Mucins and isoforms thereof and intestinal disorders

Abstract

The present invention relates to the field of mucins and mRNA isoforms thereof, more in particular the use of mucins and mRNA isoforms in subjects suspected having an intestinal disorder. Provided herein is an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto by determining the expression of at least 3 mRNA isoforms originating from genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof.

Description

[0001] MUCINS AND ISOFORMS THEREOF AND INTESTINAL DISORDERS FIELD OF THE INVENTION The present invention relates to the field of mucins and mRNA isoforms thereof, more in particular the use of mucins and mRNA isoforms in subjects suspected having an intestinal disorder. Provided herein is an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto by determining the expression of at least 3 mRNA isoforms originating from genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof. BACKGROUND TO THE INVENTION Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), remain disease entities with a high morbidity burden and are major contributors to health problems worldwide (i.e. 6.8 million cases (= 396 per 100.000) globally). IBD are characterized by chronic relapsing inflammation of the gastrointestinal (GI) tract in association with mucosal barrier dysfunction and gut dysbiosis, and usually involve severe diarrhea, abdominal pain, fatigue, and weight loss. A multitude of therapies are available for IBD patients, including a wide array of biologicals, which are mainly focused on reducing the exorbitant inflammatory response (for example antibodies such as infliximab, adalimumab, vedolizumab, risankizumab as well as small molecules, such as JAK inhibitors and sphingosine-1 phosphate (S1P) receptor agonist (ozanimod)). However, the current knowledge does not help clinicians to choose the right therapy for the right patient, forcing them to do so empirically. As a result, 30% of the patients do not respond to the initial therapy (i.e. primary non-responsive) and 50% lose response over time (i.e. secondary loss of response). Furthermore, the monitoring of IBD progression upon therapy is mainly based on symptom relief and the assessment of mucosal healing, which are not always in agreement. According to the recent guidelines, mucosal healing has been considered as a key therapeutic endpoint for IBD patients. Mucosal healing is a complex term encompassing the restoration of the mucosal barrier and the reduction of inflammation and is currently defined as a composite term of endoscopic improvement and histologic remission. Recently, advanced endoscopic techniques in combination with artificial intelligence have been shown to predict histologic remission without the need of taking biopsies. These techniques include the use of virtual chromoendoscopy (PICASSO system), automated analysis of microscopic features of leakage of vessels with single wavelength technology and automated quantification of the redness of an endoscopic image (Red Density) and have only been developed with a histologic and endoscopic ground truth. In addition, measurement of endoscopic improvement and histologic remission is, however, only based on the presence of macroscopic and microscopic inflammation without taking barrier function and thus the importance of barrier healing into account. Furthermore, objective measurements at the molecular level to monitor mucosal healing, particularly barrier healing, and to help clinicians in selecting the appropriate therapy are also lacking. The use of biomarkers, such as fecal calprotectin in stoo reactive protein in the blood to assess inflammation, have proven their worth in the follow-up of disease, but their predictive value for mucosal healing and therapy response are unsatisfactory. The current lack of predictive molecular biomarkers hence impedes treatment success in IBD patients and therefore there is an urgent and long-felt need for a suitable diagnostic method to evaluate mucosal barrier damage and healing of the intestinal tract. It was therefore an object of the present invention to provide for a new in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery. The method described herein is based on the change in expression of mucins and mRNA isoforms therefore. Mucins are the gatekeepers of the mucus barrier and aberrant mucin expression is indicative for a loss of intestinal mucosal barrier integrity which is a key hallmark of IBD. The advantage of the method of the present invention is that characterization of the intestinal mucosal barrier in IBD leads to an accurate and robust assessment of the treatment response by monitoring repairment of the mucosal barrier in addition to inflammation and thus mucosal healing at the molecular level. Disease- associated mucin mRNA isoforms can act as novel biomarkers to 1) mirror mucosal barrier healing on the one hand and 2) predict therapy response in IBD patients on the other hand. A further advantage is that such an in vitro method would be a valuable asset in the monitoring of mucosal healing and development of treat-to target strategies to control IBD in comparison to or in addition to the endoscopic and histologic parameters measuring macroscopic and microscopic inflammation. SUMMARY OF THE INVENTION In a first aspect, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto said method comprising: a) providing a biological sample from a subject suspected of having an intestinal disorder, and b) determining the expression of at least 3 mRNA isoforms originating from genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof wherein at least one of said 3 mRNA isoforms is a MUC4 mRNA isoform and wherein the expression of said selected mucin mRNA isoforms are normalized to a reference value and wherein a change in expression is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. Particularly interesting mucins for use in an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto may be MUC4 mRNA isoforms in combination with at least one other mRNA isoform selected from the list comprising: a MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC2 mRNA isoforms, MUC5AC mRNA isoforms, MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof, or any combination thereof. In a particular embodiment the MUC4 mRNA isoform is MUC4 mRNA isoform PB.1238.363. In another particular embodiment, the present invention provides an in vitro method wherein the expression of MUC4 mRNA isoforms is determined in combination with: i) MUC2 mRNA isoforms and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof; or ii) two or more mRNA isoforms selected from the list comprising: MUC5AC, MUC20 isoforms, or MUC12, or an overlapping transcript or a pseudogene thereof; or iii) two or more mRNA isoforms selected from the list comprising: MUC3A, MUC12-AS1, MUC13, or MUC19 mRNA isoforms. In a specific embodiment, said method comprises determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto wherein said barrier damage to the intestinal tract is located in a region selected from the list comprising: ileum, proximal colon, distal colon, and / or rectum. In a particular embodiment, said mucin mRNA isoform encodes for a transmembrane mucin. In another aspect, the present invention provides a combination of MUC4 mRNA isoforms and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof; optionally in combination with one or more of MUC1 mRNA isoforms, MUC2 mRNA isoforms, MUC5AC mRNA isoforms, MUC5B mRNA isoforms, MUC12 mRNA isoforms, or MUC3A_MUC12 fusion gene mRNA isoforms, for use in the diagnosis of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In a specific embodiment, the combination for use according to the invention further comprises one or more mRNA isoforms selected from the list comprising: MUC3A mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 isoforms. In a very specific embodiment, the present invention provides a combination of MUC4 mRNA isoforms, MUC2 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In yet another embodiment, the present invention provides a combination of MUC4 mRNA isoforms, MUC5AC mRNA isoforms, MUC12 mRNA isoforms, MUC12-AS1 mRNA isoforms, and MUC20 mRNA isoforms for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In a particular embodiment, said intestinal disorder is a chronic inflammatory bowel disease (IBD) or colorectal cancer, in particular an IBD selected from the group comprising: Crohn’s disease (CD), ulcerative colitis (UC), ischemic colitis, indetermin microscopic colitis, or radiotherapy-induced colitis. In another aspect, the present invention provides a diagnostic kit for performing the in vitro method according to the invention, said kit comprising agents for detecting the expression of the at least 3 mucin mRNA isoforms wherein at least one of said 3 mRNA isoforms is a MUC4 mRNA isoform in combination with one or more mucin mRNA isoforms selected from the list comprising: MUC1, MUC2, MUC3A, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof. BRIEF DESCRIPTION OF THE DRAWINGS With specific reference now to the figures, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the different embodiments of the present invention only. They are presented in the cause of providing what is believed to be the most useful and readily description of the principles and conceptual aspects of the invention. In this regard no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention. The description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice. Figure 1. Schematic overview of MUC isoform characteristics in the intestinal mucin transcriptome and human reference transcriptome. (A) Illustration of the filtering to obtain the intestinal mucin transcriptome from the SQANTI3 output (B) and subsequent classification of the isoforms according to their best matching transcript. (C) Boxplot depicting the length of each MUC isoform found in the intestinal mucin transcriptome of human reference transcriptome. (D) Illustration of the exon count for each MUC isoform found in the intestinal mucin transcriptome of human reference transcriptome. (E) Bar chart presenting the number of isoforms for each MUC gene and their coding potential in the human reference transcriptome and (F) the intestinal mucin transcriptome. (FSM, full splice match; ISM, incomplete splice match; NIC, novel in catalog; NNC, novel not in catalog). Figure 2. Model performance of classification random forest models visualised as receiver operating characteristics (ROC) curve. Complementary violin plots display the MUC isoforms used to build each predictive model and their log2-transformed counts. The specified biopsied region within the colon only applies to train and test dataset. For the external validation set, no information concerning the colonic subregion was available. (A,E) Comparison between colonic inflamed biopsies of CD patients (ntrain= 182; ntest= 45; nval= 40) and colonic biopsies of control patients (ntrain= 182; ntest= 67; nval= 35). (B, F) Comparison between colonic inflamed biopsies of CD patients (ntrain = 182; ntest = 45; nval = 40) and inflamed colonic biopsies of UC patients (ntrain = 191; ntest = 47; nval = 40). (C, G) Comparison between inflamed rectal biopsies of CD patients (ntrain = 80; ntest = 20; nval = 40) and rectal biopsies of control patients (ntrain= 80; ntest= 44; nval= 35). (D, H) Comparison between inflamed biopsies from the distal colon of CD patients (ntrain= 120; ntest= 29; nval= 40) and biopsies from the distal colon of control patients (ntrain= 120; ntest= 46; nval= 35). (CD, Cr ase) Figure 3. Model performance of classification random forest models visualised as receiver operating characteristics (ROC) curve. Complementary violin plots display the MUC isoforms used to build each predictive model and their log2-transformed counts. The specified biopsied region within the colon only applies to train and test dataset. For the external validation set, no information concerning the colonic subregion was available. (A, E) Comparison between inflamed rectal biopsies of IBD patients (ntrain= 174; ntest = 43; nval = 80) and rectal biopsies of control patients (ntrain = 180; ntest = 44; nval = 35). (B, F) Comparison between colonic inflamed biopsies of IBD patients (ntrain = 272; ntest = 93; nval = 80) and colonic biopsies of control patients (ntrain = 272; ntest = 67; nval = 35). (C, G) Comparison between Ileal inflamed biopsies of CD patients (ntrain= 97; ntest= 30; nval= 44) and ileal biopsies of control patients (ntrain= 97; ntest= 24; nval= 11). (D, H) Comparison between inflamed biopsies from the proximal colon of CD patients (ntrain = 63; ntest = 15; nval = 40) and biopsies from the proximal colon of control patients (ntrain = 63; ntest = 21; nval = 35). (IBD, inflammatory bowel disease; CD, Crohn’s disease) Figure 4. Model performance of classification random forest models visualised as receiver operating characteristics (ROC) curve. Complementary violin plots display the MUC isoforms used to build each predictive model and their log2-transformed counts. The specified biopsied region within the colon only applies to train and test dataset. For the external validation set, no information concerning the colonic subregion was available. (A, D) Comparison between colonic inflamed biopsies of UC patients (ntrain= 191; ntest= 47; nval= 40) and colonic biopsies of control patients (ntrain= 191; ntest= 67; nval= 35). The same isoform panel was used to distinguish colonic carcinoma samples (n = 20) from colonic para- carcinoma tissue (n =20). Carcinoma and para-carcinoma RNA sequencing data originate from GEO dataset GSE223119 (B, E) Comparison between inflamed rectal biopsies of UC patients (ntrain= 94; ntest= 23; nval= 40) and rectal biopsies of control patients (ntrain= 94; ntest= 44; nval= 35). (C, F) Comparison between inflamed biopsies from the distal colon of UC patients (ntrain= 155; ntest= 38; nval= 40) and biopsies from the distal colon of control patients (ntrain = 155; ntest = 46; nval = 35). (UC, ulcerative colitis) Figure 5. Model performance of classification random forest models visualised as receiver operating characteristics (ROC) curve. Complementary violin plots display the MUC isoforms used to build each predictive model and their log2-transformed counts. The specified biopsied region within the colon only applies to train and test dataset. For the external validation set, no information concerning the colonic subregion was available. (A, E) Comparison between non-inflamed biopsies from the distal colon of UC patients (ntrain= 116; ntest= 29) and biopsies from the distal colon of control patients (ntrain= 116; ntest= 46). (B, F) Comparison between colonic non-inflamed biopsies of CD (ntrain= 167; ntest= 41) and colonic non-inflamed biopsies of UC patients (ntrain = 168; ntest = 41). (C, G) Comparison between colonic non-inflamed biopsies of IBD patients (ntrain = 272; ntest = 82) and colonic biopsies of control patients (ntrain = 272; ntest = 67). (D, H) Comparison between non-inflamed rectal biopsies of IBD patients (ntrain = 160; ntest= 44) and rectal biopsies of control patients (ntrain= 160; ntest= 38). (IBD, inflammatory bowel disease; CD, Crohn’s disease; UC, ulcerative colitis). Figure 6. Model performance of the classification random forest model visualised as