sample, which may be used in analytical techniques, particularly to identify, diagnose or monitor neurodegenerative diseases or conditions and their progression, particularly Alzheimer's disease and mild cognitive impairment. Probes for diagnosis and monitoring of neurodegenerative disease The present invention relates to oligonucleotide probes, for use in assessing gene transcript levels in a sample, which may be used in analytical techniques, particularly diagnostic techniques. Conveniently the probes are provided in kit form. Different sets of probes may be used in techniques to prepare gene expression patterns and identify, diagnose or monitor neurodegenerative diseases or conditions and their progression. Neurodegenerative disease results in the progressive degeneration and/or death of nerve cells leading to problems with movement (ataxias) or mental functioning (dementias). In particular the method is concerned with identifying, diagnosing or monitoring cognitive impairment and its progression, e.g. to dementias such as Alzheimer's disease or stages thereof. Dementias account for the majority of neurodegenerative diseases in the population. The prevalence of dementia is rapidly rising as the average age of the population increases. It is estimated that more than 24 million people worldwide have dementia. Alzheimer's disease accounts for the highest number of dementia cases, particularly in the elderly. Evidence suggests that the pathophysiological process of dementia, e.g. Alzheimer's disease, begins years, if not decades, prior to the diagnosis of clinical dementia. Therapeutic interventions early in the pathophysiological process are more likely to be successful, particularly as treatments of Alzheimer's disease appear to have limited impact once the clinical symptoms appear and neuronal degradation has begun. Thus, there is a need to identify patients that might progress to ataxia or dementia as soon as possible so that treatment and management strategies may be contemplated at an early stage. Current methods for detecting dementias have poor positive predictive accuracy of up to about 61% (Visser, 2006, Principles & Practice of Geriatric Medicine, 4th Edition, Eds. Pathy et al., Section 94). In Alzheimer's disease and other dementias, the earliest clinical sign of the presence of a cognitive disorder is mild cognitive impairment (MCI) which is a predementia phase of cognitive dysfunction. MCI is a general term that defines a mildly impaired set of patients which show reduced cognitive performance. MCI patients may be divided into amnestic MCI and non- amnestic MCI but even this is not predictive of whether the MCI will progress to dementia. Not all forms of MCI will evolve into a dementia such as Alzheimer's disease and some may be stable or exhibit improvement with time. Thus MCI describes a group of patients grouped by clinical parameters rather than the underlying pathology. Within that group are sub-groups that will convert to Alzheimer's disease, that will convert to other dementias, which are stable or which will revert to normal cognitive function. The sub-group of MCI patients that convert to dementia may be considered prodromal for that dementia, e.g. to have prodromal Alzheimer's disease (AD). It is generally accepted that the progression rate of patients with MCI to AD is between 10 and 15% per year but to date there is no reliable and easy way of identifying the sub-group that will convert. Methods for identifying whether a patient will progress from MCI to Alzheimer's disease include assessment of various predictors of progression such as the ApoE ε4 carrier status, presence of atrophy on MRI, 18FDG PET pattern of Alzheimer's disease, presence of CSF markers (such as amyloid β1-42 peptide, total tau and phosphorylated tau) and a positive amyloid imaging scan (see Petersen et al., 2009, Arch. Neurol., 66(12), p1447- 1454). However, whilst these predictors may be associated with Alzheimer's disease they are not always specific to Alzheimer's disease and more than one marker is usually necessary to aid diagnosis, particularly coupled with cognitive testing. As mentioned above, to allow for early therapeutic intervention, early identification of neurodegnerative diseases or conditions is important, e.g. the identification of MCI patients that will progress to dementia. Okamura et al., 2002, Am. J. Psychiatry, 159:3, p474-476 used a combined test of CSF tau levels and regional cerebral blood flow in the posterior cingulate cortex. However, such methods are time consuming, complex and invasive with high cost and low patient compliance making introducing such diagnostic tools in a wide clinical setting challenging. Furthermore, cognitive markers have been found to be better predictors of conversion to dementia (Gomar et al., 201 1, Arch. Gen Psychiatry, 68(9); p961- 969). A simple test to identify and stage neurodegenerative disorders and diseases, particularly in relation to Alzheimer's disease would be desirable. Determination of whether dementia may be attributed to Alzheimer's disease or another cause would also be useful. In particular the use of an accurate blood based test would clearly be a valuable asset in the assessment of patients with possible neurodegenerative diseases or conditions. In earlier work, the present inventors identified the systemic effect of various diseases and conditions on gene expression in blood cells, see e.g. W098/49342 and WO04/046382, incorporated herein by reference, the latter of which describes specific probes for the diagnosis of breast cancer and Alzheimer's disease. Blood tests based on gene expression profiling in the diagnosis of brain disorders have been described. In particular, the present inventors have identified that the expression of 96 genes allows the detection of patients with Alzheimer's disease (Rye et al., 201 1, Journal of Alzheimer's Disease, 23, p 12 1- 29). However, these methods have not allowed for the determination of the stage or progression of the disease or for the identification of the sub-group within MCI patients that will progress to dementia. The identification of quick and easy methods of sample analysis for, for example, diagnostic applications, remains the goal of many researchers. End users seek methods which are cost effective, produce statistically significant results and which may be implemented routinely without the need for highly skilled individuals. We have now identified sets of probes which are of surprising utility for identifying, staging and monitoring neurodegenerative diseases and conditions, particularly Alzheimer's disease. In work leading up to this invention, the inventors examined the level of expression of various genes in patients with neurodegenerative diseases at various stages relative to normal patients. Thus in one aspect, the present invention provides a set of oligonucleotide probes, wherein said set comprises at least 10 oligonucleotides, wherein each of said 10 oligonucleotides, which are each different, are selected from: (a) an oligonucleotide which is a part of a sequence as set forth in Table 1; (b) an oligonucleotide derived from a sequence as set forth in Table 1; (c) an oligonucleotide with a sequence complementary to the sequence of the oligonucleotide of a) or b); or (d) an oligonucleotide which is functionally equivalent to an oligonucleotide as defined in (a), (b) or (c). As referred to herein, a sequence as set forth in Table 1 is the sequence to which the assay refers, e.g.
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