[0353] DNA copy number qPCR Assay: DNA copy number in the cell lines were determined using multiplexed real time quantitative polymerase chain reaction (qPCR) utilizing ABI TaqMan chemistry (Applied Biosystems).

[0354] Total DNA extraction

1) Tissue was cut into small pieces up to 25 mg, and placed in a 1.5 ml microcentrifuge tube. Buffer ATL (180 pl) was added.

2) Proteinase K (20 pl) was added, mixed thoroughly, and incubated at 56°C until the tissue was completely lysed. Vortexing was done occasionally during incubation to disperse the sample, or the sample was placed in a thermomixer, shaking water bath, or on a rocking platform.

3) Vortexing was continued for 15 s. 200 pl Buffer AL was added to the sample and mixed thoroughly.

4) 200 pl Ethanol (96-100%) was added and mixed again thoroughly by vortexing.

5) The mixture was pipetted from step 3 (including any precipitate) into the Dneasy Mini spin column placed in a 2 ml collection tube and centrifuged at 8000 rpm for 1 min. Discard flow-through.

6) About 500 pl Buffer AW 1 was added and centrifuged for 1 min at 8000 rpm. Discard flow-through.

7) About 500 pl Buffer AW2 was added, and centrifuged for 3 min at 14,000 rpm to dry the Dneasy membrane. Discard flow-through.

8) Dneasy Mini spin column was placed in a clean 1.5 ml or 2 ml microcentrifuge tube, and 200 pl Buffer AE was pipetted directly onto the Dneasy membrane. It was incubated at room temperature for 1 min, and then centrifuged for 1 min at 8000 rpm to elute.

9) Elution was repeated once as described in step 8 to maximum DNA yield. 17 samples total DNA extraction

[0355] 17 samples total DNA were isolated using Dneasy Blood & Tissue Kit. DNA quantity and quality were evaluated by NanoDrop™ spectrophotometer (A260/A280). DNA concentration and the A260/A280 ratio were shown in Table 4.

Table 4: 17 Samples Total DNA Quantification

[0356] DNA quantification: Nanodrop™ spectrophotometer detection (A260/A280). 2pl of cDNA of each sample was used for qPCR analysis in a total volume of lOpl reaction. Each sample was analyzed in triplicate. The qPCR reactions were performed with 384-well platform ABI-7900H real-time qPCR system using standard parameters suggested by the manufacturer. The CT values of the house-keeping gene are expected at a similar level. [0357] PCR amplification: ) Each sample was diluted to 5 ng/pL with nuclease-free water. ) The PCR reaction system was set as follows in Table 5:

Table 5: Reagent details

3) Required instrument setup information in Table 6:

Table 6: Instrument details

4) The procedure of PCR reaction in Table 7:

Table 7:

[0358] Data analysis

Raw data was analyzed by SDS 2.4 and processed using the AACT relative quantification method. AACT values was calculated against the TaqMan™ Copy Number Reference Assay, human, Rnase P I TaqMan™ Copy Number Reference Assay, mouse, Tfrc. Samples fold 2"^AACt x2 represents copy number of gene (see Table 8). Table 8: Q-PCR Results: 17 Cell Lines Gene Copy Number

[0359] Results and Discussion:

[0360] Seventeen cell lines of hematological cancers including AML were first evaluated for the effect of Talabostat on its cytotoxicity. More than 30% (i.e., 39.5 to 100%) cytotoxicity was observed with the treatment of Talabostat in eleven cell lines. Out of 11, six cell lines were AML cell lines, two cell lines were from Myeloma, one was from Lymphoma and two were of other leukemic origin (e.g., eosinophilic leukemia and monocytic leukemia). Rest six cell lines were not responding to Talabostat and demonstrated less than 30% cytotoxicity. Next, genomic DNA was prepared from these 13 cell lines and gene copy number were evaluated for four targets (DPP9, DPP8, DPP4 and FAP) of Talabostat by qPCR.

