Non-HLA Genetics and Application to Living Donor Candidates

Abstract

Purpose of Review:

This review examines the expanding role of non-human leukocyte antigen (non-HLA) genetic factors in kidney transplantation, with a particular focus on their implications for living donor evaluation and outcomes. It emphasizes the potential of genetic testing to improve risk stratification beyond conventional HLA matching, especially for donor candidates with a family history of hereditary kidney disease.

Recent Findings:

Non-HLA genetic mismatches, including single nucleotide variants affecting minor histocompatibility antigens, can drive alloimmune responses, leading to graft rejection and failure even in HLA-matched transplants. The presence of non-HLA antibodies further contributes to adverse immunological outcomes. Genetic testing in related living donors can uncover monogenic kidney diseases, enabling early identification of at-risk individuals and enhancing donor safety. While polygenic risk scores and gene panels show promise in predicting complications and guiding post-transplant care, most genome-wide association studies have focused on recipients. There remains a significant gap in understanding how donor-specific genetic factors influence post-donation kidney function and long-term health outcomes.

Summary:

The integration of non-HLA genetic testing into living donor evaluation supports a precision medicine approach to kidney transplantation, offering improved risk assessment and donor-recipient matching. As the field advances, longitudinal studies and robust data collection, particularly around donor genetics, are essential to optimize transplant outcomes, inform clinical decision-making, and uphold ethical standards in donor care.

1. Introduction

Advances in genetic research beyond human leukocyte antigen (HLA) have identified other polymorphic non-classical HLA antigens, non-HLA antigens and genetic loci that can influence kidney transplant outcomes^1,2. Evidence suggests that a third of immunologically mediated graft failures are unrelated to HLA mismatches, highlighting the role of non-HLA factors^3,4. This has shifted the focus in understanding risk of rejection and allograft injury toward non-HLA genetics, particularly in living donor transplants. While HLA compatibility remains central to donor-recipient matching due to its impact on transplant rejection rates and graft survival, emerging research emphasizes the significance of non-HLA genetic factors, including minor histocompatibility antigen polymorphisms and non-HLA antibodies, in shaping transplant outcomes independently of HLA matching.

Non-HLA antigens, specifically those coded by polymorphic regions outside the HLA complex, have been shown to contribute significantly to graft rejection mechanisms. Mismatches in these non-HLA loci can activate pathogenic donor-reactive T cells, particularly in genetically similar donor-recipient pairs that share certain HLA types. Evidence suggests that these genetic discrepancies are not merely incidental but can be predictive of acute and chronic rejection events post-transplantation^5,6. For instance, specific single nucleotide variants (SNVs) associated with allograft survival provide insights into how non-HLA mismatches modulate transplant outcomes^7,8. Additionally, the development of comprehensive multiplex screening assays for non-HLA antibodies has facilitated a better understanding of their clinical impact, as certain non-HLA antibodies correlate with graft loss⁹. Research has indicated that non-HLA antibodies can elicit robust immune responses detrimental to graft function, especially when present in conjunction with HLA-directed antibodies¹⁰. This highlights the necessity for a holistic assessment of both HLA and non-HLA factors in pre-transplant evaluations. In patients on the kidney transplant waiting list, for example, higher burdens of pre-existing non-HLA antibodies have correlated with increased alloimmunization risk and may influence clinical decision-making regarding donor compatibility¹¹. Furthermore, genetic risk assessment models increasingly incorporate non-HLA genetic information to enhance predictive accuracy regarding graft success and longevity.

Recognizing the complexity of alloimmunity that extends beyond traditional HLA compatibility signifies a proactive approach to tailoring immunosuppressive strategies and enhancing graft survival rates. The exploration of non-HLA genetic mismatches thus represents a pivotal frontier in transplant immunology, warranting further investigation and application in clinical settings. In parallel, the incorporation of genetic testing for living donor candidates with a family history of kidney disease is becoming increasingly important^12–14. Identifying monogenic causes of kidney disease including autosomal polycystic kidney disease (ADPKD), Alport syndrome or other hereditary kidney diseases, not only informs donor eligibility but also protects potential donors from future health risks^14–17. Single nucleotide variants (SNV) associated with hyperfiltration injury, maladaptive hypertrophy, or impaired repair capacity could also potentially predispose living donors to reduced kidney function over time¹⁸. This review explores the role of non-HLA genetic testing and its applications for the selection and management of living donor candidates.

2. The Role of Non-HLA Genetics in Transplantation

Non-HLA genetic factors in kidney transplantation encompass a variety of antigens and genetic variants outside the HLA system, which play significant roles in transplant outcomes. The increasing recognition of the insufficiency of detectable HLA antibodies as an indicator for graft acceptance highlights the importance of considering non-HLA genetic mismatches. Minor histocompatibility antigens, polymorphisms in non-HLA loci, and diverse immune responses to these factors collectively influence the success of kidney transplantation^19,20. Specific genetic variants outside the HLA system, coding non-HLA antigens, can provoke immune responses that lead to allograft rejection. Polymorphisms in genes encoding non-HLA antigens have been associated with adverse transplant outcomes, underscoring their relevance within the transplant landscape^8,9. Interactions between non-HLA genetic mismatches and the recipienťs immune system can trigger immune responses akin to those seen with HLA mismatches, thus affecting graft survival rates. Evidence suggests that mismatches at particular non-HLA loci are associated with increased risks of acute cellular rejection and graft failure^5,11.

