A method for identifying a kidney transplant recipient at an increased risk of developing interstitial fibrosis or tubular atrophy which comprises obtaining a post-transplant urine sample from the kidney transplant recipient; measuring the level of clusterin in the urine sample; comparing the level of clusterin in the patient sample to the level of clusterin in a control sample from the urine of a non-fibrotic kidney transplant recipient; diagnosing a kidney transplant recipient with a clusterin level that is significantly higher than the clusterin level in the control as being at an increased risk of developing interstitial fibrosis or tubular atrophy.

A method for characterizing the risk a subject will develop an autoimmune and/or alloimmune disease following tissue transplant includes obtaining a biological sample from the subject, wherein the subject has received the tissue transplant determining in the biological sample a level of at least one protein selected from Tables 1-4, comparing the measured level of the at least one protein to a control value, and characterizing a subject as at greater risk of developing an autoimmune disease and/or alloimmune disease if the level of at least one protein determined is increased or decreased compared to the control value.

A four-biomarker panel for diagnosis of chronic graft-versus-host disease (cGVHD) and methods of prognosing and/or diagnosing cGVHD using the biomarker panel are disclosed.

The present disclosure describes compositions and methods for increasing the abundance of commensal bacteria belonging to the order Clostridiales, including Blautia, Ruminococcus, Clostridium, Eubacterium, Holdemania and Dorea species, that are associated with reduced lethal GVHD and improved overall survival following bone marrow or hematopoietic stem cell transplant. The present disclosure, therefore, provides methods for reducing the likelihood, incidence or severity of GVHD by (1) avoiding the loss of endogenous beneficial species through antibiotic selection; (2) by administering a therapeutically effective amount of a composition comprising one or more Clostridiales associated with reduced GVHD to individuals who may lack or have lost those strains from their intestinal microbiota. Additionally, support for endogenous or reestablished Clostridiales related to reduced GVHD as a treatment option for reducing GVHD can also be provided in the form of nutritional supplementation, for example, sugars fermented by some species of Clostridiales with GVHD reducing activity.

Disclosed herein are methods for diagnosing or predicting B-cell rejection in a subject. In one example, for assessing transplant rejection, the method includes determining an antigen presenting index by comparing uptake of a donor antigen to uptake of a reference antigen in a biological sample obtained from the subject. In another example, for assessing GVHD, the method includes determining an antigen presenting index by comparing uptake of a recipient antigen to uptake of a reference antigen in a biological sample obtained from the subject.

A method for evaluating a subject for a biological condition associated with metal metabolism includes sampling positions along a biological sample of the subject to obtain several ion samples. Each ion sample corresponds to a position on the biological sample and each position represents an amount of growth of the biological sample. The obtained ions are analyzed with a mass spectrometer thereby obtaining a plurality of traces. Each such trace represents a concentration of a corresponding elemental isotope, in a plurality of elemental isotopes, over time. A set of features is derived from the traces. Each feature is determined by a variation of a single isotope or a combination of isotopes in the plurality of traces. The set of features is inputted into a trained classifier to obtain a probability that the subject has the biological condition associated with metal metabolism.

The invention relates to an isolated interleukin-34 (IL-34) polypeptide for use in preventing or treating graft rejection, autoimmune disease, unwanted immune response against therapeutic proteins and allergy. The invention also provides an in vitro method for determining whether a patient is at risk of transplant rejection, autoimmune diseases, unwanted immune response against therapeutic proteins or allergies, comprising a step of determining the expression level of IL-34 in a biological sample obtained from said patient, wherein the presence of IL-34 is indicative of a reduced risk of transplant rejection, autoimmune diseases, unwanted immune response against therapeutic proteins or allergies.

A method is provided for increasing the sensitivity of the complement-dependent cellular cytoxicity analysis that establishes whether a potential transplant recipient patient expresses donor organ-reactive antibodies that would reduce or prevent acceptance of the donor organ by a recipient. At least one gene encoding a complement inhibitor is inactivated in cells derived from a candidate transplant organ. Such modified cells, because they no longer produce at least one complement inhibitor, when placed in a serum sample from a potential transplant recipient, do not reduce the effective activity of serum complement. A lower level of recipient patient serum antibodies becomes effective in inducing detectable lysis of the donor cells.

Disclosed are biomarker panels for evaluating subjects at risk of sinusoidal obstruction syndrome (SOS) early after hematopoietic stem cell transplantation (HSCT). In particular, the present disclosure relates to the use of one or more of ST2, ANG2, L-Ficolin, HA, and VCAM1 for prognosing, diagnosing, and/or treating SOS.

By a genome-wide gene analysis of expression profiles of known or putative gene sequences in peripheral blood and biopsy samples, the present inventors have identified a consensus set of gene expression-based molecular biomarkers for distinguishing liver transplantation patients who have Acute Rejection (AR), Hepatitis C Virus Recurrence (HCV-R), both AR/HCV-R, or Acute Dysfunction No Rejection (ADNR). These molecular biomarkers are useful for diagnosis, prognosis and monitoring of liver transplantation patients.