[0361] Results are shown in table 9. It was observed that DPP9 gene copy number was correlated with the cytotoxicity of Talabostat in leukemic cell lines. Cell lines that were responding to Talabostat in a cytotoxicity assay had higher DPP9 gene copy number, and nonresponding cell lines had lower copy number. [0362] DPP9 gene copy number was highest amongst all genes evaluated. Interestingly, DPP9 gene copy number was the highest in responding cell lines and lowest in non-responding cell lines (figure 1 and 2). In all responding cell lines DPP9 gene copy number were more than four except in OCI-AML3. Although another variant of this cell line OCI-AML2 had a higher copy number. Six non-responsive cell lines had less than two DPP9 copy number.

Table 9: Association of DPP9 Copy Number With Talabostat Cytotoxicity In Leukemic

Cell Lines

NA- not available

Responding cell lines (11)- 0CI-AML2; MM.1R, EOL-1, KG-1, MV-4-11, N0M0-1, MM.l S, KARPAS-299, MONO-

MAC-6, MOLM-13 and 0CI-AML3

Non-responding cell lines (6)- THP-1, HEL, K562, Kasumil, U-937, TF1 (% Kill at 10 uM < 30% )

[0363] For human leukemic cell lines cell death in response to Talabostat treatment was found to be directly co-related to DPP9 gene copy number, (correlation coefficient = 0.81) (Figure 3). A statistically significant difference was observed between responder cell lines (cell lines that exhibit >30% cytotoxicity when treated with Talabostat) as compared to nonresponder cell lines (cell lines showing <30% cytotoxicity when treated with Talabostat). DPP9 copy number correlates with Talabostat cytotoxicity in Leukemic cell lines and is a potential predictive biomarker in Leukemias (e.g AML).

EXAMPLE 2: To measure the expression levels of a set of biomarker genes in responding and non- responding human leukemia cell lines using nanostring and RT-PCR techniques.

Procedure:

Human Leukemic cell lines from North East Biolabs

[0364] The cytotoxic activity of Talabostat was evaluated in a panel of 170 hematological and non-hematological cell lines. Four responding cell lines (KG1, MV4-11, THP1 and EOL-1, IC50 = 100 - 700 nM) and 2 non-responding cell lines (K562 and Kasumil, IC50 >60 pM) were selected based on the cytotoxicity data and their gene expression profiles were compared to identify predictive biomarkers for Talabostat. As a next step gene expression analysis was done in different human leukemic cell lines by Nanostring. The absolute gene expression values were normalized against HPRT1, a house keeping gene, to provide relative gene expression for all the genes. Nanostring analysis was performed followed by qRT-PCR using cDNA from the cell lines.

[0365] Enclosed is a list of cell lines (Table 10). They were all grown in RPMI/10 or 20% FBS. Frozen cell pellets were sent to Canopy Biosciences for RNA isolation and qPCR analysis.

Table 10.

Procedure for RNA isolation from cell lines (at Canopy Biosciences) Sample disruption and homogenization

1. The cells were harvested according to step la or lb. a) Cells grown in suspension (do not use more than 1 x 10⁷ cells):

The number of cells was determined. The appropriate number of cells were pelleted by centrifuging for 5 min at 300 x g in a centrifuge tube (not supplied). All supernatant was carefully removed by aspiration and proceeded to step 2. b) Cells grown in a monolayer (do not use more than 1 x 10⁷ cells):

Cells grown in a monolayer in cell-culture vessels could be either lysed directly in the vessel (up to 10 cm diameter) or trypsinized and collected as a cell pellet prior to lysis. Cells grown in a monolayer in cell-culture flasks should always be trypsinized.

To lyse cells directly:

The number of cells was determined. The cell-culture medium was completely aspirated, and proceeded immediately to step 2.

To trypsinize and collect cells:

The number of cells was determined. The medium was aspirated and the cells were washed with PBS.

The PBS was aspirated and 0.10-0.25% trypsin added in PBS.

After the cells were detached from the dish or flask, medium (containing serum to inactivate the trypsin), was added, the cells were I to an RNase-free glass or polypropylene centrifuge tube (not supplied), and centrifuged at 300 x g for 5 min. The supernatant was completely aspirated, and proceeded to step 2.

