Telomere Biology Disorders Research Articles

Blood Count Recovery and Telomere Elongation in a TINF2 Patient Under Treatment with a Gonadotropin-Releasing Hormone (GnRH) Agonist

Telomere biology disorders (TBDs) caused by germline variants in TINF2 are a common cause of severe disease presenting in early childhood. Progressive bone marrow failure in patients with TBDs is often treated with androgens, known to improve hematopoiesis but with a controversial impact on telomere elongation. Here, we report a unique case of a young TINF2 male patient that had a striking recovery of blood counts and robust telomere elongation in peripheral blood cells during treatment with histrelin, a gonadotropin-releasing hormone (GnRH) agonist and inhibitor of testosterone production. We investigated whether underlying clonal events were linked to blood counts and telomere length (TL) dynamics. We extracted medical information and collected peripheral blood mononuclear cells (PBMCs) and bone marrow mononuclear cells (BMMNCs) over an 10-yr period beginning at diagnosis (age 4), which was based on cytopenias, marked marrow hypocellularity, very low TL in all leukocyte subsets by Flow-FISH, and a de novo TINF2 p.K302Rfs*17 germline variant. Following 2 yrs of observation, he was started on danazol for progressive cytopenias but it was discontinued after 21 months due to the onset of danazol-related precocious puberty, for which histrelin was administered via subcutaneous implants over 4.7 yrs. Hemoglobin levels normalized while on danazol and remained stable at last follow-up. Although platelet counts increased and stabilized at ~ 40,000 on danazol, they steadily increased after initiation of histrelin up to 156,000; they then gradually declined to 108,000 over the 18 months following removal of the last histrelin implant (Fig. 1A). The absolute neutrophil count normalized while on histrelin and has remained in normal range. While TLs remained very low in all leukocyte subsets while on danazol, they either stabilized or minimally changed (+/- 0.2 kb) in lymphocytes, CD45RA+, CD45RA-, and CD57+ cells or increased by 2.8 kb or 1 kb in granulocytes and B cells, respectively. While on histrelin, TL further increased in the lymphocytes, granulocytes, and B cells to max gains of 0.4 kb, 3 kb, and 2 kb, respectively. Fourteen months after discontinuing histrelin, TL shortened in all subsets. Screening of PBMC at 8.5 yrs of follow-up for clonal hematopoiesis (CH) in myeloid and telomere-related genes by error-corrected DNA sequencing identified POT1 p.D291Y and TINF2 p.W20* variants at variant allele frequencies (VAFs) of 20% and 4%, respectively, as likely somatic genetic rescue (SGR) mechanisms (Fig. 1B). POT1 D291Ywas retrospectively tracked at a VAF of 0.7% in total DNA before any treatment and found at a VAF of 8% in PBMC collected during danazol treatment, 27% during histrelin treatment, and 14% after histrelin discontinuation. TINF2 W20* emerged while on histrelin at a VAF of 1% in PBMC; this mutation VAF slightly increased during histrelin treatment but robust clonal expansion up to a VAF of 21% was not seen until off histrelin. Hematologic improvement, particularly thrombocytopenia, and continued telomere elongation in granulocytes and B cells (CD20+) coincided with clonal expansion of the POT1 D291Y variant. Single-cell proteogenomic sequencing of BMMNCs evidenced POT1 D291Y and TINF2 W20* as independent clonal events that emerged in CD34+ hematopoietic stem cells (HSC) and were present both in the megakaryocytic and erythroid, and myeloid and lymphoid progenitor cells. During histrelin treatment, POT1 D291Y dominated the landscape and associated with increased lymphocyte counts, being present in 30% of HSC and progenitor cells, myeloid cells, and T lymphocytes. When histrelin was discontinued, hematopoiesis greatly shifted toward myeloid production, which coincided with TINF2 W20*clonal expansion and a substantial reduction of progenitors and CD8+ cells. Single-cell RNAseq of BM HSC revealed similar transcriptional profiles while on danazol and histrelin compared to baseline, with up and downregulation of inflammatory pathways and MYC targets, respectively; these programs were enhanced while on histrelin compared to danazol. In summary, we characterized a unique combination of SGR events in a patient with a TINF2 germline mutation, which can guide future research on new therapeutic strategies. As opposed to androgens, histrelin promoted the specific expansion of POT1 clones with proliferation of HSC and progenitor cells, improved hematopoiesis, and increased TL.