The clinical significance of non-HLA factors has driven advancements in screening techniques to identify relevant non-HLA antibodies, which may serve as potential biomarkers for assessing graft rejection risk¹⁰. Multiplex assays have been established to analyze the presence and effects of these antibodies, aiding clinicians in evaluating patient allosensitization profiles prior to transplantation⁹. Additionally, components such as soluble MHC class I polypeptide-related sequence A (sMICA) and HLA-G, along with their polymorphisms, have emerged as significant non-HLA genetic factors implicated in graft acceptance and rejection processes^10,19. The best known non-classical HLA molecule is MICA, and the development of MICA-specific antibodies can affect post-transplant survival, and matching for these non-classical antigens may further enhance compatibility²¹. Several specific minor histocompatibility antigens have been identified as key contributors to transplant outcomes. Notably, female recipients of kidney allografts from male donors have shown worse survival rates compared to other gender combinations²². This increased risk of acute graft rejection has been partly attributed to immune responses against Y-chromosome-encoded antigens, such as the male-enhanced antigen 1 (MEA1) gene, leading to the formation of H-Y antibodies²³. Advances in genomics have further revealed that differences in minor histocompatibility antigens between donors and recipients play a crucial role in alloimmune responses, even among HLA-matched siblings, due to the widespread distribution of minor histocompatibility antigen encoding genes across the human genome²⁴.

In recent years, with the increased availability of large, sequenced cohorts, genome wide association studies (GWAS) have identified additional genetic loci that are associated with post-transplant outcomes^3,25,26. Interpretation of the GWAS findings in these cohorts has been tempered by the failure to replicate previously reported SNV associations, even with a larger dataset²⁷. The International Genetics & Translational Research in Transplantation Network (iGeneTRAiN) has created and analyzed genome-wide datasets of >56,000 recipient-only or donor-recipient pairs to perform large scale studies on minor histocompatibility antigens and HLA genetics²⁸. The significance of genome-wide minor histocompatibility antigen mismatches remains evident even after accounting for HLA mismatches. A genome-wide analysis of transmembrane and secreted protein mismatches in 477 prospectively collected kidney transplant pairs from an iGeneTRAiN study demonstrated that non-HLA gene mismatches are independently associated with graft loss, even after adjusting for HLA eplet mismatches and serotype in a multivariable model²⁹. Moreover, non-HLA immunological responses seem to interact synergistically with HLA responses, complicating the immunological landscape of kidney transplantation. Studies suggest that non-HLA antibodies may coexist with HLA antibodies, increasing the risk of rejection and influencing post-transplant complications³⁰. A comprehensive understanding of non-HLA genetics is crucial in kidney transplants, as it enables clinicians to refine matching strategies and immunosuppressive regimens, ultimately improving graft outcomes^8,20.

An important and emerging area in non-HLA genetics is the assessment of biological risk among living kidney donor candidates^2,31. Donors who are biologically related to their recipients may carry a higher risk of developing ESKD, likely due to shared genetic predispositions³¹. Genetic disorders are estimated to account for 8%-10% of incident ESKD cases in the United States, with even higher prevalence in children and young adults³². Recent studies have shown that up to 10% of adults with ESKD harbor pathogenic variants identified through exome sequencing³³. Similarly, a large cohort study from a German transplant center reported a genetic diagnosis in 20%-25% of patients on the kidney transplant waitlist³⁴. Importantly, a subset of patients attributed with hypertensive or diabetic nephropathy may, in fact, have underlying monogenic kidney diseases that have gone unrecognized, raising concerns for their related donor candidates who may unknowingly carry the same genetic risk. Genetic testing in transplant clinics provides valuable insights beyond conventional clinical evaluations, helping to identify potential risks to both donors and recipients^35,36. As kidney genomics increasingly integrates into clinical practice, transplant programs must actively educate clinicians and patients about the capabilities, benefits, and limitations of genetic testing.

3. Key Non-HLA Genetic Variants in Transplantation

The regulation of immune response, fibrosis, drug metabolism, and ischemia-reperfusion injury involve complex genetic interactions and pathways, underscored by a growing body of research. Additionally, increasing attention has been directed toward the role of monogenic variants and the associated risks for living donor candidates. In the sections that follow, we address each of these areas in detail, supporting our discussion with relevant literature.

Variants Affecting Immune Regulation

Cytokines play a crucial role in immune modulation, with genes such as TGF-β, IL-6, and IL-10 being pivotal. TGF-β is known for its immunosuppressive role, indicating that its variants might influence susceptibility to autoimmune diseases and organ transplant acceptance³⁷. IL-6 has been implicated in exacerbating inflammation and promoting fibrosis, as seen in various pathologies, including transplant rejection⁵. Additionally, IL-10 is recognized for its anti-inflammatory properties; variations in its gene can impact cytokine production, thus shaping the immune response in clinical scenarios³⁸. In models of ischemia-reperfusion injury, elevated levels of pro-inflammatory cytokines such as TNF-α and IL-6 are observed, which contribute to inflammatory damage and have been linked to poor outcomes following organ transplantation^39,40.

