Hemanth Karnati’s research while affiliated with University of Texas Southwestern Medical Center and other places

Lynch Syndrome (LS) is a common genetic cancer condition that allows for personalized cancer prevention and early cancer detection in identified gene carriers. We used data from the All of Us (AOU) Research Initiative to assess the prevalence of LS in the general U.S. population, and analyzed demographic, personal, and family cancer history, stratified by LS genotype to compare LS and non-LS carriers. The results suggest that population-based germline testing for LS may identify up to 63.2% of carriers who might remain undetected due to lack of personal or family cancer history. LS affects about 1 in 354 individuals in this U.S. cohort, where pathogenic variants in the genes MSH6 and PMS2 account for the majority of cases. These results underscore the need to optimize the identification of LS across diverse populations and population-based germline testing may capture the most individuals who can benefit from precision cancer screening and prevention.

Celiac disease (CeD) is a heterogeneous autoimmune disorder influenced by genetic, environmental, and socioeconomic factors. However, little is known about clinical manifestations and genetic risks in minority populations. Using data from the All of Us Research Program, we analyzed 3,040 CeD patients, referred to as the AoU-CeD cohort, to identify clinical and genetic differences across racial and ethnic groups in the United States. CeD prevalence was highest among White individuals (1.08%) and significantly lower among Hispanic (0.36%) and Black (0.16%) populations. The majority of CeD patients were female (78.4%) and diagnosed between the ages of 18 and 64. Minority groups reported poorer physical and mental quality of life (QoL) and higher levels of pain. Ancestry-specific patterns emerged in CeD-associated conditions, with minorities more likely to report diarrhea and non-infectious gastroenteritis but less likely to have osteoporosis, hypothyroidism, chronic fatigue, or a family history of CeD. Compared to previously reported data showing that over 90% of CeD patients carry the HLA-DQ2.5 haplotype, genetic analysis revealed that only 49% of patients in the AoU-CeD cohort carried the high-risk HLA-DQ2.5 haplotype. Additionally, 16.5% lacked known HLA-DQ risk haplotypes, suggesting potential diagnostic or reporting inaccuracies. Minority groups exhibited higher rates of atypical symptoms, lower frequencies of the DQ2.5 haplotype, and distinct distributions of HLA-DQ genotypes. A long haplotype block spanning HLA-A1, B8, C7 and HLA-DQ2.5 was found in Europeans but absent in other ancestries. A genome-wide association study (GWAS) using over 11 million variants from whole-genome sequencing data identified 1,651 significant single-nucleotide polymorphisms (SNPs), primarily within the MHC locus, with the strongest signals observed predominantly among individuals of European ancestry. A predictive model incorporating HLA-DQ genotype, family history, and clinical features achieved 83% accuracy for identifying seropositive CeD. These results highlight the importance of ancestry-specific clinical presentations and genetic features in CeD.

The clinical penetrance of infectious diseases varies considerably among patients with inborn errors of immunity (IEI), even for identical genetic defects. This variability is influenced by pathogen exposure, healthcare access and host-environment interactions. We describe here a patient in his thirties who presented with epidermodysplasia verruciformis (EV) due to infection with a weakly virulent beta-papillomavirus (HPV38) and CD4 ⁺ T-cell lymphopenia. The patient was born to consanguineous parents living in the United States. Exome sequencing identified a previously unknown biallelic STK4 stop-gain mutation (p.Trp425X). The patient had no relevant history of infectious disease during childhood other than mild wart-like lesion on the skin, but he developed diffuse large B-cell lymphoma (DLBCL) and EBV viremia with a low viral load in his thirties. Despite his low CD4 ⁺ T-cell count, the patient had normal counts of CD3 ⁺ cells, predominantly double-negative T cells (67.4%), which turned out to be Vδ2 ⁺ γδ T cells. γδ T-cell expansion has frequently been observed in the 33 reported cases with STK4 deficiency. The Vδ2 γδ T cells of this STK4-deficient patient are mostly CD45RA ⁻ CD27 ⁺ CCR7 ⁺ central memory γδT cells, and their ability to proliferate in response to T-cell activation was impaired, as was that of CD4 ⁺ T cells. In conclusion, γδ T-cell expansion may act as a compensatory mechanism to combat viral infection, providing immune protection in immunocompromised individuals.