receiver operating characteristics (ROC) curve. Complementary violin plot displays the MUC isoforms used to build the predictive model and their log2-transformed counts. (A, B) Comparison between ileal non-inflamed biopsies of CD patients (ntrain= 82; ntest= 20) and ileal biopsies of control patients (ntrain= 82; ntest= 24). (CD, Crohn’s disease) Figure 7. Venn diagram summarizing the mucin isoforms as predictors to classify inflamed colonic biopsies of CD or UC patients from non-inflamed biopsies of control patients and inflamed ileal biopsies of CD patients from non-inflamed biopsies of control patients. Isoforms present in the colon, rectum, distal and / or proximal CD panel are combined as are the isoforms present in the colon, rectum and / or distal UC panel. Figure 8. Venn diagram summarizing the mucin isoforms as predictors to classify inflamed biopsies from the proximal colon, distal colon and rectum from CD patients from their non-inflamed control counterparts. Figure 9. Venn diagram summarizing the mucin isoforms as predictors to classify inflamed biopsies from the distal colon and rectum from UC patients from their non-inflamed control counterparts. The colors represent the mucin gene from which the isoform originates, the letters refer to the specific mucin isoform and the size of the circle for each isoform indicates in how many panels it occurs. Figure 10. Graphical overview of the different mucin isoform panels obtained for each anatomical region in Crohn’s disease and ulcerative colitis patients. Significant up- and downregulation when compared to mucin isoform expression in control samples is indicated with arrows in front of each isoform. Figure 11. Venn diagram presenting an overview of the mucin isoforms obtained by the feature selection Random Forest throughout multiple models involving only non-inflamed biopsies. The mucin isoforms as predictors to classify non-inflamed colonic biopsies of CD or UC patients from non-inflamed biopsies of control patients and non-inflamed ileal biopsies of CD patients from non-inflamed biopsies of control patients are summarized. The colors represent the mucin from which the isoform originates, the letters refer to the specific isoform and the size of the circle for each isoform indicates in how many panels it occurs. DETAILED DESCRIPTION OF THE INVENTION As already detailed herein above, in a first aspect, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto said method comprising: a) providing a biological sample from a subject suspected of having an intestinal disorder, and b) determining the expression of at least 3 mRNA isoforms originating from mucin genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof wherein at least one of said 3 mRNA isoforms is a MUC4 mRNA isoform and wherein the expression of said selected mucin mRNA isoforms are normalized to a reference value and wherein a change in expression is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In the context of the present invention, several correlations between mRNA isoforms on the one hand, and intestinal barrier damage related aspects on the other hand have been identified. In particular MUC4 mRNA isoforms are an essential discriminator for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In the context of the present invention, the term ““mucin mRNA isoform” is meant to be a member of a set of similar mRNA molecules, which originate from a single mucin (pseudo)gene or an overlapping mucin gene thereof, and that are the result of genetic differences. The term also includes mucin mRNA isoform fusion genes (e.g. MUC3A-MUC12 fusion gene). These isoforms may be formed from variable promotor usage, alternative stop codons, or formed from alternative splicing or other post-transcriptional modifications of the gene. Through RNA splicing mechanisms, mRNA has the ability to select different protein-coding segments (exons) of a gene, or even different parts of exons from RNA to form different mRNA sequences, i.e. isoforms. Each unique RNA isoform sequence encodes a specific form of a protein. The presence of genetic differences in mucin genes can result in different mRNA isoforms (i.e. splice variants via alternative splicing) produced from the same mucin gene locus. While most isoforms encode similar biological functions, others have the potential to alter the protein function resulting in progression toward disease. Thus, it should be clear to the person skilled in the art that the mRNA isoforms as used herein refer to mRNA isoform transcripts and not to the corresponding encoded protein products. In particular, and as an example for clarification, the invention is directed, to MUC4 mRNA isoforms obtained via alternative splicing, which are genetic variants of the full-length MUC4 reference transcript generated via constitutive splicing. Constitutive splicing is the process of intron removal and exon ligation of the majority of the exons in the order in which they appear in a gene while aternative splicing is a deviation from this preferred sequence where certain exons are skipped resulting in various forms of mature mRNA. The invention is in particular based on MUC4 mRNA isoforms which may give rise to aberrant proteins (through alternative splicing) or act as non-coding RNA molecules interfering in signaling pathways of the intestinal tract, and are therefore specifically suitable in for example the diagnosis of barrier damage to the intestinal tract. Accordingly, the present invention is specifically directed to the identification and / or us mucin mRNA isoforms in various intestinal tract disorders. The present invention in particular provides mucin mRNA isoforms as defined herein, specifically MUC4, MUC1, MUC2, MUC3A, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof (see Table 1 and Table 2). In particular, the mucin mRNA isoforms are represented by a specific isoform ID that can be selected from one or more of any one of Table 1 or Table 2, wherein at least one is a MUC4 mRNA isoform. Even more specifically, the present invention provides different combinations of mucin mRNA isoforms as represented in any one or more of Fig.2E-H, Fig.3E-H, Fig.4D-F, Fig.5E-H, Fig. 6B, or represented by the Venn diagrams of Fig.7-9, 11 and summarized by Fig.10. It further provides uses of such mucin mRNA isoforms as detailed in the present application. The skilled artisan will appreciate that, except where otherwise noted, nucleic acid sequences set forth in the instant application may recite “T”s in a representative DNA sequence but where the sequence represents RNA, the “T”s would be substituted for “U”s. Thus, any of the DNA sequences disclosed herein and identified by a particular sequence identification number herein, is also intended to disclose its corresponding RNA sequence complementary to the DNA, where each “T” of the DNA sequence is substituted with “U”. The term “isoform” according to the present invention refers to mRNA transcript variants (which are genetic variants of the full-length reference transcript) of a gene. Such transcription variants result, for example, from alternative splicing or from a shifted transcription initiation. Based on the different transcript variants, different polypeptides are generated. It is possible that different transcript variants have different translation initiation sites. A person skilled in the art will appreciate that the amount of an isoform can be measured by adequate techniques for the quantification of mRNA as far as the isoform relates to a transcript variant which is an mRNA. Examples of such techniques are polymerase chain reaction-based methods, in situ hybridization-based methods, microarray-based techniques and whole transcriptome long-read sequencing. Further, a person skilled in the art will appreciate that the amount of an isoform can be measured by adequate techniques for the quantification of polypeptides as far as the isoform relates to a polypeptide. Examples of such techniques for the quantification of polypeptides are ELISA (Enzyme-linked Immunosorbent Assay)-based, gel-based, blot-based, mass spectrometry- based, and flow cytometry-based methods. In the context of the present invention, the term “overlapping transcript” is defined within the context of gene overlap and is to be understood as having at least one nucleotide shared between the boundaries of the primary mRNA transcripts of two or more genes, such that a nucleotide mutation at any point of the overlapping region would affect the transcripts of all genes involved. An example of such an overlapping gene is MUC20 and MUC20 overlapping transcript (MUC20-OT1). As used herein, the term “pseudogene” is to be understood as non-functional sequences of genomic DNA originally derived from functional genes. An example of such a pseudogene is Mucin 20, Cell Surface Associated Pseudogene 1 (MUC20-P1). Accordingly, when reference is MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, it is also meant to be to include overlapping transcript such as MUC20-OT1 and / or pseudogenes thereof such as MUC20-P1. Likewise, when reference is made to a particular MUC mRNA isoform, it also includes any variant thereof such as a fusion gene (e.g. MUC3A_MUC12 fusion gene) as well as antisense RNA. For example, when reference is made to MUC12 mRNA isoform, it also includes MUC12-AS1 which is an RNA gene that is affiliated with the lncRNA class. In a particular embodiment, said mucin mRNA isoform encodes for a transmembrane mucin, which is a type of integral membrane protein that spans the entirety of the cell membrane. These mucins form a gateway to permit / prevent the transport of specific substances across the membrane. Particularly interesting mucins for use in an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto may be MUC4 mRNA isoforms, MUC1 mRNA isoforms, MUC16 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC2 mRNA isoforms, MUC5AC mRNA isoforms, MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof. In particular, determining the expression of at least 3 mRNA isoforms wherein one of said 3 mRNA isoforms is MUC4 mRNA isoform, in particular MUC4 isoform PB.1238.363, is highly suitable in the determination of intestinal barrier damage in a subject having an intestinal tract disorder or has received therapy therefore, or is in recovery therefrom. It has been found that it is important to determine at least the expression of MUC4 mRNA isoform to have an accurate prediction of intestinal barrier damage. Accordingly, the present invention provides different combinations of mucin mRNA isoforms such as but not limited to: MUC4 mRNA isoform and MUC1 mRNA isoform, MUC4 mRNA isoform and MUC2 mRNA isoform, MUC4 mRNA isoform and MUC3A mRNA isoform, MUC4 mRNA isoform and MUC3A_MUC12 fusion gene mRNA isoform, MUC4 mRNA isoform and MUC5AC mRNA isoform, MUC4 mRNA isoform and MUC5B mRNA isoform, MUC4 mRNA isoform and MUC6 mRNA isoform, MUC4 mRNA isoform and MUC12 mRNA isoform or an overlapping transcript or a pseudogene thereof, MUC4 mRNA isoform and MUC12-AS1 mRNA isoform, MUC4 mRNA isoform and MUC13 mRNA isoform, MUC4 mRNA isoform and MUC16 mRNA isoform, MUC4 mRNA isoform and MUC17 mRNA isoform, MUC4 mRNA isoform and MUC19 mRNA isoform, MUC4 mRNA isoform and MUC20 mRNA isoform or an overlapping transcript or a pseudogene thereof. In a particular embodiment, the present invention provides combinations of mucin mRNA isoforms as previously presented but wherein said mRNA isoform is represented by a specific mucin isoform number and associated transcript mRNA isoforms as represented in Fig.10, or by the letters A-U in Figs.7 to 9 or the letters B-BM in Fig.11. In a particular embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract ediction of therapy response and recovery thereto by determining the expression of any of the following combinations: MUC4 mRNA isoform and MUC1 mRNA isoform, MUC4 mRNA isoform and MUC2 mRNA isoform, MUC4 mRNA isoform and MUC5AC mRNA isoform, MUC4 mRNA isoform and MUC12 mRNA isoform or an overlapping transcript or a pseudogene thereof, MUC4 mRNA isoform and MUC16 mRNA isoform, MUC4 mRNA isoform and MUC20 mRNA isoform or an overlapping transcript or a pseudogene thereof; either or not further in combination with one or more other mucin mRNA isoforms selected from the list comprising MUC1 mRNA isoforms, MUC3A mRNA isoforms, MUC3A_MUC12 fusion gene mRNA isoforms, MUC5B mRNA isoforms, MUC6 mRNA isoforms, MUC12-AS1 mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 mRNA isoforms. In a particular embodiment, the present invention provides an in vitro method wherein said method comprises determining the expression of MUC4 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, and MUC2 mRNA isoforms; alternatively MUC4 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, and MUC5AC mRNA isoforms; alternatively MUC4 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, and MUC16 mRNA isoforms; alternatively MUC4 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, and MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof, either or not further in combination with one or more other mucin mRNA isoforms selected from the list comprising MUC1 mRNA isoforms, MUC3A mRNA isoforms, MUC3A_MUC12 fusion gene mRNA isoforms, MUC5B mRNA isoforms, MUC6 mRNA isoforms, MUC12-AS1 mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 mRNA isoforms. In another particular embodiment, the present invention provides an in vitro method wherein said method comprises determining the expression of MUC4 mRNA isoforms, MUC2 mRNA isoforms, and MUC5AC mRNA isoforms; alternatively MUC4 mRNA isoforms, MUC2 mRNA isoforms, and MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof, either or not further in combination with one or more other mucin mRNA isoforms selected from the list comprising MUC1 mRNA isoforms, MUC3A mRNA isoforms, MUC3A_MUC12 fusion gene mRNA isoforms, MUC5B mRNA isoforms, MUC6 mRNA isoforms, MUC12-AS1 mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 mRNA isoforms. In yet another embodiment, the present invention provides an in vitro method wherein said method comprises determining the expression of MUC4 mRNA isoforms, MUC5AC mRNA isoforms, and MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof, either or not further in combination with one or more other mucin mRNA isoforms selected from the list comprising MUC1 mRNA isoforms, MUC3A mRNA isoforms, MUC3A_MUC12 fusion gene mRNA isoforms, MUC5B mRNA isoforms, MUC6 mRNA isoforms, MUC12-AS1 mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC1 oforms, or MUC19 mRNA isoforms. In another particular embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, wherein the expression of MUC4 mRNA isoforms in particular MUC4 isoform PB.1238.363, is determined in combination with: i) MUC2 mRNA isoforms and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, in particular MUC20 and / or MUC20-OT1, optionally in combination with MUC1, MUC16, and / or MUC12 mRNA isoforms; or ii) two or more mRNA isoforms selected from the list comprising: MUC5AC, MUC20 isoforms or MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof, optionally in combination with MUC1, MUC2 and / or MUC16 mRNA isoforms; or iii) two or more mRNA isoforms selected from the list comprising: MUC3A, MUC12-AS1, MUC13, or MUC19 mRNA isoforms. In a very specific