2. The cells were disrupted by adding Buffer RLT Plus.

For pelleted cells, the cell pellet was loosen thoroughly by flicking the tube. The appropriate volume of Buffer RLT Plus (see Table 11) was added. It was vortexed or pipeted to mix, and proceeded to step 3. Table 11. Volumes of Buffer RLT Plus for lysing pelleted cells

For direct lysis of cells grown in a monolayer, the appropriate volume of Buffer RLT Plus (see Table 12) was added to the cell-culture dish. The lysate was collected with a rubber policeman.

The lysate was pipetted into a microcentrifuge tube, vortexed or pipetted to mix and ensured that no cell clumps were visible before proceeding to step 3.

Table 12. Volumes of Buffer RLT Plus for direct cell lysis

3. The lysate was homogenized according to step 3a, 3b or 3c. If processing U1 x 105 cells, they can be homogenized by vortexing for 1 min. After homogenization, proceed to step

4.

Note: Incomplete homogenization led to significantly reduced RNA yields and could cause clogging of the AllPrep DNA and RNeasy spin columns. Homogenization with a rotor-stator or QIA shredder homogenizer generally result in higher nucleic acid yields than with a syringe and needle. a) The lysate was pipetted directly into a QIA shredder spin column placed in a 2 ml collection tube, and centrifuged for 2 min at maximum speed. Proceed to step 4. b) The lysate was homogenized for 30 s using a rotor-stator homogenizer. Proceed to step 4. c) The lysate was passed at least 5 times through a 20-gauge needle (0.9 mm diameter) fitted to an RNase-free syringe. Proceed to step 4. 4. The homogenized lysate was transferred to an AllPrep DNA spin column placed in a 2 ml collection tube (supplied). The lid was closed gently, and centrifuged for 30 s at V8000 x g (VI 0,000 rpm).

5. The AllPrep DNA spin column was placed in a new 2 ml collection tube (supplied), and stored at room temperature (15-25°C) or at 4°C for later DNA purification in steps 14-17. The flow-through was used for RNA purification in steps 6-13.

[0366] Total RNA purification

6. Added 1 volume (usually 350 pl or 600 pl) of 70% ethanol to the flowthrough from step 5 and mixed well by pipetting. Do not centrifuge.

Proceed immediately to step 7.

7. Up to 700 pl of the sample, including any precipitate that may have formed, was transferred to an RNeasy spin column placed in a 2 ml collection tube (supplied). The lid was closed gently, and centrifuged for 15 s at V8000 x g (VI 0,000 rpm). Discard the flow-through.

Reuse the collection tube in step 8.

If the sample volume exceeded 700 pl, successive aliquots were centrifuged in the same RNeasy spin column. Discard the flow-through after each centrifugation.

8. 700 pl Buffer RW 1 was added to the RNeasy spin column. The lid was closed gently, and centrifuge for 15 s at V8000 x g (VI 0,000 rpm) to wash the spin column membrane. Discard the flow-through.

Reuse the collection tube in step 9.

9. 500 pl Buffer RPE was added to the RNeasy spin column. The lid was closed gently, and centrifuged for 15 s at V8000 x g (VI 0,000 rpm) to wash the spin column membrane. Discard the flow-through.

Reuse the collection tube in step 10.

10. 500 pl Buffer RPE was added to the RNeasy spin column, lid was closed gently, and centrifuged for 2 min at V8000 x g (VI 0,000 rpm) to wash the spin column membrane.

The long centrifugation dries the spin column membrane, ensuring that no ethanol was carried over during RNA elution. Residual ethanol may interfere with downstream reactions. 11. Optional: The RNeasy spin column was placed in a new 2 ml collection tube (supplied), and the old collection tube discarded with the flowthrough.

Centrifuged at full speed for 1 min.

This step was performed to eliminate any possible carryover of Buffer RPE, or if residual flowthrough remained on the outside of the RNeasy spin column after step 10.

12. The RNeasy spin column was placed in a new 1.5 ml collection tube (supplied). 30-50 pl RNase-free water was added directly to the spin column membrane. The lid was closed gently, and centrifuged for 1 min at V8000 x g (VI 0,000 rpm) to elute the RNA.