Genes Influencing Allograft Rejection and Fibrosis

Allograft rejection and fibrosis are multifactorial processes influenced by genetic variations. LIMS1 rs893403 variant has been tied to kidney transplant rejection, survival and the development of fibrosis post-transplant, highlighting its expression quantitative trait locus (eQTL) functions⁵. Studies have indicated that variations in LIMS1 can lead to significant differences in graft survival and fibrosis development, suggesting that their study is critical in transplant immunology⁵. The LIMS1 locus, which also functions as a copy-number variant (CNV), encodes a minor histocompatibility antigen that can be expressed on the cell surface, making it a potential endothelial cell antigen. Notably, recipients homozygous for the LIMS1 variant rs893403 exhibited significantly reduced mRNA levels³. Furthermore, kidney transplant recipients with a donor-recipient mismatch at LIMS1, where the recipient was variant-homozygous and the donor variant-heterozygous, had a 63% increased risk of acute rejection. The detection of LIMS1-specific antibodies confirmed an alloimmune response against this mismatched non-HLA antigen, providing indirect evidence of its role in transplant rejection²⁹. Kiryluk et al.³ introduced the concept of “genomic collision,” in which donor non-HLA kidney proteins absent in the recipient, such as the LIMS1 protein, trigger the development of antibodies directed against the expressed protein in the donor kidney. Initially, the LIMS1 rs894303 variant was thought to exemplify mutation-induced loss-of-function. In affected patients, reduced endothelial LIMS1 protein expression was thought to trigger an immune response against this non-HLA antigen. However, follow up studies did not show any association of LIMS1 rs893403 and antibody mediated rejection^4,41. Our group demonstrated that recipient LIMS1 risk genotype is associated with an increased risk of T cell mediated rejection (TCMR) after kidney transplantation, confirming the role of the LIMS1 locus in allograft rejection^4,41. However, we found no association between LIMS1 risk genotype and antibody mediated rejection⁴. Further investigation revealed that the LIMS1 locus plays a role in lymphocyte infiltration into the internal aspect of the tubular basement membranes⁴¹.

Sun et al⁵ investigated how donor-recipient mismatches beyond HLAs contribute to kidney allograft loss, particularly focusing on intronic mismatches⁵. Using SNV data from two well-characterized transplant cohorts (GoCAR and CTOT-01/17), the researchers identified the LIMS1 locus as the top gene where donor-recipient mismatches are associated with death-censored graft loss (DCGL). A previously unreported LIMS1 intronic haplotype of 30 SNVs was independently linked to DCGL in both cohorts, showing a dosage effect, where minor-allele introduction to major-allele-carrying recipients increased DCGL risk. The study also found that the LIMS1 haplotype and SNV rs893403 function as eQTLs for GCC2, a gene involved in mannose-6-phosphate receptor (M6PR) recycling. Further transcriptome and in vitro analyses suggested that GCC2 and LIMS1 SNVs regulate the TGF-β1/SMAD pathway, which plays a crucial role in immune response. Specifically, GCC2 modulation affected M6PR-dependent regulation of active TGF-β1 in T cells, linking LIMS1 mismatches to immune-mediated graft loss. The study by Sun et al.⁵ identifies a novel mechanism by which LIMS1 locus mismatches impact kidney transplant outcomes through GCC2-mediated regulation of TGF-β1 signaling in T cells, providing new insights into non-HLA-mediated allograft rejection. Mirioglu et al observed an increased fraction of regulatory T cells (Treg) in the recipients with LIMS1 risk genotype (rs893403-GG)⁴². The higher fraction of Treg subpopulation in kidney transplant patients with GG genotype was not accompanied by higher BKV DNAemia levels. However, they suggest a regulatory effect of rs893403-GG genotype on distribution of T-cell subpopulations, particularly FoxP3+ Treg cells⁴².

These findings may have clinical implications for the prediction and clinical management of kidney transplant rejection through pretransplant genetic testing of both recipients and donors for the LIMS1 risk genotype. Expanding research into non-HLA genetic regions will be essential for improving transplant outcomes and refining precision donor-recipient matching.

Variants Affecting Drug Metabolism and Response

The cytochrome P450 enzyme CYP3A5 and the ATP-binding cassette transporter ABCB1 are essential for the metabolism of immunosuppressive drugs like tacrolimus. Genetic variants in these genes can lead to significant interindividual variability in drug disposition and efficacy^37,43. For instance, studies have demonstrated that CYP3A5 gene variants can predict tacrolimus dosing requirements in different populations, thereby impacting transplantation outcomes⁴⁴. A pharmacoeconomic study found that first-year Medicare reimbursement differed significantly by CYP3A5 genotype, categorizing rapid metabolism phenotype without loss of function alleles, intermediate phenotype for 1 loss of function allele, and slow phenotype for 2 loss of function alleles⁴⁵. After adjustment for donor and recipient characteristics, care for patients with intermediate metabolism was $4790 less expensive (P=0.003)⁴⁵. Furthermore, ABCB1 haplotypes have been demonstrated to influence tacrolimus pharmacokinetics, although often confounded with CYP3A5 variants, suggesting a critical area for further genotyping in transplant settings^37,46.