embodiment, in any one of the previous or following combination, MUC4 mRNA isoform is preferably PB.1238.363, MUC1 mRNA isoform is preferably ENST00000620103.4, MUC16 mRNA isoform is preferably ENST00000397910.8, and MUC20 isoform is preferably ENST00000447234.7. In the context of the present invention, the phrase ‘determining the expression of mucins’, is meant to be a step in the method in which the expression level of mucin mRNA isoforms is determined, in order to detect the presence and / or amount of expression of such mucin mRNA isoforms. This can be determined on the level of protein or RNA (or mRNA) expression levels, by means of suitable techniques including but not limited to: western blotting, ELISA assays, next-generation sequencing, RT-PCR methods, mass spectrometry,… In a specific embodiment, in case expression levels are determined on the level of mRNA expression levels, the expression of a selected mucin mRNA isoform is normalized to a reference value wherein a change in expression is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In a particular embodiment, said change in expression level can be an upregulation or downregulation wherein respectively a high expression or low expression is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. Specific reference is made to Figure 10 wherein a combination of MUC isoforms are up- or downregulated for a specific region along the intestinal tract such as along the small intestine and colon, more specifically the (terminal) ileum, proximal colon, distal colon, and / or rectum. The specific set of disorders focused on in this application, is that they are characterized by intestinal barrier damage or dysfunction. The term “barrier dysfunction” is meant to be the partial or complete disruption of the natural function of an internal m rrier of the intestinal tract of a subject. The intestinal mucosal barrier separates the luminal content from host tissues and plays a pivotal role in the communication between the microbial flora and the mucosal immune system. Emerging evidence suggests that loss of barrier integrity, also referred to ‘leaky gut’, is a significant contributor to the pathophysiology of gastrointestinal diseases, including IBD (Inflammatory Bowel Diseases). In a particular embodiment, the method according to the invention is particularly suitable for the determination of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto in a subject having an intestinal disorder which can be a Irritable Bowel Syndrome (IBS), chronic inflammatory bowel disease (IBD), colorectal cancer, in particular an IBD selected from the group comprising: Crohn’s disease (CD), ulcerative colitis (UC), ischemic colitis, indetermined colitis, microscopic colitis, or radiotherapy-induced colitis. As used herein, the term “Crohn’s disease” refers to a chronic inflammatory condition of the gastrointestinal tract. It is a type of inflammatory bowel disease (IBD) that can affect any part of the gastrointestinal tract from the mouth to the anus, but most commonly affects the end of the small intestine and the beginning of the colon. The inflammation caused by Crohn's disease can lead to a variety of symptoms, including abdominal pain, severe diarrhea, fatigue, weight loss, and malnutrition. As used herein, the term "ulcerative colitis" is defined as a chronic inflammatory bowel disease (IBD) that specifically affects the colon (large intestine) and rectum. It is characterized by inflammation and ulceration of the innermost lining of the colon, leading to symptoms such as abdominal pain, diarrhea, rectal bleeding, and an urgent need to defecate. In a very specific embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of at least MUC4 mRNA isoforms, in particular MUC4 isoform PB.1238.363, in combination with: i) MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7, further in combination with one or more mRNA isoforms selected from the list comprising: MUC1, in particular ENST00000620103.4, MUC3A, MUC5AC, MUC5B mRNA isoforms, MUC16, in particular ENST00000397910.8; in particular wherein the intestinal disorder is Crohn’s disease (CD); or ii) MUC20 or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7, and one or more mRNA isoforms selected from the list comprising MUC3A, MUC12-AS1, MUC13, MUC19 mRNA isoforms, mRNA isoforms; in particular wherein the intestinal disorder is chronic inflammatory bowel disease (IBD): or iii) one or more mRNA isoforms selected from the list comprising: MUC5AC mRNA isoforms and MUC20 or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7, optionally in combination with MUC1, MUC2, MUC3A_MUC12 fusion gene, MUC12, and / or MUC16; in particular wherein the intestinal disorder is ulcera (UC). In an alternative embodiment, wherein the intestinal disorder is Crohn’s disease (CD), the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC2 and MUC13 mRNA isoforms further in combination with one or more mRNA isoforms selected from the list comprising: MUC1, MUC3A, MUC5AC, MUC5B mRNA isoforms. In a specific embodiment, wherein the intestinal disorder is CD, the method comprises determining expression of MUC4, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC2, and MUC1 mRNA isoforms. In another alternative embodiment, wherein the intestinal disorder is IBD, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC5AC and MUC1 mRNA isoforms, further in combination with one or more mRNA isoforms selected from the list comprising: MUC3A, MUC3A_MUC12 fusion gene, MUC12-AS1, MUC13, MUC19 mRNA isoforms. In a specific embodiment, wherein the intestinal disorder is IBD, the method comprises determining expression of MUC4, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC1, MUC2, MUC5AC, MUC19 mRNA isoforms. In the context of the present invention, the term ‘biological sample’ or ‘sample’ is meant to be sample obtained from a subject, such as for example a tissue or liquid sample or biopsy from the intestinal tract, an endoscopically derived sample, luminal brush sample, aspirated intestinal fluid sample, mucus sample, faecal sample, urinal sample, blood sample, or a serum sample. In a specific embodiment, in case a sample is obtained from endoscopy, it may be obtained from a specific region along the intestinal tract such as along the small intestine and colon, more specifically the ileum, caecum, proximal colon, distal colon, and / or rectum. In a very specific embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of at least MUC4 mRNA isoforms, in particular MUC4 isoform PB.1238.363, in combination with: i) MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, further in combination with one or more mRNA isoforms selected from the list comprising: MUC2, MUC5AC; in particular wherein said sample is obtained from the colon; or ii) MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, further in combination with one or more mRNA isoforms selected from the list comprising: MUC1, MUC2, MUC3A_MUC12 fusion gene, MUC5AC; in particular wherein said sample is obtained from the distal colon; or iii) MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof in combination with one or more mRNA isoforms selected from the list comprising: MUC3A, MUC12-AS1, MUC13, MUC19; in particular wherein the sa btained from the ileum; or iv) one or more mRNA isoforms selected from the list comprising: MUC1, MUC3A, MUC5AC, MUC5B; in particular wherein the sample is obtained from the proximal colon; or v) MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, further in combination with one or more mRNA isoforms selected from the list comprising: MUC5AC, MUC16, MUC1, MUC2, MUC12, in particular wherein the sample is obtained from the rectum. In an alternative embodiment, wherein the sample is obtained from the colon, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC2 and MUC13 mRNA isoforms, optionally in combination with one or more mRNA isoforms selected from the list comprising: MUC1, MUC5AC, MUC5B, MUC12, MUC16, MUC17. In another alternative embodiment, wherein the sample is obtained from the colon, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC5AC and MUC13 mRNA isoforms, further in combination with MUC1 and / or MUC16 mRNA isoforms. In a specific embodiment, wherein the sample is obtained from the colon, the method comprises determining expression of MUC4, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC2, MUC5AC, and MUC13 mRNA isoforms. In an alternative embodiment, wherein the sample is obtained from the distal colon, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC5AC or MUC3A_MUC12 fusion gene mRNA isoforms, further in combination with one or more mRNA isoforms selected from the list comprising: MUC1, MUC2, MUC12, MUC16. In another alternative embodiment, wherein the sample is obtained from the distal colon, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC2 mRNA isoforms, further in combination with MUC3A_MUC12 fusion gene and / or MUC5AC mRNA isoforms. In a specific embodiment, wherein the sample is obtained from the distal colon, the method comprises determining expression of MUC4, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, MUC2, MUC3A_MUC12 gene fusion, MUC5AC mRNA isoforms. In an alternative embodiment, wherein the sample is obtained from the ileum, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with one or more mRNA isoforms selected from the list comprising: MUC3A, MUC12-AS1, MUC13, MUC19, further in combination with MUC1 and / or MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof. In a specific embodiment, wherein the sample is obtained from the ileum, the method comprises determining expression of MUC1, MUC3A, MUC4, MUC12-AS1, MUC13, MUC19, MUC20-OT1 mRNA isoforms. In an alternative embodiment, wherein the sample is obtained from the rectum, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC5AC mRNA isoforms, further in combination with one or mor soforms selected from the list comprising: MUC1, MUC2, MUC12, MUC16. In yet another alternative embodiment, wherein the sample is obtained from the rectum, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC16 mRNA isoforms, further in combination with one or more mRNA isoforms selected from the list comprising: MUC2, MUC3A, MUC5AC, MUC13. In a specific embodiment, wherein the sample is obtained from the rectum, the method comprises determining expression of MUC4, MUC5AC, MUC16, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof. In a further embodiment, the method of the present invention is particularly suitable to distinguish between an inflamed or non-inflamed condition of a patient having intestinal barrier damage or dysfunction; and this is particularly useful in determining whether a treatment or therapy of an inflamed condition is effective to reduce said inflammation or is also useful to determine the recovery after said treatment or therapy. In this regard, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of at least MUC4 mRNA isoforms in combination with: i) MUC1 mRNA isoforms, MUC16 mRNA isoforms and MUC17 mRNA isoforms, further in combination with one or more mRNA isoforms selected from the list comprising MUC3A, MUC3A_MUC12 gene fusion, MUC5AC, MUC20 mRNA isoforms; in particular in a subject having an inflammation status in said intestinal tract; or ii) MUC13 mRNA isoforms and MUC19 mRNA isoforms, further in combination with one or more mRNA isoforms selected from the list comprising: MUC2, MUC3A, MUC3A_MUC12 gene fusion, MUC5AC, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof; in particular in a subject having a non-inflamed status in said intestinal tract; or iii) the combination of MUC mRNA isoforms as represented in Fig.11 or any combination thereof, in particular isoform J in combination with any one of isoform O, N, BJ, BI and / or BK, in particular in a subject having a non-inflamed status in said intestinal tract. In an alternative embodiment, wherein the subject has an inflammation status in said intestinal tract, the method comprises determining the expression of at least MUC4 mRNA isoforms in combination with MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof in combination with MUC1 mRNA isoforms. Therefore, the present method described herein comprises determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto wherein said barrier damage to the intestinal tract is located in a region selected from the list comprising: ileum, proximal colon, distal colon, and / or rectum. In a very specific embodiment, wherein the subject has a non-inflammation status of the intestinal disorder CD, and wherein the sample is obtained from the ileum or colon, the method comprises determining the expression of at least MUC mRNA isoform BI (PB.2810.2552), optionally in combination with any one of C, AZ, BA, BB, AY, or a combination thereof in case the sample is obtained from colon, or any one of BM, BD, BH, D, M, V, U, F, BF, BE, E, U, BG, Z, X, W, Y, BC, BJ, O, J, N, BK, or a combination thereof in case the sample is obtained from the colon as represented in Fig.11. In even a further specific embodiment, wherein the subject has a non-inflammation status of the intestinal disorder UC or CD, and wherein the sample is obtained from the colon, the method comprises determining the expression of at least MUC mRNA isoform BJ, O, N, J and / or BK, or any combination thereof as represented in Fig.11. Particularly interesting mucin mRNA isoforms are those listed in Table 1 and 2 (i.e. intestinal mucin mRNA landscape), Fig.10 and Fig.11. In this regard, when reference is made to a particular mucin mRNA isoform (e.g. MUC4), the specific isoform ID can be selected from one or more mRNA isoforms mentioned in that list for MUC4. In a particular embodiment, the MUC4 mRNA isoform can be selected from any one or more of the following isoforms: Iso_00176220, Iso_00176219, Iso_00175826, Iso_00175821, Iso_00176208, Iso_00176203, Iso_00175824, or Iso_00175838. Some mRNA isoforms are known isoforms (e.g. Iso_00175826 = ENST00000349607.8.4) while others are previously unidentified sequences (e.g. Iso_00176219 = PB.1238.355 [SEQ ID 17]). In some embodiments, reference is made to letters referring to the specific mucin isoform number and associated transcript which can be used interchangeably throughout the description, for example: Further, when reference is made to determine the expression of a combination of mRNA isoforms originating from mucin genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof, it can be any combination of specific isoform ID or associated transcript as represented in Table 1 and Table 2, or as represented by Fig.10 or the letters in Figs.7-9 and 11. Accordingly, the present invention also provides the use of one or more of the following mRNA isoforms as set forth in Table 1 or Table 2 which are compatible for all mentioned embodiments in the determination of a disorder characterized by barrier dysfunction, in particular an intestinal disorder. Particularly interesting combinations are represented in any one or more of Fig.2E-H, Fig.3E-H, Fig. 4D-F, Fig.5E-H, Fig.6B, and Fig.7-11 or any one of Tables 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42. With respect to Figure 7-9, the letters (A-U), or with respect to Figure 11 (B-BM) refer to the specific mucin isoform and the size of the circle for each isoform indicates in how many panels it occurs. In