Replication stress, microcephalic primordial dwarfism, and compromised immunity in ATRIP deficient patients.

Ataxia telangiectasia and Rad3-related (ATR) kinase and its interacting protein ATRIP orchestrate the replication stress response. Homozygous splice variants in the ATRIP gene, resulting in ATRIP deficiency, were identified in two patients of independent ancestry with microcephaly, primordial dwarfism, and recurrent infections. The c.829+5G>T patient exhibited lymphopenia, poor vaccine responses, autoimmune features with hemolytic anemia, and neutropenia. Immunophenotyping revealed reduced CD16+/CD56dim NK cells and absent naïve T cells, MAIT cells, and iNKT cells. Lymphocytic defects were characterized by TCR oligoclonality, abnormal class switch recombination, and impaired T cell proliferation. ATRIP deficiency resulted in low-grade ATR activation but impaired CHK1 phosphorylation under genotoxic stress. ATRIP-deficient cells inadequately regulated DNA replication, leading to chromosomal instability, compromised cell cycle control, and impaired cell viability. CRISPR-SelectTIME confirmed reduced cell fitness for both variants. This study establishes ATRIP deficiency as a monogenic cause of microcephalic primordial dwarfism, highlights ATRIP's critical role in protecting immune cells from replication stress, and offers new insights into its canonical functions. Approximately 10 million PBMCs were isolated each for one ATRIP-deficient patient and three sex/age matched controls (human). Additionally, approximately 4000 viable CD19+ B cells were sorted for each sample by FACS. In sequencing lane 1, approximately 6000 viable PBMCs each from both the ATRIP-deficient patient and healthy control 1 were hashed (total approximately 12000 cells) and loaded for CITE-sequencing and TCR-sequencing. In lane 2, approximately 6000 viable PBMCs each from both healthy control 2 and healthy control 3 were hashed (total approximately 12000 cells) and loaded for CITE-sequencing and TCR-sequencing. In sequencing lane 3, approximately 3000 CD19+ B cells were loaded for each of the samples (total approximately 12000 cells). Due to concerns of underloading of sequencing lane 3, an additional 4000 B-cells were sorted per sample, and loaded onto sequencing lane 4 (approximately 12000 cells).