Genes Associated with Ischemia-Reperfusion Injury and Inflammation

Ischemia-reperfusion injury (IRI) is a significant concern in various clinical settings, particularly in transplant surgery. Various genes have been implicated in exacerbating or mitigating this injury. For example, the NLRP3 inflammasome has been shown to contribute to detrimental inflammatory responses during IRI, indicating its potential as a therapeutic target⁴⁷. Moreover, studies have highlighted the role of cytokines, particularly TNF-α and IL-6, as mediators of inflammatory responses during IRI, suggesting that genetic predisposition can significantly influence patient outcomes following ischemic events^39,40. Other investigations have also identified pathways involving oxidative stress, suggesting that modulation of these pathways can diminish IRI effects and improve recovery following transplant surgeries⁴⁸.

Genes Associated with Post-transplant Outcomes

The iGeneTRAiN conducted GWAS to identify genetic loci influencing kidney function 5 years post-transplant and also looked at factors that increase skin cancer risk²⁵. A strong genetic predisposition to skin cancer was observed, differentiated by polygenic risk scores (PRS)s²⁵. Further, other studies have identified genetic loci associated with additional post-transplant complications, such as allograft rejection and diabetes^49,50. These studies highlight the potential of GWAS to uncover genetic associations that in turn could lead to the identification of genetic variants that affect the susceptibility to transplant-related outcomes and complications^1,3,4. (Tables 1 and 2)

Table 1.

Genome wide associations studies identifying recipient single nucleoti⁹⁸de variants associated with transplant outcomes

Study	Year	Discovery	Replication	Outcome	Significant genes	SNP's	PMID
O'Brien et al.26	2013	326		Graft function at 5 years	ZNF516 TRAV19, TRAV20 SHANK2 LINC01070, SOX1-OT	rs6565887-G rs3811321-C rs3017493-G rs9324268-A	23432519
McCaughan et al.49	2014	707		NODAT	CCL2	rs10484821, rs7533125, rs2861484, rs11580170, rs2020902, rs1836882, rs198372, rs4394754	24309190
Dabrowska-Zamojcin et al.98	2016		315	NODAT Validation	CCL2	rs1024611	26802601
Ghisdal et al.99	2017	4,127	2,765	Acute allograft rejection	PTPR, CCDC67	rs11543947, rs2279804, rs17421009, rs2476601, rs3087243, rs3087456, rs7528684, rs4839469, rs10804682	27272414
Oetting et al.100	2018	DeKAF 1,342		Tacrolimus blood concentration	CYP3A4	rs35599367-A	29160300
Oetting et al.101	2018		1,923	Tacrolimus blood concentration	CYP3A4 CYP3A5		29318894
Oetting et al.102	2019	DeKAF 1,948 EA and 391 AA	698 EA and 176 AA	Tacrolimus blood concentration	CYP3A5	rs776746-?, rs35599367-?, rs776746-?, rs41303343-?	30801552
Steers et al.3	2019	705	2,004	Acute allograft rejection	LIMS1	rs893403	31091373
Caliskan et al.4	2021		841	Acute allograft rejection	LIMS1	rs893403	33909908
Reindl-Schwaighofer et al.6*	2019	477 Pairs		Graft loss	*	1,892 non-synonymous SNP mismatches	30773281
Stapleton et al.103	2019	European 10,844 Pairs		Posttransplant eGFR change	LRATD1, NBAS SRRM1P2, CYP51A1P1 RUNX1T1, FLJ46284 LHPP, RNU6–63P, MTIF3,ZNF551	rs2705863-T, rs73117799-T rs13269272-A, rs12569498-T rs150558112-A, rs1966325-T	30920136
				Posttransplant eGFR in 1 year	SYT16, HPGD, GLRA3 DIO2-AS1, N6AMT1 GPR85, HRAT17, OR1D4, OR1D3P, TNIK, MAP3K7CL	rs113730106-T, rs2555639-T rs10142839-A, rs1997606-C rs7791116-T, rs59125474-A rs67616801-A, rs2471950-A	30920136
				Posttransplant eGFR in 5 years	MICAL2, ISCA1P3, KIF2B VN1R18P, PPIAP62, PIK3R1, LINC02198, ADGRL2 TUBBP8, LCIIAR, SH3GL3 HDAC4, LMCD1-AS1	rs11022188-A, rs9891228-T rs79939438-T, rs2925732-A rs9324185-T, rs7169056-A rs56026818-T, rs4852063-A rs923381-T	30920136
Sun et al.5	2025	58,326 AA	7,274	Graft failure	LILRB3	rs139094141, rs549267286, rs567676351, rs761515451	40065170

^*1,892 nsSNP mismatches were identified as related to graft loss between donors and recipients.

Abbreviations: EA, European American; African American; eGFR, estimated glomerular filtration rate

Table 2.