a specific embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of: i) the combination of MUC mRNA isoforms as represented in Fig.2E, or Fig.2F, or Fig.2G, or Fig. 2H, or Fig.3G, or Fig.3H, or Fig.5F, or Fig. 6B, or Fig.10, or any combination thereof; in particular wherein the intestinal disorder is Crohn’s disease (CD); or ii) the combination of MUC mRNA isoforms as represented in Fig.3E, or Fig.3F, or Fig.5G, or Fig.5H, or Fig.10 or any combination thereof; in particular wherein the intestinal disorder is chronic inflammatory bowel disease (IBD); or iii) the combination of MUC mRNA isoforms as represented in Fig.2F, or Fig.4D, or Fig.4E, or Fig.4F, or Fig.5E, or Fig.5F, or Fig.10 or any combination thereof; in particular wherein the intestinal disorder is ulcerative colitis (UC). iv) the combination of MUC mRNA isoforms as represented in Fig. 8 or any combination thereof, in particular isoform D in combination with any one of isoform A, B, C, E to L, in particular isoform D in combination with any one of isoform A, B, C, E, F, G, H, I, and / or J, even more in particular isoform D in combination with any one of isoform A, B, C, and / or E, in particular wherein the intestinal disorder is Crohn’s disease (CD), more in particular in a subject having an inflamed status of CD; v) the combination of MUC mRNA isoforms as represented in Fig. 7 or any combination thereof, in particular isoform D in combination with any one of isoform A, B, C, E to U, even more in particular isoform D in combi any one of isoform A, B, C, F, G, and / or J, most in particular isoform D in combination with any of A, B, F, and / or J, in particular wherein the intestinal disorder is IBD, more in particular in a subject having an inflamed status of IBD; vi) the combination of MUC mRNA isoforms as represented in Fig. 9 or any combination thereof, in particular isoform D in combination with any one of isoform B, J, F, G, M, N, O, P, Q and / or A, even more in particular isoform D in combination with any one of isoform B, F, G, and / or J, most in particular isoform D in combination with any one of isoform B, D and / or J, in particular wherein the intestinal disorder is ulcerative colitis (UC), more in particular in a subject having an inflamed status of UC. In a preferred embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of: at least MUC4 mRNA isoform (D; PB.1238.363) in combination with MUC20 isoform (B; ENST00000447234.7), optionally in combination with MUC16 mRNA isoform (A; ENST00000397910.8), MUC1 isoform (C; ENST00000620103.4), and / or MUC1 isoform (G; ENST00000462317.5), in particular wherein the intestinal disorder is CD, IBD or UC, more in particular in a subject having an inflamed status of CD, IBD or UC. In a specific embodiment, the present invention provides an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery, said method comprises determining the expression of: i) the combination of MUC mRNA isoforms as represented in Fig.2E, or Fig.2F, or Fig.3F, or Fig. 4D, or Fig. 5E, or Fig. 5F, or Fig. 5G, or Fig. 10, or any combination thereof; in particular wherein said sample is obtained from the colon; or ii) the combination of MUC mRNA isoforms as represented in Fig.2H, or Fig.4F, or Fig.5E, or Fig.10, or any combination thereof; in particular wherein said sample is obtained from the distal colon; or iii) the combination of MUC mRNA isoforms as represented in Fig.3G, Fig.6B, or Fig.10, or any combination thereof; in particular wherein said sample is obtained from the ileum; or iv) the combination of MUC mRNA isoforms as represented in Fig.3H and / or or Fig.10; in particular wherein said sample is obtained from the proximal colon; or v) the combination of MUC mRNA isoforms as represented in Fig.2G, or Fig.3E, or Fig.4E, or Fig.5H, or a combination thereof; in particular wherein said sample is obtained from the rectum. In an alternative embodiment, the method comprises determining the expression of: the combination of MUC mRNA isoforms as represented in Fig. 2E, Fig. 2F, and / or Fig. 5F, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from A, B, C, and / or E as represented in Fig.8, wherein the intestinal disorder is CD and wherein the sample is obtained from the colon; or the combination of MUC mRNA isoforms as represented in Fig.2G, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from A, B, C, E, L and / or K as represented in Fig.8, wherein the intestinal disorder is CD and wherein the sample is obtained from the rectum; or the combination of MUC mRNA isoforms as represented in Fig.2H, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from A, B, C, E and / or F as represented in Fig.8, wherein the intestinal disorder is CD and wherein the sample is obtained from the distal colon; or the combination of MUC mRNA isoforms as represented in Fig.3G, and / or Fig.6B, or the combination of MUC mRNA isoforms comprising at least MUC4 isoform S (ENST00000349607.8 ; i.e. PB.1238.112) and any one isoform selected from C, G, R, T and / or U, or any combination thereof as represented in Fig.7, wherein the intestinal disorder is CD and wherein the sample is obtained from the ileum; or the combination of MUC mRNA isoforms as represented in Fig.3H, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from G, H, I, and / or J as represented in Fig.8, wherein the intestinal disorder is CD and wherein the sample is obtained from the proximal colon; or the combination of MUC mRNA isoforms as represented in Fig.3E and / or Fig.5H, wherein the intestinal disorder is IBD and wherein the sample is obtained from the rectum; or the combination of MUC mRNA isoforms as represented in Fig.3F and / or Fig.5G, wherein the intestinal disorder is IBD and wherein the sample is obtained from the colon; or the combination of MUC mRNA isoforms as represented in Fig.2F, Fig.4D, Fig.5E, and / or Fig.5F, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from B, F, G, J and / or M as represented in Fig.9, wherein the intestinal disorder is UC and wherein the sample is obtained from the colon; or the combination of MUC mRNA isoforms as represented in Fig.4E, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from B, F, G, J, A, O, P and / or Q, as represented in Fig.9, wherein the intestinal disorder is UC and wherein the sample is obtained from the rectum; or the combination of MUC mRNA isoforms as represented in Fig.4F and / or Fig.5E, or the combination of MUC mRNA isoforms comprising at least isoform D and any one isoform selected from B, J and / or N as represented in Fig.9, wherein the intestinal disorder is UC and wherein the sample is obtained from the distal colon. In an alternative embodiment, wherein the inflamed intestinal disorder is CD or UC and wherein the sample is obtained from the ileum or colon, the method comprises determining the expression of MUC1 mRNA isoform, in particular isoform G (ENST00000462317.5), optionally in combination with any one of A-F or H-U or a combination thereof as represented in Fig.7, in particular at least in combination with MUC4 isoform D (PB.1238.363). In another alternative embodiment, wherein the inflamed intestinal disorder is CD and wherein the sample is obtained from the ileum or colon, the me prises determining the expression of MUC1 mRNA isoform, in particular isoform C (ENST00000620103.4), optionally in combination with any one of A, B, D-U or a combination thereof as represented in Fig.7, in particular at least in combination with isoform G (ENST00000462317.5). In an alternative embodiment, wherein the intestinal disorder is CD and wherein the sample is obtained from the rectum, the method comprises determining the expression of MUC mRNA isoforms L and / or K, optionally in combination with any one of A, B, C, D, E or a combination thereof as represented in Fig.8. In an alternative embodiment, wherein the intestinal disorder is CD and wherein the sample is obtained from the distal colon, the method comprises determining the expression of MUC mRNA isoform F, optionally in combination with any one of A, B, C, D, E or a combination thereof as represented in Fig. 8. In an alternative embodiment, wherein the intestinal disorder is CD and wherein the sample is obtained from the proximal colon, the method comprises determining the expression of MUC mRNA isoforms G, H, I, J or a combination thereof, optionally in combination with D as represented in Fig.8. In an alternative embodiment, wherein the intestinal disorder is UC and wherein the sample is obtained from the colon, the method comprises determining the expression of MUC mRNA isoform M, optionally in combination with any one of B, D, F, G, J, or a combination thereof as represented in Fig.9. In an alternative embodiment, wherein the intestinal disorder is UC and wherein the sample is obtained from the rectum, the method comprises determining the expression of MUC mRNA isoforms A, O, P, Q, or a combination thereof, optionally in combination with any one of B, D, F, G, J, or a combination thereof, as represented in Fig.9. In an alternative embodiment, wherein the intestinal disorder is UC and wherein the sample is obtained from the distal colon, the method comprises determining the expression of MUC mRNA isoform N, optionally in combination with any one of B, D, J, or a combination thereof as represented in Fig.9. In one very specific embodiment, the method of the present invention comprises determining the expression of any isoform as represented in Fig.10, or any combination thereof; wherein the change in expression of said selected mucin mRNA isoforms as normalized to a reference value is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at least mRNA isoform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoform MUC 1 (ENST00000462317.5), MUC3A (PB.2118.153), MUC5AC (PB.2811.15) and / or MUC5B (ENST00000525715.5), in particular an increase in expression of any one of said MUC1, MUC5AC, and / or MUC5B isoforms, more in particular wherein the sample is obtained from the proxim and even more in particular wherein the intestinal disorder is CD. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at least mRNA isoform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoform MUC 1 (ENST00000462317.5), MUC1 (ENST00000338684.9), MUC1 (ENST00000620103.4), MUC1 (PB.381.4), and / or MUC20-OT1 (ENST00000631087.1), in particular determining an increase in expression in any one or more of said MUC1 isoforms and / or determining a decrease in expression of said MUC20-OT1 isoform, more in particular wherein the sample is obtained from the ileum and more even in particular wherein the intestinal disorder is CD. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at least mRNA isoform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoforms MUC1 (ENST00000620103.4), MUC2 (PB.2810.148), MUC12 (ENST00000473098.5), MUC16 (ENST00000397910.8), and / or MUC20 (ENST00000447234.7), in particular determining an increase in expression of any one or more of said MUC1, MUC2, MUC16 isoforms and / or determining a decrease in expression of any one or more of said MUC12, or MUC20 isoforms, more in particular wherein the sample is obtained from the distal colon and even more in particular wherein the intestinal disorder is CD. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at least mRNA isoform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoforms MUC1 (ENST00000620103.4), MUC2 (PB.2810.148), MUC12 (PB.2118.1621), MUC16(ENST00000397910.8), MUC20 (ENST00000447234.7), and / or MUC20 (ENST00000436408.6), in particular determining an increase in expression of any one or more of said MUC1, MUC4, MUC16 isoforms and / or determining a decrease in expression of any one or more of said MUC12 or MUC20 isoforms, more in particular wherein the sample is obtained from the rectum and even more in particular wherein the intestinal disorder is CD. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at least mRNA isoform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoform MUC5AC (PB.2811.15), MUC3A_MUC12 overlap (PB.2118.1322), and / or MUC20 (ENST00000447234.7), in particular determining an increase in expression of said MUC5AC isoform and / or determining a decrease in expression of any one or more of said MUC3A_MUC12 overlap, or MUC20 isoform, more in particular wherein the sample is obtained from the distal colon, and even more in particular wherein the intestinal disorder is UC. In a specific embodiment and as represented in Fig.10, the method of the present invention comprises determining an increase in expression of at leas soform MUC4 (PB.1238.363), optionally in combination with determining expression of any one of isoform MUC 1 (ENST00000462317.5), MUC5AC (PB.2811.15), MUC5B (PB.2816.52), MUC16( ENST00000397910.8), MUC12 (ENST00000473098.5), MUC12 (PB.2118.1409), MUC20 (ENST00000447234.7), and / or MUC20 (PB.1239.830), in particular determining an increase in expression in any one or more of said MUC1, MUC5AC, MUC5B, MUC16 isoforms and / or a decrease in expression of any one or more of said MUC12 or MUC20 isoforms, more in particular wherein the sample is obtained from the rectum, and even more in particular wherein the intestinal disorder is UC. In a specific embodiment, said change in expression level is at least 5%, such as at least 10%, at least 11%, at least 12%, at least 13%; at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%,in particular at least 20%, such as at least 21%, at least 22%, at least 23%, at least 24%, preferably at least 25%, at least 26%, at least 27%, at least 28%, at least 29% more preferably at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40% compared to said reference value. In another aspect, the present invention provides a combination of MUC4 mRNA isoforms, in particular PB.1238.363 and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7; optionally in combination with one or more of MUC1 mRNA isoforms, MUC2 mRNA isoforms, MUC5AC mRNA isoforms, MUC5B mRNA isoforms, MUC12 mRNA isoforms, MUC16 mRNA isoforms, in particular ENST00000397910.8; or MUC3A_MUC12 fusion gene mRNA isoforms, for use in the diagnosis of barrier damage to the intestinal tract and / or prediction of therapy response or recovery thereto. In a specific embodiment, the combination for use according to the invention further comprises one or more mRNA isoforms selected from the list comprising: MUC3A mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 isoforms. In a very specific embodiment, the present invention provides a combination of MUC4 mRNA isoforms, MUC2 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response or recovery thereto. In yet another embodiment, the present invention provides a combination of MUC4 mRNA isoforms, MUC5AC mRNA isoforms, MUC12 mRNA isoforms, MUC12-AS1 mRNA isoforms, and MUC20 mRNA isoforms for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response or recovery thereto. In a further embodiment, the present invention provides a combination of MUC4 mRNA isoforms, in particular PB.1238.363, MUC16 mRNA isoforms, in particular ENST00000397910.8, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7, optionally in combination with MUC1 mRNA isof articular ENST00000620103.4, for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response or recovery thereto. The invention also provides a diagnostic kit for performing the in