13. If the expected RNA yield is >30 pg, step 12 was repeated using another 30-50 pl of RNasefree water, or using the eluate from step 12 (if high RNA concentration was required). Reuse the collection tube from step 12.

If using the eluate from step 12, the RNA yield was 15-30% less than that obtained using a second volume of RNase-free water, but the final RNA concentration was higher.

[0367] Evaluation of gene expression using nanostring

Before the start

1. The working station was prepared by cleaning it with Sanihol, RNAse Away, and another layer of Sanihol.

2. The nCounter® 12 Well Notched Strip Tube was labelled with date and project name as well as appropriate set (for example: A,B,C, etc) and places on tube holder.

3. The nCounter® 12 Well Notched Strip Tube and its accompanying lid was cut in half.

4. The thermal cycler was programmed using the following settings: 65°C target temperature, 15 pL volume, 70°C lid temperature, for 18 hours and then ramped down to 4°C and hold. A program which has these specific settings has already been set up on the Applied Biosystems Proflex. The program is called “Nanostring 65”.

5. The thermal cycler was preheated, the run was started and paused immediately when the heating block reached 65°C.

6. Go to the CoreDx Team Folder > Nanostring> Templates> Nanostring Worksheet Template and the “Nanostring Worksheet” was completed and saved under appropriate project and date. “Dilutions” tab was completed if dilutions are needed. [0368] RNA Sample Normalization

7. After RNA samples were thawed, each sample was mixed by flicking the tube followed by a brief spin down in the centrifuge.

8. Refer to the “Nanostring Worksheet” and the required volume of RNAse Free Water was added to each strip tube well.

9. RNA samples were placed on a cold block to avoid excessive RNA degradation and let thawed. Each tube was mixed by flicking followed by a brief spin in the table top centrifuge. (Refer to the “Nanostring Worksheet” to aliquot the appropriate amount of RNA into the strip tubes).

Note: Unless otherwise stated normalization was lOOng. The total volume was 7uL. RNA+water = 7uL.

[0369] Hybridization Setup

10. The appropriate Reporter CodeSet was removed and the ProbeSet was captured from the -80°C and thawed at room temperature at working station. It was mixed by flicking or inverting the tubes and briefly spinned down in the mini centrifuge.

11. A Hybridization Mastermix (MM) was made by adding 70pL of Hybridization Buffer [kept at room temperature (RT)] into the Reporter Code Set tube and mixed by flicking the tube and briefly spinned down.

12. 8pL of the MM was added to each well in the labeled Strip Tube and mixed by flicking the tube and spinned down.

13. The Capture ProbeSet was mixed by flicking and briefly spinning down. 2pL of the Capture ProbeSet was pipetted to each well, tips for each sample were changed and verified that capture Probeset was entirely added. The nCounter® Strip Tube was covered with a lid, spinned down to make sure Capture ProbeSet was added into the sample and not stuck on the wall of the tube. It was mixed by flicking the tube and spinned down again. It was made sure to minimize the time between the addition of the Capture ProbeSet and incubation at 65 °C.

14. The tubes were placed into the thermal cycler, using the designate settings for the nCounter XT Gene Expression Assay and run for 18 hours. (Indicate the Lot # of Hybridization Buffer, Reporter Codeset and Capture Codeset in the Lab Notebook). [0370] Evaluation of Gene Expression using RT-PCR

A. Reverse Transcription

1. The following kit components were thawed on ice: a. 1 OX RT Buffer b. 25X dNTP Mix (100 mM) c. 10X RT Random Primers d. MultiScribe Reverse Transcriptase e. RNase Inhibitor

2. In a PCR strip tube on ice, 200 ng RNA was normalized to 13.2 pL in nuclease-free water. a. Our standard RNA input amount was 200 ng for each 20 pL RT reaction. Up to 2 pg of RNA could be used per reaction with this kit. b. Each RT reaction would yield 20 pL of cDNA. Depending on number of replicates and probes running with it, multiple RT reactions per sample were set up and pooled them before qPCR.