Genome wide associations studies identifying donor single nucleotide variants associated with transplant outcomes

Study	Year	Discovery	Replication	Outcome	Significant genes	SNP's	PMID
Yan et al.65	2017	189		Posttransplant eGFR after 1 month	SHROOM3, ABCB1	rs17319721, rs1045642	27779570
Stapleton et al.103	2019	European 10,844 Pairs		Posttransplant eGFR change	CHRNA9, OSBP2	rs114219703-T, rs136237-A	30920136
				Posttransplant eGFR in 1 year	COL4A1, MRPS21P6, RPS27P18, EMP1, FAM234B, RN7SKP27, LINC02923, BFSP1, POT1-AS1, GRM8	rs3783107-A, rs72834903-A, rs7952921-A, rs1002159-A, rs6044852-A, rs148931567-A	30920136
				Posttransplant eGFR in 5 years	LINC00378, GPR139, SNRPEP3, TPRX1, RPL23AP80, PKP4-AS1, SYNPO2, RNA5SP200, STC2, CSMD1	rs1041331-A, rs9921767-A, rs11671550-C, rs723539-A, rs17263971-A, rs11747973-T, rs2627395-T	30920136
Reindl-Schwaighofer et al.6*	2019	477 Pairs		Graft loss	*	1,892 non-synonymous SNP mismatches	30773281
Divers et al.104	2020	DeKAF 978		Graft survival time	ACTBP8, RNGTT, MIR31HG, LINC02719, GUCY1A2, NUDT7, VAT1L	rs1923418-?, rs12552330-?, rs113665227-?, rs9319516-?	32080893
				Graft survival time x APOL1 interaction	ATAD3B, MIR4431, ASB3, CRLF3P1, TMEM182, SEC63, PVT1, LINC01228, DYNLRB2-AS1	rs1695847-?, rs76455983-?, rs7582966-?, rs6906957-?, rs73710129-?, rs4889062-?	32080893
Verma et al.105	2024	VA Million Veteran Program 635,000		Kidney replaced by transplant (PheCode 587)	NAALADL2, ADAM29, KATNBL1P4, RNA5SP182, RNU6–1060P, SPTLC1P2, CEP41, APOL1	rs564279849-T, rs558277096-T, rs373906611-C, rs189512721-G, rs376434190-C, rs73885319-A	39024449

^*1,892 nsSNP mismatches were identified as related to graft loss between donors and recipients.

Abbreviations: eGFR, estimated glomerular filtration rate; VA, Veterans Affairs

APOL1 Renal Risk Variants (RRVs)

The discovery of APOL1 risk alleles has also significantly influenced the field of kidney transplantation, particularly in assessing donor suitability and predicting allograft outcomes. The G1 and G2 variants of the APOL1 gene, found almost exclusively in individuals of recent African ancestry, arose due to evolutionary selection for protection against Trypanosoma brucei, the parasite responsible for African sleeping sickness.⁵¹ However, these same genetic variants have been strongly associated with an increased risk of chronic kidney disease (CKD) and ESKD. In the United States, an estimated 13% of African American people carry two APOL1 RRVs, significantly elevating their susceptibility to kidney disease^36,51. Despite the strong genetic association, not all individuals with two APOL1 RRVs develop kidney disease, suggesting that additional “second-hit” factors, such as inflammation, infections, or hypertension may be required to trigger disease progression⁵². APOL1-associated nephropathy is linked to increased cellular stress, mitochondrial dysfunction, and podocyte injury, ultimately leading to glomerulosclerosis and renal failure.

The presence of high-risk APOL1 genotypes in kidney donors and recipients has important clinical implications⁵³. Recipients of kidneys from deceased donors with two APOL1 RRVs have been shown to experience significantly higher rates of allograft failure, often occurring prematurely, independent of traditional risk factors. These findings underscore the potential impact of donor APOL1 status on transplant outcomes and long-term graft survival. The ongoing APOLLO (APOL1 Long-term Kidney Transplantation Outcomes Network) study is prospectively assessing: (1) allograft outcomes in U.S. transplant recipients according to donor and recipient APOL1 genotypes; (2) renal outcomes in living kidney donors after nephrectomy according to APOL1 genotype^51,54. The results of this study are anticipated to guide evidence based recommendations on APOL1 testing in transplantation. In current practice, considerable variability exists regarding whether and how to incorporate APOL1 testing into donor evaluations. While some transplant programs may decline living donors with high-risk genotypes due to concerns about future ESKD risk, others may proceed cautiously, particularly in cases of urgent need or within families, following thorough genetic counseling. However, the potential for implicit coercion or guilt among related donors remains a concern and underscores the need for standardized, ethically grounded approaches^52,53,55,56.

4. Impact of donor genetic variants on long-term kidney function

The impact of donor genetic variants on long-term kidney function is an increasingly critical area of research in the field of transplantation medicine. Genetic factors, particularly variations in specific genes such as APOL1 and CAV1, play substantive roles in determining both donor kidney viability and recipient outcomes post-transplantation^57,58. The integration of genetic screening into donor evaluation processes offers a more refined selection framework, optimizing transplant success and ensuring donor safety.