vitro method according to present invention, said kit comprising agents for detecting the presence of at least 3 mucin mRNA isoforms wherein at least one of said 3 mRNA isoforms is a MUC4 mRNA isoform in combination with one or more mucin mRNA isoforms selected from the list comprising: MUC1, MUC2, MUC3A, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof. The term “diagnosing” as used herein means assessing whether a subject suffers from a disease as disclosed herein or not. As will be understood by those skilled in the art, such an assessment is usually not intended to be correct for all (i.e.100%) of the subjects to be identified. The term, however, requires that a statistically significant portion of subjects can be identified. The term diagnosis also refers, in some embodiments, to screening. Screening for diseases, in some embodiments, can lead to earlier diagnosis in specific cases and diagnosing the correct disease subtype can lead to adequate therapy. In another particular embodiment, the present invention provides a mucin mRNA isoform panel as defined herein, for use as a biomarker for diagnosis and disease surveillance or monitoring or recovery. By monitoring the progression or recovery by the change of mucin mRNA isoform status of the individual using the methods of the present invention, the clinician or practitioner is able to make informed decisions relating to the treatment or therapy approach adopted for any one individual. For example, in certain embodiments, it may be determined that patients having specific mucin mRNA isoforms may or may not react to a particular treatment or therapy. Thus, by monitoring the response of mucin mRNA isoform carriers to various treatment approaches using the methods of the present invention, it is also possible to tailor an approach which combines two or more treatments, each targeting different subsets of isoforms in the individual. The term “patient” is generally synonymous with the term “subject” and includes all mammals including humans. Preferably, the patient is a human. In another particular embodiment, the present invention provides mucin mRNA isoforms as defined herein, for use as a new therapeutic target. In particular, said mucin mRNA isoforms may be specifically targeted by monoclonal antibodies, small molecules or antisense technology or CAR-T technology. EXAMPLES EXAMPLE 1: Mucin mRNA isoform landscape in patients with inf bowel diseases (I Here, we unravelled the mucin mRNA isoform landscape in inflamed and non-inflamed ileal and colonic tissues from IBD patients using a targeted isoform sequencing approach to identify novel mucin mRNA isoform biomarker panels for the monitoring of IBD. Methods Sample collection IBD patients undergoing an endoscopy based on medical indications were recruited via the policlinic of the University Hospital of Antwerp (UZA). Ileal and colonic biopsies were collected from macroscopically inflamed and non-inflamed regions in patients undergoing endoscopy for the diagnosis or follow-up of IBD. Patients without a history of IBD undergoing an endoscopy due to a positive immunological fecal occult blood test (iFOBT) and without endoscopic abnormalities were included as controls. Biopsies were immediately submerged in RNA later and frozen in liquid nitrogen. Biopsies were stored at -80°C until RNA extraction. Approval for the study protocol was granted by the Ethics Committee of the UZA, Belgium. RNA isolation Total RNA was extracted from 106 intestinal biopsies using the Nucleospin RNA Plus kit. The purity of the RNA was assessed through spectrophotometric analysis with the NanoDrop ND-1000. Concentration and RNA quality were evaluated with the Qubit Fluorometer and 2100 Bioanalyzer. Multiplex targeted iso-seq library preparation and SMRT sequencing The PacBio sequel platform was used to sequence 106 intestinal biopsies randomly allocated in different batches. Barcoded oligo-dT primers were used to allow for multiplexing (maximum 12-plex) after which targeted capture was performed by using a custom-designed pool of probes (IDT), developed for the capture of MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC7, MUC12, MUC13, MUC15, MUC16, MUC17, MUC19, MUC20, MUC21 and MUC22 gene transcripts. After SMRTbell library preparation, the samples were sequenced on a SMRTcell 1M v3 LR tray. RNA-seq library preparation and Illumina sequencing Total RNA from 48 intestinal biopsies was also used to obtain a poly-A enriched library for bulk RNA sequencing on the Illumina NovaSeq 6000 platform (v1.5 Reagent kit) with 150 bp paired-end reads. Bioinformatics analysis Public datasets Publicly available datasets GSE165512 (170 samples) [2] and GSE193677 (2489 samples) [3] comprising Illumina short read sequencing data o nd ileal biopsies of IBD and control patients were retrieved from the Gene Expression Omnibus (GEO) with the sratoolkit (v3.0.0). From the GSE193677 dataset we removed 36 samples. All Illumina short read data was trimmed with fastP (v0.20.0) prior to the analysis. PacBio Iso-seq and combined MUC transcriptome assembly PacBio Iso-seq raw reads were analysed using the IsoSeq 3 pipeline in Linux bash. In short, starting from the raw sequencing reads from SMRTlink, circular consensus sequences (CCS) reads were generated (ccs, v6.4.0). From the resulting isoform sequences (≥Q20), primers were removed and the samples demultiplexed (lima, v2.6.0). Poly(A) tails and concatemers were removed from the obtained full-length reads (isoseq refine, v3.8.0) and successively, the full-length non-concatemer reads were clustered (isoseq cluster, v3.8.0). The resulting high-quality isoforms were aligned to the human genome assembly GRCh38 (pbmm2, v1.9.0) and redundant isoforms collapsed in order to obtain count information on unique isoforms (coverage 99% and identity 95%, isoseq collapse, v3.8.0). For further classification, quality control and rigorous filtering (Figure 1A) of the isoforms, SQANTI3 (v3.5.1) was used in conjunction with supporting short reads (Illumina) from a subset of 48 samples also sequenced on the PacBio platform and from the publicly available dataset GSE165512 by using STAR (v2.7.10a) and Kallisto (v0.48.0). In addition to the default SQANTI3 filter, we incorporated four supplementary rules being that all isoforms should have a count higher or equal to two in three or more PacBio sequenced samples, have an expression higher than zero according to the Illumina sequenced samples (except when the transcript is classified as a full-splice match), are bite negative and map to a mucin gene. Failure to comply with one of these rules causes the isoform to be filtered out. The obtained mucin intestinal transcriptome was merged with the human reference transcriptome GRCh38 (Gencode release 42) by using gffcompare (v0.12.6). Classification random forest Bulk RNA sequencing data from the GSE193677 dataset was quantified based on the transcripts present in the combined MUC transcriptome (Kallisto v0.48.0) for colon and ileum samples separately. Only MUC isoforms with a minimal count of 5 in 30 or more samples were retained and transcripts of which the expression was highly correlated (>75%) were removed (caret v6.0.94). The GSE193677 dataset was split in train and test datasets. GSE165512 was used as external validation dataset. For model training, the data was balanced when necessary. On the training dataset, important MUC isoforms were identified based on a random forest algorithm adapted from Brieuc et al. [3]. In short, for each binary comparison, importance values for every MUC isoform is estimated with a random forest algorithm. Based on their importance, MUC isoforms are divided in groups. The group with the lowest out-of-bag error rate is selected and used for backwards purging to obtain the final MUC isoform selection for that specific classification. To minimize the chance on overfitting, the number of isoforms used for each classification was optimized by selecting the panel with the fewest isoforms within the 2% range of the panel with the lowest OOB-ER. Subsequently, this panel was used to classify the samples in the training, test and external validation data. Results Mucin transcriptome characterisation Intestinal mucin transcriptome Through targeted PacBio Iso-Seq of intestinal biopsies from IBD and control patients, a total of 20,206 unique isoforms were identified. After rigorous filtering, 877 isoforms were retained, from which 208 transcripts (henceforth referred to as the intestinal mucin transcriptome) originated from a MUC-gene (Figure 1A). More specifically, the intestinal mucin transcriptome consists of isoforms derived from MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC7, MUC12, MUC13, MUC17 and MUC20. In addition, one transcript mapped to the MUC20 pseudogene MUC20P1, one mapped to a not previously identified region on the antisense strand at the chromosomal location of MUC2 (MUC2- AS), two transcripts contained exons from both MUC3A and MUC12 (MUC3A_MUC12) and one contained exons that mapped to sequences in both MUC20 and MUC20-OT1 (MUC20_MUC20-OT1). Isoform lengths remained relatively stable between the different MUC genes in the intestinal mucin transcriptome (Figure 1B, C). The exon count was similar between MUC isoforms in the reference and the intestinal mucin transcriptome (Figure 1D). The majority of the isoforms in the intestinal mucin transcriptome were predicted to be coding for a protein (Figure 1E), in contrast to the reference mucin transcriptome, where the isoforms are more evenly distributed between being coding or non-coding (Figure 1F). Combined MUC transcriptome Upon merging the human reference transcriptome (Gencode v42), containing 268 MUC transcripts, with our intestinal mucin transcriptome, the combined MUC transcriptome consisted of 386 unique MUC isoforms. After mapping the Illumina bulk RNA seq data of the GSE193677 dataset to this combined transcriptome and removal of lowly expressed transcripts, 289 MUC isoforms were found in the colonic biopsies and 261 MUC isoforms exceeded the expression threshold in the ileum biopsies. Random forest classification using combined MUC transcriptome To assess whether the isoforms within the combined MUC transcriptome can be used as biomarkers to distinguish biopsies from inflamed regions of CD and UC patients from each other, and from control patient biopsies without inflammation, we selected a specific MUC isoform panel for each comparison based on their OOB-ER. This isoform panel was then used to train a random forest model for binary classification. The discriminative performance of each model is presented as ROC curves along with expression values of the MUC isoforms which were used to train the model (Figures 2 – 6). An overview of the identified mucin mRNA isoforms is shown in Table 1. General IBD classification Feature selection used to distinguish IBD patients with colonic inflammation from non-inflamed colon in control patients resulted in a panel of ten MUC isoforms (Figure 3F; Table 1). The random forest model trained with this panel performed well in the train and test dataset (AUC 92.3% and 92.5% respectively), but its performance decreased in the external validation dataset to an AUC of 53.9% (Figure 3B). The panels identified to compare inflamed colonic bi CD and UC patients with control patients separately consisted of five (Figure 2E; Table 1) and six (Figure 4D; Table 1) MUC isoforms, respectively. The AUC of CD versus control in the external validation dataset increased to 59.2%, whereas the AUC of the train- and testdata was 89.1% and 86.6% (Figure 2A & E; Table 1). For UC versus C the AUC for the external validation increased to 74.1%. The AUC for the train and test data was 93.0% and 89.3% (Figure 4A &D; Table 1). Interestingly, we also applied an external RNA data set of colorectal cancer (CRC) patients on the UC versus control colon inflamed model (Figure 5A) and identified an AUC of 61.1% to distinguish CRC patients from control patients. This highlights the potential of the UC-specific colonic inflamed isoform panel (Figure 5D) for the stratification of CRC patients as well. The AUC of the model when distinguishing CD-derived inflamed colonic biopsies from UC-originating inflamed colonic biopsies was 74.9%, 57.1% and 53.3% for the train, test and external validation data, respectively (Figure 2B &F; Table 1). Training the model to distinguish non-inflamed colonic biopsies of IBD patients from control patients based on MUC isoform expression resulted in an AUC of 78.4% for the train data and 68.2% test data (Figure 5C &G; Table 1). When only training the model on rectal samples of IBD patients, AUC of 81.1% and 69.9% were obtained for train and test data respectively (Figure 5D &H; Table 1). For the comparison between non-inflamed colonic samples from CD and UC patients this was 72.9% and 56.9% respectively (Figure 5B & F; Table 1). Region-specific CD classification Based on the previous results, we further investigated if the random forest classification could be improved by only using biopsies from specific colonic regions or the terminal ileum. When only using the biopsies from the proximal colon (i.e. caecum, ascending and transverse colon) of CD patients, the AUC of the train and test dataset were respectively 94.0% and 75.9%. The AUC of the external validation data was 60.6% (Figure 3D & H; Table 1) . When using biopsies from the distal colon (i.e. descending colon, sigmoid and rectum) from CD patients instead, the AUC when applying the random forest model to the train, test and external validation datasets was respectively 91.1%, 96.0% and 55.9% (Figure 2D &H; Table 1). Upon using only rectal biopsies from CD patients for model training, the AUC of the external validation increased to 61.1%. The performance of the model on the train and test dataset (AUC 94.8% and 86.6%; Figure 2C & G; Table 1) were in line with results from the proximal and distal colon. Distinguishing CD patients from control patients based on MUC isoform expression of inflamed ileal biopsies proved effective with AUC for train, test and external validation data being 91.1%, 89.0% and 74.5% respectively (Figure 3C & G; Table 1). When performing the same comparison but with non- inflamed ileal biopsies of CD patients, AUC of train and test data was 80.8% and 64.4% respectively (Figure 6A & B; Table 1). Region-specific UC classification Due to the nature of the disease, inflamed colonic biopsies of ulcerative colitis patients were predominantly present in the distal colon. Random forest models trained solely on biopsies from the distal colon performed well on the train, test and external validation datasets (AUC 93.3%, 95.0% and 76.6% respectively) (Figure 4C& F; Table 1). Only training on mucin isoform expression data originating from the rectal biopsies resulted in minor changes in the AUC of the train and test dataset (95.3% and 94.5% respectively) while the AUC of the external validation data decreased to 65.0% (Figure 4B & E; Table 1) For the classification of non-inflamed biopsies from the distal colon of UC patients and control patients an AUC of 82.3% and 76.6% was obtained for the train and test data, respectively (Figure 5A & E; Table 1). Table 1. Overview of all isoforms used in the prediction models and their associated isoform identifier.