3. The RT master mix was created according to the table below. The tube was flicked to mix and quickly spinned down in a picofuge and kept on ice.

Table 13.

It was made sure to calculate for an extra sample when setting up the master mix.

4. 6.8 pL RT master mix was added to each normalized RNA sample in the strip tube.

5. The strip tube contents were gently mixed and spin down.

6. The following RT program was run on the thermal cycler.

Table 14.

Leave heated lid set to 105°C (default). 7. cDNA was used immediately or stored at -20°C.

B. 7500 Real Time PCR System Setup

1. Logged into the connected laptop and the 7500 Software was opened.

2. Under “Set Up”, “Advanced Setup” was selected to start programming. a. To use an existing template, “Template” was selected or browsed to it directly in Windows.

3. The “Setup” tab in the left panel was selected.

4. The “Experimental Properties” sub-tab was selected in the left panel. a. The experiment was named and the project name was included and the date of run. b. “7500 (96 Wells)” as the instrument type was selected. c. “TaqMan Reagents” as the reagent type was selected. d. “Standard” ramp speed was selected e. The experiment was saved by clicking “Save As.” The filename reflected the name given to the experiment and could be saved as a Template.

5. “Plate Setup” sub-tab in the left panel was selected. a. “Define Targets and Samples” heading was selected. b. Each target was added and its reporter type (typically FAM or sometimes VIC) and a quencher type (usually NFQ-MGB) was assigned. c. Each sample was added in the right panel. It was made sure to include standards and NTC if applicable. d. The “Assign Targets and Samples” heading was selected. e. The wells in the graphic on the right were highlighted. Each well could be assigned a target and a sample. It was ensured all targets were of type “Unknown” (blue ‘U’ button). You cannot have two targets with the same reporter in the same well. f. “ROX” as the passive dye was selected.

6. The “Run Method” sub-tab was selected in the left panel, and then the “Tabular View” heading. a. Input a reaction volume of 20 pL. b. Holding Stage 1 : 50°C for 2 minutes, 100% ramp rate. c. Holding Stage 2: 95°C for 20 seconds, 100% ramp rate. d. Cycling Stage: 95°C for 3 seconds, then 60°C for 1 minute with acquisition. Ramp rates 100%. The standard number of cycles was 60.

7. “Save” from the top menu was selected. The instrument was ready to run. [0371] C. qPCR Reaction Setup

1. The entire plate setup was performed in a designated pre-PCR hood.

2. TaqMan probes and TaqMan Fast Advanced Master Mix (2X) were thawed on ice.

3. The table below (table 15) was used to create a master mix for each probe according to the number of plate wells in which it was used. Calculated for an extra 20% in volume.

Table 15.

If multiplexing, adjust water volume for a 17 pL final volume. If using 60X probes, dilute to

20X in nuclease-free water before adding.

4. A new MicroAmp Optical 96-Well Reaction Plate was placed in an ice block.

5. A 125 pL VIAFLO was programmed to repeatedly dispense 17 pL.

6. 17 pL of probe master mix was pipeted into each corresponding well in the plate.

7. A 12.5 pL VIAFLO was programmed to repeatedly dispense 3 pL.

8. 3 pL of cDNA was pipetted into each corresponding well in the plate.

9. The plate was sealed with an adhesive PCR plate seal.

10. It was mixed well by vortexing and a secondary plate was used to vortex as direct contact of the vortex rubber with the optical wells could leave behind debris or scratches and interfere with detection.

11. The plate was quick spinned to 1000 ref.

12. The plate was placed inside of the 7500 instrument with well Al in the top left comer.

13. “Start Run” was selected in the software.

Table 16. Gene Expression Levels of 20 Genes in Responding and Non-Responding Cell Lines Evaluated By Nanostring Technique

Res: responding cell line to Talabostat

Non-Res: non-responding cell line to Talabostat

Table 17. Data Represents Transcripts Expression Levels (Nanostring Data) of 20

Genes Validated By Q-PCR (RT-PCR)

R: Responding cell line to Talabostat

NR: non-responding cell line to Talabostat

Data shown is the expression values relative to HPRT1, a house keeping gene

[0372] Results: The analysis identified 20 genes as potential predictive biomarkers. Twenty genes were found to be differentially expressed (transcripts levels) in rlonding (R) vs nonresponding (NR) human leukemic cell lines. Twenty genes are involved in the inflammasome pathway (including DPP9) and other immune signaling were found to be differentially expressed (transcripts levels) ilesponding (R) compared to non-responding (NR) human leukemic cell lines.