As mentioned previously, the APOL1 gene has garnered attention due to its association with kidney disease, particularly among individuals of African descent. Research suggests that donors who possess high-risk APOL1 genotypes (specifically, the G1 and G2 alleles) have kidneys that may function poorly post-transplant. Doshi et al. demonstrated that APOL1 high-risk genotype in living kidney donors of African ancestry associated with greater decline in post-donation kidney function¹. However, the trajectory of renal function was similar between donors and nondonors. The association between APOL1 high-risk genotype and poor renal outcomes in kidney donors requires validation in larger studies. Furthermore, kidneys from deceased African American donors with two APOL1 risk alleles may fail more rapidly compared to kidneys from donors with fewer or no risk alleles (the topic of the APOLLO Study), emphasizing the importance of considering APOL1 variants in living donors, especially those with African ancestry^59,60.

Complement system genes, particularly polymorphisms in the complement C3 gene, also demonstrate a significant influence on transplant outcomes. Certain complement gene variants in donors correlate with long-term kidney allograft survival, suggesting that genetic matching may enhance transplant outcomes beyond traditional HLA systems⁶¹. These findings suggest that integrating donor genetic screening can refine selection criteria for kidney donors, potentially enhancing long-term outcomes for recipients⁶². CAV1 gene variations have also been linked to graft function. Studies have established that variants within the CAV1 gene can influence renal allograft failure and fibrosis^58,63. The structural role of caveolin-1 makes it a candidate for influencing tissue integrity and preventing fibrosis, critical factors for maintaining long-term renal function after transplantation.

Multiple studies have demonstrated that CKD-associated SNVs in the SHROOM3 gene, when present in the donor, are associated with adverse graft outcomes, particularly in the context of anti-non-HLA immunity in HLA-disparate pairs^64–66. Donor SHROOM3 SNVs, especially rs17319721, have been shown to increase SHROOM3 expression in the allograft, potentiating TGF-β1 signaling and promoting interstitial fibrosis, which correlates with reduced estimated glomerular filtration rate (eGFR) and increased risk of chronic allograft nephropathy^64–66. These effects are independent of HLA matching and are more pronounced in HLA-disparate pairs, where non-HLA alloimmune responses are more likely to be clinically relevant^6,67–70. Genome-wide analyses confirm that non-HLA donor-recipient mismatches, including those at the SHROOM3 locus, contribute to alloimmune injury and graft loss, with the development of donor-specific antibodies against non-HLA antigens in HLA-mismatched transplants^6,70. Importantly, the impact of donor SHROOM3 variants is not limited to HLA-matched individuals; the risk is amplified in HLA-disparate pairs due to increased non-HLA antigenic differences, which drive anti-non-HLA immune responses and chronic antibody-mediated rejection^6,68,70. These findings support the paradigm that donor SHROOM3 SNVs are a risk factor for allograft fibrosis and dysfunction, especially in the setting of HLA mismatch, where non-HLA immunity plays a significant role.

Another critical genetic consideration in living donor evaluation involves familial variants identified in recipients with hereditary kidney diseases. For biologically related donor candidates, these shared variants may pose significant, yet often unrecognized, risks on kidney functions. Comprehensive genetic testing of living donors can reveal pathogenic or likely pathogenic familial variants that may not only impact the donor’s future health but also provide critical information for recipient management. Singh et al. highlighted that proactive genetic testing strategies could identify significant incidental findings that might directly impact donor safety and recipient outcomes⁷¹. This approach not only fosters personalized matching but also illuminates potential genetic predispositions that could lead to complications in either party involved in the transplant. The evolving literature reflects a paradigm shift towards utilizing genetic profiling as a routine part of donor evaluation processes, thereby optimizing kidney allocation strategies and potentially improving long-term graft survival outcomes. With advancements in genetic understanding, it becomes plausible to adopt tailored approaches to transplant medicine, enhancing both donor safety and recipient success rates^72,73. As the field continues to emphasize the importance of genetics in organ transplantation, future studies are warranted to expand the scope of genetic markers utilized in donor evaluations, facilitating better clinical practices in kidney transplantation.

5. Genetic Risk Stratification for Living Donor Candidates

Genetic diseases can impact living kidney donor candidates, even if they appear healthy and asymptomatic at the time of kidney donation. This is especially relevant for biologically related kidney donors who have about a 1.5 to 2-fold increased risk of developing kidney failure compared to unrelated donors, likely due to shared genetic variants^14,74,75. Although healthy donor candidates might carry familial genetic variants that could lead to kidney disease, genetic testing can identify asymptomatic donors who are likely to develop clinical manifestations. Therefore, assessing their risk of developing future genetic kidney disease is important. The APOL1 RRVs are a prominent example of how non-HLA genetics can influence donor eligibility and transplant outcomes. While APOL1 testing has the potential to guide donor selection and protect long-term health, it raises complex ethical and legal questions. For example, it remains unclear whether individuals with high-risk APOL1 variants should be informed about their potential risks for kidney disease that may affect their donor eligibility. Similarly, it is also unknown whether potential recipients of kidney transplants should be informed of the donor’s APOL1 genotype, especially if there is a risk of developing kidney disease later in life.