[0002] In the context of the present invention, the DNA sequences of the above table may also be replaced by the corresponding RNA sequences in which ‘T’ is replaced by ‘U’ in the sequences as defined herein. EXAMPLE 2: Mucin mRNA isoform landscape in patients with inflammatory bowel diseases (IBD) METHODS Mucin RNA isoform landscape discovery and model building based on Random Forest classification: See Example 1. GSE83687 (134 samples), comprising Illumina short read sequencing data of colonic and ileal biopsies of IBD and control patients and retrieved from the Gene Expression Omnibus (GEO) using the sratoolkit (v3.0.0), was used as a dataset for external validation. Results Mucin RNA isoform features as discriminators for general IBD and subtype classification To determine whether mucin RNA isoforms can be used as discriminators to classify biopsies derived from IBD patients and its subtypes (i.e. UC and CD) in the presence / absence of inflammation from control patients, Random Forest-based feature selection was carried out on the combined mucin RNA isoform landscape extracting specific mucin RNA isoform panels associated with IBD, UC or CD compared to control patients based on their OOB-ER. An equal distribution of sex between the groups for each model and no significant correlation between the expression of mucin isoforms, selected for the panels, and age was found. The expression level of each mucin RNA isoform in the panel was then used to train, test, and validate the model for binary classification. The discriminative performance and the expression levels of the mucin RNA isoforms of each respective panel are shown Tables 3-42. The characteristics of the combined mucin RNA isoform landscape are summarized in Table 2. The mucin RNA isoforms occurring throughout both the inflamed and non-inflamed panels are schematically depicted as Venn diagrams in Figs.7-11. Feature selection to distinguish IBD patients with colonic inflammation from control patients without inflammation in their intestinal tract unveiled a panel of 10 mucin RNA isoforms originating from 8 different mucin genes and half of them were identified as novel (Table 3 and 4 and Table 2). This panel performed well in the training and test dataset (AUC of 92.3% and 92.5% respectively). Its performance decreased slightly in the external validation dataset to an AUC of 72.2% (Table 3). All 10 isoforms were significantly increased in the IBD cohort compared to the control patients, except for the MUC20 (ENST00000447234.7) and MUC12 (ENST00000473098.5) RNA isoforms which were significantly downregulated in the IBD patient group (Table 4). By using the same approach, we identified several panels to distinguish UC and CD patients from control patients. These included a panel of 6 mucin RNA isoforms that accurately discriminated inflamed colonic biopsies of UC patients from non-inflamed colonic control biopsies (i.e. AUC of 93.0% (based on the training data), AUC of 89.3% (test data); Tables 2,5-6), a panel of 5 mucin RNA isoforms as major determinant for inflammation in the colon of CD patients (AUC of 89.1% (training data), AUC of 86.6% (test data); Tables 2, 7-8) and a panel of 6 mucin RNA isoforms that associated with inflammation in the ileum of CD patients compared to control patients (AUC of 91.1% (training data), AUC of 89.0% (test data); Tables 2, 9-10). Within these panels, each mucin RNA isoform originated from a different mucin gene (Tables 6-8) except for the CD ileum inflamed panel where 4 RNA isoforms originated from the MUC1 gene (Table 10). Performance of the UC colon and CD colon inflamed models when applied to the external validation dataset remained remarkably high (i.e. AUC-values of 89.0% and 77.2%, respectively; Tables 5 and 7). Interestingly, the MUC4 (PB.1238.363) and MUC20 (ENST00000447234.7) RNA isoforms were shared by the UC colon inflamed and CD colon inflamed panels (Tables 6, 8; Figs.7-10) whereas the MUC1 RNA isoform (ENST00000462317.5) was common between the UC colon inflamed and CD ileum inflamed panels (Tables 6, 10; Figs.7-10) and the MUC1 RNA isoform (ENST00000620103.4) between the CD colon inflamed and CD ileum inflamed panels (Tables 8, 10; Figs.7-10). Most of the mucin RNA isoforms from the three models were upregulated upon inflammation in the UC or CD group (Tables 6, 8 and 10). Only the MUC12 (ENST00000473098.5; UC colon inflamed panel; Table 6), MUC20 (ENST00000447234.7; UC and CD colon inflamed panel; Tables 6, 8) and MUC20-OT1 (ENST00000631087.1; CD inflamed ileum panel; Tables 10) RNA isoforms were downregulated in the presence of inflammation. In addition, we also designed prediction models to classify IBD patients from control patients in the absence of inflammation. However, due to the absence of non-inflamed biopsies in the IBD cohort of the external validation dataset, ROC curves and AUC values could only be obtained for the training and test data. Training the model to distinguish non-inflamed colonic biopsies of IBD patients from non- inflamed control biopsies based on a panel of 10 mucin RNA isoforms resulted in an AUC of 78.4% for the training data and 68.2% for the test data. Interestingly, MUC5AC (PB.2811.15) that resided in the IBD colon inflamed panel was also found to be overexpressed in the IBD non-inflamed panel (Tables 2, 4, 23-24). In addition, the MUC5B (ENST00000525715.5, ENST00000527802.1 and PB.2816.52), 8.1123) and MUC2 (PB.2810.148) RNA isoforms were also overexpressed in the non-inflamed IBD group, while MUC20-OT1 (ENST00000446521.1) was downregulated (Table 24). Performance of the models distinguishing betwee amed biopsies from CD or UC patients and control patients was similar in the test and training datasets (Tables 25-28). Only the MUC5AC (PB.2811.15) and MUC20 (ENST00000447234.7) RNA isoforms of the UC colon inflamed panel (Table 6) were also identified in the UC colon non-inflamed panel (Table 26), whereas the MUC2 (PB.2810.148) and MUC1 (ENST00000620103.4) RNA isoforms were shared among the CD colon and ileum inflamed / non-inflamed panels, respectively (Tables 2, 8, 10, 28 and 30). Notably, the MUC5AC (PB.2811.15) RNA isoform was overexpressed and MUC20 (ENST00000447234.7) RNA isoform downregulated in UC patients compared to the control group independent of inflammation (Tables 6 and 26). In the biopsies of CD patients, the MUC1 (ENST00000620103.4) and MUC2 (PB.2810.148) RNA isoforms were upregulated in both the inflamed and non-inflamed biopsies compared to the controls (Tables 8, 10, 28 and 30). Setting up a prediction model that distinguished between colonic biopsies from CD and UC patients in the presence / absence of inflammation was shown to be difficult as reflected by the lower AUC values for the different datasets (Tables 11 and 21). Both panels encompassed a high number of mucin RNA isoforms (Tables 12 and 32), particularly in the presence of inflammation, in which the majority of isoforms was not differentially expressed. Region-specific mucin isoform panels for UC and CD patient subpopulation stratification One of the key features that attribute to disease heterogeneity is the variable inflammatory pattern expressed in the intestinal tract of IBD patientsKlik of tik om tekst in te voeren.. More specifically, UC patients have a more uniform mucosal inflammation that starts in the rectum and further extends towards the distal part of the colon whereas patchy and transmural inflammatory areas are seen in the terminal ileum and throughout the colon of CD patients. Here, we further investigated if the Random Forest approach for IBD subtype classification could be improved when integrating the colonic disease location, i.e. proximal colon (encompassing caecum, ascending and transverse colon), distal colon (encompassing descending colon, sigmoid and rectum), and rectum (tables 13-42). Feature selection to distinguish UC patients with inflammation in the distal colon from control patients unveiled a panel of 4 differentially expressed mucin RNA isoforms with similar high performance (i.e. AUC-values of 93.3% (training data), 95.0% (test data) and 89.5% (external validation data); tables 2,13-14) compared to the UC colon inflamed panel (table 6). Interestingly, the MUC4 (PB.1238.363), MUC5AC (PB2811.15) and MUC20 (ENST00000447234.7) RNA isoforms were common in both panels (tables 6, 14; Fig.9). The prediction model built to discriminate UC patients with rectal inflammation from control patients revealed a panel of 9 differentially expressed mucin RNA isoforms (tables 2, 15 and 16), of which 5 were common with the UC colon inflamed panel (tables 14, 16; Fig.9) and 3 with the UC distal colon inflamed panel (tables 14, 16. Fig.9). The panel for discriminating inflamed rectal biopsies of UC patients with non-inflamed control biopsies also performed very well in the training, test and external validation datasets with an AUC of 95.3%, 94.5% and 96.1%, respectively (table 15) (note that for the rectal UC inflamed model, all distal colonic UC samples (including sigmoid and colon descendens) were used for external validation due to an insufficient number of rectal biopsies in this dataset). When training the Random Forest model to distinguish, inflamed proximal colon biopsies of CD patients from their non- inflamed control counterpart, the AUC decreased to 75.9% in the test dataset and 61.9% in the external validation dataset (table 17). However, the isoform build to discriminate inflamed distal colon or rectal biopsies of CD patients from their non-inflamed control counterparts, demonstrated a slightly improved performance for the training (distal colon: AUC = 91.1%; rectum: AUC = 94.8%; tables 19 and 21), test (distal colon: AUC = 96.0%; rectum: AUC = 86.6%; tables 19 and 21) and external validation datasets (distal colon: AUC = 78.3%; rectum: AUC = 81.6%; tables 19 and 21) compared to the CD colon inflamed model (table 7) (also for the rectal CD inflamed model, all distal colonic CD samples (including sigmoid and colon descendens) were used for external validation due to an insufficient number of rectal biopsies in this dataset). The isoforms in all three region-specific CD models were differentially expressed except for the MUC3A (PB.2118.153) RNA isoform in the CD proximal colon inflamed panel and the MUC2 (PB.2810.148) RNA isoform in the CD rectum inflamed panel (tables 18 and 22). Interestingly, the CD colon distal inflamed and rectum inflamed panels encompassed all mucin RNA isoforms from the CD colon inflamed panel, in addition to 1 (MUC12: ENST00000473098.5) and 2 (MUC12: PB.2810.148; MUC20: ENST00000436408.6) RNA isoforms, respectively (tables 2, 8, 20 and 22; Fig.8). On the contrary, the CD proximal colon inflamed panel consisted of completely different mucin RNA isoforms (n = 5), except for the MUC4 (PB.1238.363) RNA isoform, compared to the CD colon inflamed panel (tables 2, 18; Fig.8). Finally, we also investigated the performance of the region-specific UC and CD models in the absence of inflammation. Similarly, and due to the absence of non-inflamed biopsies in the UC and CD cohorts of the external validation dataset, ROC curves and AUC values could only be obtained for the training and test datasets (tables 33-42). Distinguishing region-specific non-inflamed biopsies in the colon of UC and CD patients compared to control patients resulted in high AUC values for the training data but performance decreased in the test data, specifically for UC and CD rectum models (tables 33-42). The UC distal colon non-inflamed panel contained 3 mucin RNA isoforms (MUC3A_MUC12 (PB.2118.1322), MUC5AC (PB.2811.15) and MUC20 (ENST00000447234.7)) which also resided in the UC distal colon inflamed panel but with MUC3A_MUC12 (PB.2118.1322) no longer being downregulated (tables 14 and 34), whereas all mucin RNA isoforms from the UC rectum non-inflamed panel were differentially expressed and occurred in the UC rectum inflamed panel (tables 16 and 36). On the contrary, the CD proximal inflamed and non-inflamed panels had no mucin RNA isoforms in common (tables 18 and 38). Of all 13 mucin RNA isoforms in the CD distal colon non-inflamed panel, only the MUC12 (ENST00000473098.5) RNA isoform was also present (and downregulated) in the CD distal colon inflamed panel (tables 20 and 40). Of the 23 RNA isoforms from the CD rectum non- inflamed panel, only the MUC4 (PB.1238.363) RNA isoform was present (and upregulated) in its inflamed counterpart (tables 22 and 42) Furthermore, the MUC4 (PB.1238.363) and MUC12 (ENST00000473098.5) RNA isoforms were respectively up- and downregulated in both their inflamed and non-inflamed CD region-specific panels (tables 20, 22, 41 and 42). Structural characterization of abundant mucin RNA isoforms in IBD Several mucin RNA isoforms frequently occurred throughout the different panels highlighting their importance for further investigation. More specifically, the MUC1 RNA isoform ENST00000462317.5 appeared in the panels comparing inflamed biopsies of CD ileal, CD proximal, UC colonic and UC rectal with (region-matched) non-inflamed control biops 7-10). Interestingly, this 7 exon-long MUC1 (ENST00000462317.5) RNA isoform lacks the first 2 exons compared to the canonical MUC1 (ENST00000620103.4) isoform, which encodes for a part of the extracellular region and gains 1 exon near the 3’ end of the transcript. The canonical MUC1 (ENST00000620103.4) RNA isoform also appeared in different panels, however its presence was limited to the CD inflamed panels, with the exception of the CD proximal colon inflamed panel (Fig.8), and to the CD non-inflamed ileum panel (Fig.11). In all models comparing inflamed IBD with non-inflamed control colonic biopsies, the MUC4 (PB.1238.363) RNA isoform was selected by the feature selection procedure suggesting its high discriminative value (Fig.7-10). In addition, MUC4 (PB.1238.363) also appeared in the CD rectum non- inflamed panel (Fig. 11). Compared to the 25 exon-long canonical MUC4 (ENST00000463781.8) sequence, MUC4 (PB.1238.363) comprises only 7 exons and misses a large part at its 3’ end which encodes the intracellular, transmembrane and part of the extracellular region. Since it also contained novel splice sites, it was categorised as a “novel_not_in_catalog” isoform (Table 2). The canonical MUC20 (ENST00000447234.7) and novel MUC5AC (PB.2811.15) RNA isoforms occurred with a high frequency in the inflamed colon of CD and UC panels, while also being present in some non-inflamed panels for UC (MUC20 (ENST00000447234.7)) or both CD and UC (MUC5AC (PB.2811.15)) (Figs.7- 11). MUC20 (ENST00000447234.7) is a relatively small isoform, only having 4 exons, which stands in steep contrast with many other isoforms like MUC5AC (PB.2811.15) having 17 exons. Identical to MUC4 (PB.1238.363), the MUC5AC (PB.2811.15) RNA isoform was categorised as “novel_not_in_catalog” due to the presence of splice sites that were previously not identified for MUC5AC. In addition, this isoform lacks a major part at its 5’ end thereby missing the sequence that encodes for the signal peptide, several Von Willebrand factor type D domains and the PTS domain, rich in proline, threonine and serine34. Finally, like MUC20 (ENST00000447234.7) and MUC1 (ENST00000620103.4), the 84 exon-long MUC16 (ENST00000397910.8) occurred in all inflamed colonic CD panels, except for the proximal colonic panels (Fig. 8), and was also present in the UC rectum inflamed panel (Fig.9 and 10). Of note, a large number of unique mucin RNA isoforms were identified in the UC and CD non-inflamed panels (Fig.11), suggesting the Random Forest approach has difficulty in finding discriminative isoforms to classify the non-inflamed IBD subgroups and the control patients from one another.

