Genomic Collision May Explain Why Many Kidney Transplants Fail

A genomic collision could explain why many kidney transplants fail, even when donors and recipients are thought to be well-matched, according to a new study from researchers at Columbia University Vagelos College of Physicians and Surgeons. This genomic collision is a genetic incompatibility between kidney donor and recipient, causing the recipient to mount an immune attack against the donor protein. 

The findings, published online today in the New England Journal of Medicine, could lead to more precise matching between donors and patients and reduce kidney transplant failures. The same genomic collision may also potentially occur in heart, liver, and lung transplants. 

A Different Possible Mechanism for Kidney Rejection

A successful organ transplant depends in large part on assuring genetic compatibility between donor and recipient. This is done by matching the donor and recipient’s human leukocyte antigens (HLAs)—cell surface proteins that help the immune system determine which cells are foreign—as closely as possible.

But HLA mismatches can explain only about two-thirds of transplants that fail for immunological reasons. “The rest of those failures are probably due to less common antigens, or so-called minor histocompatibility antigens. However, the identity of most of these antigens and how they lead to rejection is largely not known,” says co-senior author Krzysztof Kiryluk, MD, the Herbert Irving Assistant Professor of Medicine at Columbia University Vagelos College of Physicians of Surgeons. 

The researchers hypothesized that a person whose genome carries a kidney gene with a deleted section might be especially sensitive to organs from a donor whose genome carries the full-sized gene. “The recipient would then be exposed to a protein their immune system would sense as foreign,” says Kiryluk.

To test their hypothesis, researchers screened 705 kidney recipients transplanted at Columbia University Irving Medical Center for deletions in 50 kidney genes that were present as full-sized versions in the donor. The deletions associated with rejection were then confirmed in an additional 2,004 donor-recipient pairs from three international transplant cohorts.

What the Study Found

The study found that kidney recipients with two copies of a deletion near a gene called LIMS1 had a significantly higher risk of rejection when the donor kidney had at least one full-sized version of the same gene. The risk of rejection was 63% higher among the donor-recipient pairs with this genomic collision, compared to those without this mismatch. “To put this into perspective, the risk of rejection from LIMS1 mismatch is roughly three times as high as the risk due to a single allele mismatch in the HLA,” Kiryluk says.

Kidney transplant recipients with two copies of the deletion who developed rejection had detectable levels of anti-LIMS1 antibodies in their blood—further evidence that this genomic collision contributes to rejection.

“The exact mechanism by which this deletion exerts its effects is unknown,” says Kiryluk. “It’s likely that it reduces the amount of LIMS1 protein produced, since we find that individuals with two copies of the deletion have lower levels of LIMS1 gene transcript in their kidneys. When these individuals are exposed to a high level of LIMS1 protein in a newly transplanted organ, their immune system is more likely to recognize the LIMS1 antigen as foreign, resulting in rejection.” 

Transplanted organs commonly experience a significant period of low oxygenation, which appears to compound the genomic collision. In cells that produce LIMS1, the researchers found that low oxygen levels increase LIMS1 production on the cell surface, which may increase the risk of an immune attack. 

One in 7 Transplants in Some Populations May Be Affected

An LIMS1 mismatch would be expected to occur in approximately 12% to 15% of transplants from unrelated donors among persons of European and African ancestry, but it would be very rare among persons of East Asian ancestry because the deletion is very rare in these populations.

“LIMS1 mismatches could be avoided by pre-transplant genetic screening,” Kiryluk says. “But first we need to validate our findings in larger studies.”

The findings may apply to other types of organ transplants since LIMS1 is also expressed in the lung, heart, and liver. Similarly, other genetic incompatibilities may also be contributing to rejection of these organs.

“This project illustrates how genetic analysis is empowering clinical care by enabling better matching, and the antibody test potentially presents a noninvasive method for screening for organ rejection in individuals with an existing transplant,” says co-senior author Ali G. Gharavi, MD, professor of medicine at Columbia University Vagelos College of Physicians and Surgeons.

The LIMS1 gene has gone previously undetected in earlier searches, partly due to the limited sample size of previous studies, Kiryluk says. “We estimate that a traditional genome-wide association study would need to analyze a minimum of 13,000 kidney recipients to find this gene. The genomic collision approach provides a new method to find additional mismatches in a smaller number of donor-recipient pairs. And, coupled with new methods of antibody detection, is likely to propel future discoveries in this area.”


The study is titled “Genomic Mismatch at LIMS1 Locus and Kidney-Allograft Rejection.” The full list of contributing authors can be found here. 

The research was supported by the Columbia University Transplant Center, a NewYork-Presbyterian Hospital Translational Pilot Grant funded by the New York State Empire Clinical Research Investigator Program, a Columbia University Precision Medicine Pilot Award funded by the Dean of the Vagelos College of Physicians & Surgeons, and the Columbia Clinical and Translational Science Award Precision Medicine Pilot Program funded by a grant from the NIH National Center for Advancing Translational Sciences (UL1TR001873) and by grants from the National Institute of Diabetes and Digestive and Kidney Diseases (T35-DK093430 and T32-DK108741). Replication studies in the Torino cohort were supported by a Department of Excellence Grant 2018–2022 funded by the Italian Ministry of Education to the Department of Medical Sciences of the University of Turin. The Columbia Center for Translational Immunology Flow Cytometry Core is supported in part by a grant (S10RR027050) from the NIH Office of the Director, and the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University is supported by a grant (P30CA013696) from the NIH National Cancer Institute.

Financial disclosure forms provided by the authors are available with the full text of this article at