The Living donor Extended Time Outcomes (LETO) study is a critical ancillary project to the APOLLO Network, designed to address key limitations of the APOLLO Consortium’s prospective design. APOLLO, while the largest national effort to date, is constrained by relatively short follow-up and the declining number of living kidney donors with two APOL1 RRVs due to changes in donor selection practices and increased awareness of APOL1-associated risk^60,76,77. LETO overcomes these limitations by employing a hybrid design: it combines home-based research visits for direct data collection with linkage to national registry data, enabling long-term follow-up of a large, nationally representative cohort of 1,100 African American living kidney donors from 2001–2005. This approach allows LETO to capture outcomes nearly two decades post-donation, providing unique insight into the risk of clinically significant CKD (eGFR <45 mL/min/1.73 m2) in African American living donors with two APOL1 RRVs, a question that prior studies with shorter follow-up and smaller sample sizes could not adequately address^1,78. LETO also aims to determine whether other independent or APOL1-interactive gene variants confer additional CKD risk, and to evaluate the impact of donor APOL1 RRVs and other genetic factors on graft survival and recipient outcomes. LETO’s comprehensive, long-term, and genetically informed approach is likely to provide definitive data on these critical questions, which have remained unresolved in the field.

Kidney transplantation mirrors the physiology of unilateral nephrectomy, with early hyperfiltration and hypertrophic responses that can become maladaptive, leading to podocyte loss, proteinuria, and reduced graft survival^18,79. Converging evidence from clinical, genetic, population, and transcriptomic studies indicates that elevated recipient-derived circulating insulin-like growth factor 1 (IGF-1), particularly in younger recipients or carriers of the IGF1 rs35767 risk allele, drives this maladaptation, increasing the risk of death-censored graft failure by approximately 50%⁸⁰. IGF-1 is a key mediator of compensatory hyperfiltration in the remaining kidney after living kidney donation^81–84. Following unilateral nephrectomy, IGF-1 promotes renal hypertrophy and increases GFR through vasodilation of renal arterioles and expansion of glomerular volume, primarily by decreasing afferent and efferent arteriolar resistance and increasing the glomerular ultrafiltration coefficient^81–84. Experimental models demonstrate that inhibition of IGF-1 signaling, using monoclonal antibodies or tyrosine kinase inhibitors, attenuates compensatory hyperfiltration, confirming IGF-1’s mechanistic role⁸³. The rise in IGF-1 activity after nephrectomy is associated with increased renal plasma flow and GFR, which are sustained over time and contribute to adaptive hyperfiltration rather than pathologic glomerular hypertension in most donors⁸⁴. This process is considered physiologically benign for the majority of living kidney donors, although rare individuals may be at increased risk for progressive kidney disease if additional insults occur^84,85. Based on current clinical cohort data, increasing the transplanted kidney dose may attenuate the detrimental impact of high IGF-1 exposure.

Recognizing the growing importance of genetic risk, the American Society of Transplantation’s (AST) Living Donor Community of Practice (LDCOP) Working Group recently recommended targeted genetic testing in selected living donor candidates, particularly those with a family history of kidney disease¹⁴. Their proposed evaluation algorithm begins with genetic counseling for both the at-risk donor candidate and the affected family member, who is often the intended recipient¹⁴. If the affected individual agrees to testing, they undergo genotyping using a phenotype-driven panel, a broad multigene panel, or whole exome sequencing (WES). The results of this initial testing help identify any pathogenic or likely pathogenic variants, which can then guide the evaluation of the potential donor. If a shared variant is found, the donor candidate is subsequently tested for the familial variant to assess their genetic risk and suitability for donation¹⁴. A negative result for a known familiar variant generally rules out the risk of that specific inherited kidney disease in the donor candidate, thereby supporting the safety of proceeding with donation. In contrast, a positive result suggests a future risk of developing the disease, which often, but not always, leads to a recommendation against donation, depending on the varianťs penetrance, disease severity, and clinical context. However, it is important to note that a negative result does not entirely exclude the possibility of genetic kidney disease, as some pathogenic variants may be missed due to limitations in the testing panel or gaps in current genetic knowledge. In some cases, testing of the affected family member (typically the recipient) may identify variants of uncertain significance (VUS), which require further interpretation before any clinical decisions can be made. To navigate these complexities, transplant teams have access to a range of resources, including variant classification databases, interpretation tools, and the expertise of genetic counselors and clinical geneticists, who play a vital role in guiding both donor and recipient evaluations^12,14. The AST LDCOP Working Group recommended that all living donor candidates who pass preliminary testing should be educated about APOL1 risk alleles and offered testing. However, the Working Group recommends against mandatory testing and emphasizes shared-decision making if the APOL1 genotype is the primary risk factor determining candidacy. A positive test should not automatically exclude a donor candidate but rather be evaluated in the context of other risk factors^{14,52,86–88}.