[0373] Genes like CARD8, CASP1, DPP8, DPP9 and PYCARD were found to be upregulated in responder cell lines as compared to non-responders and correlated with the Talabostat cytotoxic activity. Other genes involved were serine/threonine kinase AKT3, along with other immune signaling molecules IL4R, IL6R, IL17RA, CARD9, IRF8, CXCR4, TARP, ITGAL and ITGB2 (Table 16, 17). Cell adhesion gene EPCAM was found to be elevated in non- responders while MHC class II associated genes HLA-DMA, HLA-DRA and HLA-DRB3 and an associated protease PSMB8 were found to be upregulated in responder cell lines. The results from Nanostring based study were confirmed using RT-PCR for the 20 genes which show differential expression between responder and non-responder human leukemic cell lines. Results from RT-PCR confirmed the results obtained earlier by Nanostring (Fig 4A, 4B). It concluded that a set of these gene expression (i.e.gene panel) could be predictive biomarker for the selection of patients for treatment with Talabostat in leukemia. Most of the genes have 2 -to- 1,000-fold higher expression in at least 3 responding cell lines in comparison to nonresponding cell lines. On the other hand, EPCAM gene has 7,000-fold higher expression in non-responding cell lines vs responding cell lines. Example 3: To evaluate human data for selected genes samples (according to example 2) were collected from AML patients (n=10), RNA from patient PBMCs were isolated and gene expression was assessed using RT-PCR.

Procedure:

[0374] RNA isolation from PBMCs

1. RNEasy Mini Kit Preparation:

1.1. RLT - lOpl P-ME per ml of RLT buffer was added just before use, stored at RT for upto one month. 350pl RLT (with PME) was used for cell numbers <5 x 10 6. For cell numbers 5 x l0⁶ - l x l0⁷ use 600pl. If cell numbers were not known but a visible large pellet can be seen, 600pl of RLT was used.

1.2. It was ensured that appropriate amount of EtOH was added to RPE (instructions on bottle) and stored at room temperature (RT).

1.3. DNase I Stock: 550 pl of the RNase-free water was added to the vial of DNAse I, mixed gently by inversion, Do not Vortex. It was stored in aliquots of 130pl or 65pl at -20°C.

1.4. DNase I working: For 12 samples, 130pl of DNAse I stock was mixed with 910pl of buffer RDD.

2. Preparation of lysate:

2.1. 350/600pl of RLT- PME was added to each tube containing PBMC pellet and mixed well by pipetting.

2.2. The entire mixture was transferred to labeled Qiashredder columns on collection tube.

2.3. It was centrifuged at 16000xg(RCF) for 2 minutes.

2.4. Do not discard flow-through! ! ! Transfer flow-through to a fresh labeled Eppendorf tube avoiding pellet. Discard Qiashredder columns.

3. RNA purification:

3.1. Equal volume (350/600pl) of 70% EtOH was added to the flow-through from 2.4 and mixed well by pipetting up and down at least 20 times.

3.2. Up to 700pl of tie was transfered to RNEasy Mini spin columns.

3.3. It was centrifuged at 8000xg(RCF) for 30s. Discard flowthrough.

3.4. Repeated step 3.2 and 3.3 until all lysate was processed.

3.5. 350 pl RW1 Buffer was added to the column and centrifuged at 8000xg(RCF) for 30s. Discard flowthrough.

3.6. 80pl DNAse I working mix was added directly to the column matrix. 3.7. It was incubated at room temperature (20-30°C) for 15 minutes.

3.8. 350 pl RW1 Buffer was added to the column and centrifuged at 8000xg(RCF)for 30s. Discard flow-through.