[0003] -34- Table 2: Characteristics of MUC isoform landscape with expression in the colon and / or ileum. Features of known isoforms were extracted from the Gencode v42 annotation. Chr, Chromosome; CDS, coding sequence Table 3: inflamed colonic biopsies of IBD patients (nTrain= 272; nTest= 93; next. val.= 42) versus non-inflamed colonic biopsies of control patients (nTrain= 272; nTest= 67; next. val.= 49). Overview 5 of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. 10 Table 4: inflamed colonic biopsies of IBD patients (nTrain = 272; nTest = 93; next. val. = 42) versus non-inflamed colonic biopsies of control patients (nTrain = 272; nTest = 67; next. val. = 49). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon 5 inflammation for training data (80% of GSE193677). Differential mucin isoform expression was assessed using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 5: inflamed colonic biopsies of UC patients (nTrain= 191; nTest= 47; next. val.= 30) vs non- 10 inflamed colonic biopsies of control patients (nTrain= 191; nTest= 67; next. val.= 49). Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. 15 Table 6: inflamed colonic biopsies of UC patients (nTrain= 191; nTest= 47; next. val.= 30) vs non- inflamed colonic biopsies of control patients (nTrain= 191; nTest= 67; next. val.= 49). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). Differential mucin isoform expression was assessed using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni 20 method. Table 7: inflamed colonic biopsies of CD patients (nTrain = 182; nTest = 45; next. val. = 12) vs non- inflamed colonic biopsies of control patients (nTrain = 182; nTest = 67; next. val. = 49). Overview of 5 model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. Table 8: inflamed colonic biopsies of CD patients (nTrain= 182; nTest= 45; next. val.= 12) vs non- inflamed colonic biopsies of control patients (nTrain = 182; nTest = 67; next. val. = 49). Mucin RNA 10 isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). Differential mucin isoform expression was assessed using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 15 Table 9: inflamed ileal biopsies of CD patients (nTrain = 97; nTest = 30; next. val. = 30) vs non-inflamed ileal biopsies of control patients (nTrain = 97; nTest = 24; next. val. = 11). Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation 5 (GSE83687) datasets. Table 10: inflamed ileal biopsies of CD patients (nTrain= 97; nTest= 30; next. val.= 30) vs non- inflamed ileal biopsies of control patients (nTrain= 97; nTest= 24; next. val.= 11). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation 10 for training data (80% of GSE193677). Differential mucin isoform expression was assessed using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 11: inflamed distal colonic biopsies of CD patients (nTrain = 120; nTest = 38; next. val. = 9) vs inflamed distal colonic biopsies of UC patients (nTrain= 120; nTest= 29; next. val.= 27). Overview of 15 model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. Table 12: inflamed distal colonic biopsies of CD patients (nTrain= 120; nTest= 38; next. val.= 9) vs inflamed distal colonic biopsies of UC patients (nTrain = 120; nTest = 29; next. val. = 27). Mucin RNA 20 isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). Differential mucin isoform expression was assessed using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 13: Distal colonic biopsies: UC inflamed vs control. Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. inflamed distal colonic biopsies of UC patients (nTrain = 155; nTest = 38; next. val. = 27) vs 5 non-inflamed biopsies of control patients (nTrain = 155; nTest = 46; next. val. = 23). Table 14: Distal colonic biopsies: UC inflamed vs control. Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data 5 (80% of GSE193677). inflamed distal colonic biopsies of UC patients (nTrain = 155; nTest = 38; next. val.= 27) vs non-inflamed biopsies of control patients (nTrain= 155; nTest= 46; next. val.= 23). Differential mucin isoform expression was determined using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 10 Table 15: Rectal colonic biopsies: UC inflamed vs control. Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. inflamed rectal biopsies of UC patients (nTrain= 94; nTest= 23; next. val.= 27) vs non- inflamed biopsies of control patients (nTrain= 94; nTest= 44; next. val.= 23) (the external validation consisted of all distal colon samples to increase the sample size). 15 Table 16: Rectal colonic biopsies: UC inflamed vs control. Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). inflamed rectal biopsies of UC patients (nTrain = 94; nTest = 23; next. val. = 27) vs non-inflamed biopsies of control patients (nTrain= 94; nTest= 44; next. val.= 23) (the external 20 validation consisted of all distal colon samples to increase the sample size). Differential mucin isoform expression was determined using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 17: Proximal colonic biopsies: CD inflamed vs control. Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. inflamed proximal colonic biopsies of CD patients (nTrain = 63; nTest = 15; next. val. = 2) vs 5 non-inflamed proximal colonic biopsies of control patients (nTrain= 63; nTest= 21; next. val.= 21). Table 18: Proximal colonic biopsies: CD inflamed vs control. Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). inflamed proximal colonic biopsies of CD patients (nTrain = 63; nTest = 10 15; next. val. = 2) vs non-inflamed proximal colonic biopsies of control patients (nTrain = 63; nTest = 21; next. val.= 21). Differential mucin isoform expression was determined using the Wilcoxon rank- sum test corrected for multiple testing using the Bonferroni method. Table 19: Distal colonic biopsies: CD inflamed vs control. Overview of model performance for 15 training (80% of GSE193677), test (20% of GSE193677) and external validation (GSE83687) datasets. inflamed distal colonic biopsies of CD patients (nTrain = 120; nTest = 29; next. val. = 9) vs non-inflamed distal colonic biopsies of control patients (nTrain= 120; nTest= 46; next val= 23). Table 20: Distal colonic biopsies: CD inflamed vs control. Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data 5 (80% of GSE193677). inflamed distal colonic biopsies of CD patients (nTrain = 120; nTest = 29; next. val.= 9) vs non-inflamed distal colonic biopsies of control patients (nTrain= 120; nTest= 46; next.val.= 23). Differential mucin isoform expression was determined using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 10 Table 21: Inflamed rectal biopsies of CD patients (nTrain = 80; nTest = 20; next. val. = 9) vs non- inflamed rectal biopsies of control patients (nTrain= 80; nTest= 44; next. val.= 23) (the external validation consisted of all distal colon samples to increase the sample size). Overview of model performance for training (80% of GSE193677), test (20% of GSE193677) and external validation 15 (GSE83687) datasets. Table 22: Inflamed rectal biopsies of CD patients (nTrain= 80; nTest= 20; next. val.= 9) vs non- inflamed rectal biopsies of control patients (nTrain= 80; nTest= 44; next. val.= 23) (the external 20 validation consisted of all distal colon samples to increase the sample size). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training data (80% of GSE193677). Differential mucin isoform expression was determined using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 23: Non-inflamed colonic biopsies of IBD patients (nTrain= 272; nTest= 82) vs non-inflamed colonic biopsies of control patients (nTrain = 272; nTest = 67). Mucin RNA isoform expression levels 5 as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. Table 24: Non-inflamed colonic biopsies of IBD patients (nTrain = 272; nTest = 82) vs non-inflamed colonic biopsies of control patients (nTrain = 272; nTest = 67). Differential mucin isoform expression 10 was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 25: Non-inflamed colonic biopsies of UC patients (nTrain = 168; nTest = 41) vs non-inflamed colonic biopsies of control patients (nTrain = 168; nTest = 67). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. 5 Table 26: Non-inflamed colonic biopsies of UC patients (nTrain = 168; nTest = 41) vs non-inflamed colonic biopsies of control patients (nTrain= 168; nTest= 67). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 10 Table 27: Non-inflamed colonic biopsies of CD patients (nTrain = 167; nTest = 41) vs non-inflamed colonic biopsies of control patients (nTrain = 167; nTest = 67). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. 15 Table 28: Non-inflamed colonic biopsies of CD patients (nTrain= 167; nTest= 41) vs non-inflamed colonic biopsies of control patients (nTrain = 167; nTest = 67). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the 20 Bonferroni method. Table 29: Non-inflamed ileal biopsies of CD patients (nTrain = 82; nTest = 20) vs non-inflamed ileal biopsies of control patients (nTrain = 82; nTest = 24). 5 Table 30: Non-inflamed ileal biopsies of CD patients (nTrain= 82; nTest= 20) vs non-inflamed ileal biopsies of control patients (nTrain = 82; nTest = 24). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 10 Table 31: Non-inflamed distal colonic biopsies of CD patients (nTrain= 112; nTest= 27) vs non- inflamed distal colonic biopsies of UC patients (nTrain = 112; nTest = 46). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. 15 Table 32: Non-inflamed distal colonic biopsies of CD patients (nTrain = 112; nTest = 27) vs non- inflamed distal colonic biopsies of UC patients (nTrain = 112; nTest = 46). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 33: Non-inflamed distal colonic biopsies of UC patients (nTrain = 116; nTest = 29) vs non- 5 inflamed biopsies of control patients (nTrain = 116; nTest = 46). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. Table 34: Non-inflamed distal colonic biopsies of UC patients (nTrain = 116; nTest = 29) vs non- 10 inflamed biopsies of control patients (nTrain= 116; nTest= 46). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 35: Non-inflamed rectal biopsies of UC patients (nTrain = 84; nTest = 20) vs non-inflamed biopsies of control patients (nTrain = 84; nTest = 44). Mucin RNA isoform expression levels as 5 variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. Table 36: Non-inflamed rectal biopsies of UC patients (nTrain = 84; nTest = 20) vs non-inflamed biopsies of control patients (nTrain= 84; nTest= 44). Differential mucin isoform expression was 10 determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 37: Non-inflamed proximal colonic biopsies of CD patients (nTrain = 56; nTest = 13) vs non- inflamed proximal colonic biopsies of control patients (nTrain = 56; nTest = 21). Mucin RNA isoform 15 expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation for training (80% of GSE193677) and test (20% of GSE193677) data. Table 38: Non-inflamed proximal colonic biopsies of CD patients (nTrain = 56; nTest = 13) vs non- inflamed proximal colonic biopsies of control patients (nTrain= 56; nTest= 21). Differential mucin 20 isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. Table 39: Non-inflamed distal colonic biopsies of CD patients (nTrain= 112; nTest= 17) vs non- inflamed distal colonic biopsies of control patients (nTrain= 116; nTest= 29). Mucin RNA isoform expression levels as variables associated with IBD and subtypes (UC or CD) upon inflammation 5 for training (80% of GSE193677) and test (20% of GSE193677) data. Table 40: Non-inflamed distal colonic biopsies of CD patients (nTrain = 112; nTest = 17) vs non- inflamed distal colonic biopsies of control patients (nTrain = 116; nTest = 29). Differential mucin isoform expression was determined by using the Wilcoxon rank-sum test corrected for multiple 10 testing using the Bonferroni method. Table 41: Non-inflamed rectal biopsies of CD patients (nTrain = 76; nTest = 18) vs non-inflamed rectal biopsies of control patients (nTrain = 76; nTest = 44). Mucin RNA isoform expression levels 5 as variables associated with IBD and subtypes (UC or CD) upon inflammation for for training (80% of GSE193677) and test (20% of GSE193677) data. Table 42: Non-inflamed rectal biopsies of CD patients (nTrain = 76; nTest = 18) vs non-inflamed rectal biopsies of control patients (nTrain= 76; nTest= 44). Differential mucin isoform expression 10 was determined by using the Wilcoxon rank-sum test corrected for multiple testing using the Bonferroni method. 5 REFERENCES [1] Massimino, L., Lamparelli, L. A., Houshyar, Y., D’Alessio, S., Peyrin-Biroulet, L., Vetrano, S., ... & Ungaro, F. (2021). The inflammatory bowel disease transcriptome and metatranscriptome meta-analysis (IBD TaMMA) framework. Nature Computational Science, 1(8), 511-515. 10 [2] Argmann, C., Hou, R., Ungaro, R. C., Irizar, H., Al-Taie, Z., Huang, R., ... & Suárez-Fariñas, M. (2023). Biopsy and blood-based molecular biomarker of inflammation in IBD. Gut, 72(7), 1271-1287. [3] Brieuc, M. S., Waters, C. D., Drinan, D. P., & Naish, K. A. (2018). A practical introduction to Random Forest for genetic association studies in ecology and evolution. Molecular ecology 15 resources, 18(4), 755-766.