6. Future Directions and Research Challenges,

Research in the genetics of kidney transplantation continues to advance the field toward more precise and individualized care by refining predictive models, improving donor-recipient matching, and supporting personalized treatment strategies aimed at enhancing both graft and patient outcomes. One promising area is the application of PRS, which may help predict complications such as new-onset diabetes after transplantation (NODAT), post-transplant skin cancer, and long-term allograft failure^89–91. Future research should focus on refining PRS models, validating their utility across diverse populations, and integrating them into clinical workflows to improve patient outcomes. Optimizing PRS for NODAT prediction requires integrating genetic data with clinical risk factors, such as immunosuppressive regimens and metabolic profiles, while also investigating donor-recipient genetic interactions to better understand post-transplant glucose dysregulation⁸⁹. Similarly, for skin cancer, large-scale, multi-ethnic studies are needed to improve PRS calibration and explore its integration with environmental and clinical factors to develop personalized surveillance strategies⁹². In kidney transplantation, incorporating genetic markers related to inflammation, immune response, and allograft fibrosis could enhance PRS-based predictions.

Despite these advances, a significant gap remains in our understanding of genetic predictors of donor outcomes. Most GWAS in transplantation have focused on recipients and graft survival, with limited data on how donor genetic factors influence post-donation kidney function and long-term donor health^8,90. Expanding GWAS to investigate non-HLA genetic contributions to donor outcomes is essential, especially as living donation grows and the importance of safeguarding donor well-being gains increasing recognition. Future longitudinal studies that assess the impact of PRS-guided risk stratification on both recipient and donor management will be critical to ensure safe, ethical, and effective clinical implementation.

Beyond PRS, precision medicine is transforming the landscape of kidney transplantation by tailoring treatment strategies to the genetic, molecular, and environmental profiles of both donors and recipients. Advances in NGS and other genomic technologies now enable more refined donor-recipient matching beyond HLA loci, offering the potential to enhance long-term graft survival and reduce rejection risk. While pharmacogenomics has identified variants affecting drug metabolism, such as CYP3A5 and TPMT in kidney transplantation, broader integration with donor-recipient compatibility assessments remains limited⁹³. Ethical challenges, including informed consent with informed choice, communication and follow-up of incidental genetic findings, and disparities in access to genetic testing in certain populations, further complicate implementation^87,94. Gene-editing technologies, particularly CRISPR/Cas9, have introduced the possibility of modifying donor organs to enhance compatibility and reduce rejection risk. Recent studies have demonstrated the feasibility of gene-edited pig kidneys achieving long-term survival in non-human primates, which has paved the way for preliminary studies in humans. There is a long way to go before it can become mainstream, but the results show promise^95,96. Additionally, personalized genomics plays a crucial role in optimizing transplant outcomes by identifying genetic variations that influence graft longevity and function⁹⁰. Initiatives like iGeneTRAiN aim to uncover these genetic factors, facilitating tailored immunosuppressive regimens and improving patient management⁹⁷.

The integration of gene editing, PRS, and personalized genomics represents a paradigm shift in transplantation, enhancing donor-recipient matching, reducing rejection risks, and optimizing post-transplant care. Multi-omic approaches including transcriptomics, proteomics, and epigenetics combined with artificial intelligence and machine learning, offer promising avenues for precision medicine in transplantation. However, ethical and policy considerations must be addressed to ensure equitable access to genetic testing and prevent disparities in organ allocation. Future research should prioritize refining predictive models, validating genetic risk assessments, and incorporating personalized strategies into clinical practice. By addressing these challenges, the field of transplantation can move towards more precise, individualized approaches that improve long-term graft, patient and donor outcomes.

7. Conclusion

Recognizing the definition and scope of non-HLA genetic factors in kidney transplantation reveals their critical and multifaceted role in shaping the alloimmune response and influencing transplant outcomes. While significant progress has been made in understanding genetic contributors to graft survival and recipient health, a substantial gap remains in our knowledge of how donor genetic factors affect post-donation outcomes, including long-term kidney function and overall donor well-being. To date, most GWAS in transplantation have concentrated on recipients and allograft outcomes, with limited attention to the genetic predictors of donor outcomes. As living kidney donation continues to increase, so does the ethical and clinical imperative to ensure the long-term safety and health of living donors. Expanding GWAS and other genomic studies to include non-HLA genetic variants that influence donor outcomes is essential to provide a more complete risk profile and inform safe donation practices. While the clinical application of tools such as PRS remains in early stages, future longitudinal studies will be critical to validate their utility in both donor and recipient management. PRS-guided risk stratification, when integrated with clinical and demographic factors, holds the promise of improving transplant outcomes, enabling personalized care, and optimizing the allocation of scarce donor organs. At the same time, genetic testing is rapidly emerging as a transformative tool in the evaluation of both transplant recipients and their potential living donors. It offers unprecedented opportunities for identifying hidden familial risk, stratifying disease susceptibility, and informing decisions about eligibility and donor-recipient matching. For donors who are biologically related to their recipient or have a family history of kidney disease, genetic testing provides precision risk assessment not achievable through standard clinical evaluation alone.

In conclusion, the continued advancement of genomics and immunogenetics will be pivotal for unlocking new layers of understanding in kidney transplantation. Incorporating non-HLA genetic factors into clinical practice will enhance precision in donor-recipient matching, improve predictive models for graft and donor outcomes, and promote individualized therapeutic strategies that safeguard the health and future of all those involved in transplantation.