3.9. 500 pl RPE was added to column and centrifuged at 8000xg for 30s. Discard flowthrough.

3.10. 500 pl RPE was added to column and centrifuged at 8000xg for Imin. Discard collection tube.

3.11. The column was placed on a new collection tube and centrifuged at 16000xg (RCF) for 1 min. Discard collection tube.

3.12. The column was placed on a new 1.5ml tube. 32pl of Nuclease free water was added to the column matrix and incubated at room temperature for 2 minutes.

3.13. It was centrifuged at 16000 x g (RCF) for 1 minute.

3.14. Steps 3.12 and 3.13 were repeated and eluted into the same tube.

3.15. Proceeded with Nanodrop quantification. Eluted RNA was stored at -80°C.

[0375] Evaluation of Gene Expression using RT-PCR: The procedure same as given under Example 2 was followed.

[0376] Results: Gene expression values were normalized against HPRT1, a house keeping gene. The data obtained from AML patients (Fig. 5 and Table 18) exhibit similar expression levels as that of responding and non-responding cell lines. The expression levels of 20 genes were low or high in various PBMCs samples from bone marrow of 10 AML patients.

Table 18. Expression Relative to HPRT1

Claims

CLAIMS What is claimed is:

1. A method of treating a subj ect with a cancer using a dipeptidyl peptidase (DPP) inhibitor, comprising a) obtaining a biological sample from the subject; b) determining DNA copy number of DPP9 gene in the biological sample; and c) administering an effective amount of the DPP inhibitor to the subject if the DNA copy number of the DPP9 gene is equal to or higher than a predetermined DPP9 gene threshold.

2. A method for identifying and/or predicting the likelihood of response to treatment with dipeptidyl Peptidase (DPP) inhibitor in a subject with a cancer, comprising a) obtaining a biological sample from the subject; and b) determining DNA copy number of DPP9 gene in the biological sample; wherein a DNA copy number of DPP9 gene is equal to or higher than a predetermined DPP9 gene threshold indicates that the subject is likely to respond favorably to DPP inhibitor.

3. The method of claim 1 or 2, wherein the cancer is hematological cancer selected from the group consisting of leukemia, lymphoma, myeloma, chronic lymphocytic leukemia, chronic myelogenous leukemia or acute lymphocytic leukemia, acute myeloid leukemia (AML), Hodgkin and non-Hodgkin lymphoma. Chronic myelomonocytic leukemia, Chronic neutrophilic leukemia, hairy cell leukemia, chronic idiopathic myelofibrosis, plasma cell leukemia; Heilmeyer-Schbner disease; panmyelosis; acute panmyelosis with myelofibrosis; lymphosarcoma cell leukemia; acute leukaemia of unspecified cell type; blastic phase chronic myelogenous leukemia; Stem cell leukemia; Chronic leukaemia of unspecified cell type; Subacute leukaemia of unspecified cell type; Accelerated phase chronic myelogenous leukemia; Polycythemia vera; Adult T-cell leukemia/lymphoma; Aggressive NK-cell leukemia; B-cell prolymphocytic leukemia; B-cell leukemia, Anaplastic large cell lymphoma; Angioimmunoblastic T-cell lymphoma; Hepatosplenic T-cell lymphoma; Follicular lymphoma; mucosa-associated lymphatic tissue lymphoma; B-cell chronic lymphocytic leukemia; Mantle cell lymphoma; Burkitt lymphoma; Mediastinal large B cell lymphoma; Nodal marginal zone B cell lymphoma; Splenic marginal zone lymphoma; Intravascular large B-cell lymphoma; Primary effusion lymphoma; Nodular lymphocyte predominant Hodgkin's lymphoma; Lymphomatoid granulomatosis, multiple myeloma; Kahler's disease; Myelomatosis, plasmacytoma, extramedullary; Malignant plasma cell tumour NOS; Plasmacytoma NOS, myelodysplastic syndromes(MDS), myeloproliferative neoplasms (MPN), amyloidosis, Waldenstrom’s macroglobinaemia (WM) and aplastic anaemia.