Claims

CLAIMS1 . An in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto said method comprising: a) providing a biological sample from a subject suspected of having an intestinal disorder, and b) determining the expression of at least 3 mRNA isoforms originating from genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12- AS1 , MUC13, MUC16, MUC17, MUC19, MUC20 or any overlapping transcript or a pseudogene thereof wherein at least one of said 3 mRNA isoforms is a MUC4 mRNA isoform, in particular MUC4 mRNA isoform PB.1238.363; and wherein the expression of said selected mucin mRNA isoforms are normalized to a reference value and wherein a change in expression is indicative for barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto.

2. The in vitro method of claim 1 , wherein said method comprises determining the expression of MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof.

3. The in vitro method of claim 1 or 2, wherein said method comprises determining the expression MUC2 mRNA isoforms.

4. The in vitro method of claim 1 or 2, wherein said method comprises determining the expression of MUC5AC mRNA isoforms.

5. The in vitro method of claim 1 or 2, wherein said method comprises determining the expression of MUC12 mRNA isoforms or an overlapping transcript or a pseudogene thereof.

6. The in vitro method of claim 1 , wherein said method comprises determining the expression of at least MUC4 mRNA isoforms in combination with: i) MUC2 mRNA isoforms and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof; or ii) two or more mRNA isoforms selected from the list comprising: MUC5AC, MUC20, or MUC12 or an overlapping transcript or a pseudogene thereof; or ill) two or more mRNA isoforms selected from the list comprising: MUC3A, MUC12-AS1 , MUC13, or MUC19 mRNA isoforms.

7. The in vitro method of any of claims 1 to 5, wherein said barrier damage to the intestinal tract is located in a region selected from the list comprising: ileum, proximal colon, distal colon, and / or rectum.

8. The method according to any one of claims 1 to 7, wherein said mucin mRNA isoform encodesfor a transmembrane or secreted mucin.

9. A combination of MUC4 mRNA isoforms, in particular PB.1238.363 and MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof, in particular ENST00000447234.7; optionally in combination with one or more of MUC1 mRNA isoforms, MUC2 mRNA isoforms, MUC5AC mRNA isoforms, MUC5B mRNA isoforms, MUC12 mRNA isoforms, MUC16 mRNA isoforms, or MUC3A_MUC12 fusion gene mRNA isoforms, for use in the diagnosis of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto.

10. The combination for use as defined in claim 9, further comprising one or more mRNA isoforms selected from the list comprising: MUC3A mRNA isoforms, MUC13 mRNA isoforms, MUC16 mRNA isoforms, MUC17 mRNA isoforms, or MUC19 isoforms.

11. A combination of MUC4 mRNA isoforms, MUC2 mRNA isoforms, MUC20 mRNA isoforms or an overlapping transcript or a pseudogene thereof for use in determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto. 12 The in vitro method of any one of claims 1 to 8, or the combination of mucin mRNA isoforms for use according to claim 9 to 11, wherein said MUC4 mRNA isoform is MUC4 mRNA isoform PB.1238.

363.

13. The in vitro method of any one of claims 1 to 8, or the combination of mucin mRNA isoforms for use according to claim 9 to 11 wherein said MUC4 mRNA isoform is isoform PB.1238.363, said MUC16 mRNA isoform is isoform ENST00000397910.8, and said MUC20 mRNA isoforms is ENST00000447234.

7.

14. The in vitro method of any one of the preceding claims, wherein the intestinal disorder is a chronic inflammatory bowel disease (IBD) or colorectal cancer, in particular an IBD selected from the group comprising: Crohn’s disease (CD), ulcerative colitis (UC), ischemic colitis, indetermined colitis, microscopic colitis, or radiotherapy-induced colitis.

15. A diagnostic kit for performing the in vitro method according to any one of the claims 1 to 8, said kit comprising agents for detecting the expression of the at least 3 mucin mRNA isoforms as defined in anyone of claims 1 to 13, wherein said kit comprises agents for detecting at least a MUC4 mRNA isoform PB.1238.363.

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