4. The method of claim 3, wherein the hematological cancer is acute myeloid leukemia.

5. The method of claim 1 , wherein the cancer is a solid tumor/cancer selected from the group consisting of urogenital cancers (such as prostate cancers including small cell neuroendocrine prostate cancer; (SCNC), neuroendocrine prostate cancer (NEPC), treatment emergent neuroendocrine prostate cancer (tNEPC), castration resistant prostate cancer (CrPC), metastatic castration resistant prostate cancer (mCrPC) and adenocarcinoma type prostate cancer), renal cell cancer, bladder cancer), neuroendocrine cancer, thyroid cancer, colon cancer, kidney cancer, liver cancer, testicular cancer, vulvar cancer, wilm's tumor, hormone sensitive or hormone refractory prostate cancer, gynecological cancers (such as ovarian cancer, cervical cancer, endometrial cancer, uterine cancer), lung cancer, non-small cell lung cancer, small cell lung cancer, gastrointestinal stromal cancers, gastrointestinal cancers (such as non- metastatic or metastatic colorectal cancers, pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellular cancer, cholangiocellular cancer), ovarian cancer, breast cancer, gastric cancer, astroglial, astrocytoma, neuroectodermal tumors, head and neck cancer, gastroesophageal cancer, malignant glioblastoma, malignant mesothelioma, non-metastatic or metastatic breast cancer (such as hormone refractory metastatic breast cancer, triple negative breast cancer), malignant melanoma, mucosal melanoma, uveal melanoma, uterine sarcoma, metastatic melanoma, skin cancer, merkel cell carcinoma or bone and soft tissue sarcomas, oral cancer, oral squamous cell carcinoma, glioblastoma, brain cancer, spinal cord cancer, germ cell tumors, basal cell carcinoma, pleomorphic sarcoma, leiomyosarcoma, squamous cell carcinoma of unknown primary, dedifferentiated liposarcoma, osteosarcoma, Ewing sarcoma, Rhabdomyosarcoma, adrenocortical carcinoma, neuroblastoma, advanced metastatic, an inflammatory myofibroblastic tumor (IMT), cholangiocarcinoma, cystadenocarcinoma, ameloblastoma, chondrosarcoma, dermatofibrosarcoma, ganglioglioma, leiomyosarcoma, medulloblastoma, osteoblastoma and inoperable non-inflammatory locally advanced disease and other advanced solid cancers/tumors

6. The method of claim 1 or 2, wherein the DPP inhibitor is a DPP2/DPP4/DPP8/DPP9/FAP inhibitor.

7. The method of claim 6, wherein the DPP2/DPP4/DPP8/DPP9/FAP inhibitor is Talabostat or a pharmaceutically acceptable salt thereof.

8. The method of claim 7, wherein the DPP2/DPP4/DPP8/DPP9/FAP inhibitor is Talabostat mesylate.

9. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is about 3 or higher.

10. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is between 3 and 13.

11. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is between 2 and 13.

12. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is between 3 and 10.

13. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is between 3 and 6.

14. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is between 3 and 4.

15. The method of claim 1 or 2, wherein the predetermined DPP9 gene threshold is about 3.

16. The method of claim 1 or 7, wherein the effective amount of Talabostat or a pharmaceutically acceptable salt thereof ranges from about 100 mcg to about 1 mg.

17. The method of claim 1 or 7, wherein the effective amount of Talabostat or a pharmaceutically acceptable salt thereof ranges from about 100 mcg to about 600 mcg.

18. The method of claim 1 or 7, wherein Talabostat or a pharmaceutically acceptable salt thereof is administered at a dose of about 0.2 mg twice daily on one or more days of a treatment cycle.

19. The method of claim 1 or 7, wherein Talabostat or a pharmaceutically acceptable salt thereof is administered at a dose of about 0.3 mg twice daily on one or more days of a treatment cycle.

20. The method of claim 1 or 2, wherein the DNA copy number of DPP9 gene is determined using quantitative polymerase chain reaction (qPCR) or next generation sequencing.

21. The method of claim 1 or 2, wherein DNA copy number of DPP9 gene is determined using PCR amplification of the gene .