A Zebrafish Model of Parn-Deficiency Reveals Conserved Mechanisms Underlying Marrow Failure and Opportunities for Therapeutic Amelioration of Hematopoiesis

Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome (IBMFS) and a telomere biology disorder that is characterized by physical malformations such as nail dystrophy, oral leukoplakia, reticular hyperpigmentation, multilineage cytopenia and immunodeficiency. Definitive treatment for the hematological complications is hematopoietic stem cell transplantation (HSCT), which is associated with high risk of organ toxicity and engraftment failure in this population. Further, DC patients are prone to developing myelodysplastic syndrome (MDS) and solid tumors. Germline mutations in the poly(A)-specific ribonuclease (PARN) gene are associated with Hoyeraal-Hreidarsson syndrome, the most severe form of DC. PARN encodes a deadenylase enzyme involved in the 3'-end processing of various RNAs including the telomerase RNA component (TERC). The clinical heterogeneity of phenotypes and the paucity of primary human samples necessitate the use of animal models such as zebrafish ( Danio rerio), given their highly conserved genetic program, to elucidate underlying biology. Zebrafish have a single PARN ortholog with 64% sequence identity at the amino acid level. Using CRISPR-Cas9 mutagenesis, we generated a 1.3 kb deletion in the zebrafish parn gene, predicted to result in premature protein truncation. To measure the hematopoietic output of the parn mutants, we performed whole-mount in situ hybridization (WISH) for key hematopoietic lineage markers. At 48 hours post-fertilization (hpf), we found a reduction in lcp1 + total leukocytes, mpx + neutrophils and hbbe3 + mature erythrocytes. Impaired erythroid differentiation was accompanied by an accumulation of gata1 + erythroid progenitors. This finding was further corroborated by o-dianisidine staining, showing reduced hemoglobinized erythrocytes. Thus, erythrocyte and leukocyte differentiation are compromised in our zebrafish parn mutant, phenocopying the multilineage cytopenia observed in DC patients. Flow cytometry of the whole kidney marrow (WKM, human bone marrow equivalent) at 12 months of age revealed an increase in hematopoietic stem and progenitor cells in the parn mutants. Giemsa staining of WKM touchpreps further identified an increase in myeloid-biased progenitors. Next, we investigated the consequences of Parn loss on telomerase activity. Using the telomere repeat amplification protocol, we found reduced telomerase activity in the WKMs of parn mutant zebrafish. Using 3' rapid amplification of cDNA ends, we observed longer ends in the terc amplicons of the parn mutants, reminiscent of defective deadenylation of human TERC RNA in the setting of PARN mutations. Exogenous thymidine supplementation has been shown to support telomere elongation in human cells. Following treatment of zebrafish embryos with thymidine nucleoside, we observed an improvement in erythrocyte numbers in the parn mutants by o-dianisidine staining at 48 hpf. Collectively, our preliminary findings suggest that telomerase-dependent mechanisms may contribute to the erythropenia seen in parn-mutant zebrafish. In summary, we generated a robust zebrafish model carrying a germline parn mutation that phenocopies the molecular and hematologic features seen in DC patients. Our model holds promise as a new in vivo tool for investigating DC-related disease mechanisms and as a platform for preclinical therapeutic screening.

Immune Signature in Telomere-Biology Disorders

Excessive telomere shortening caused by pathogenic germline variants in telomere-biology genes may result in bone marrow failure, hematopoietic malignancy and extramedullary complications, such as idiopathic pulmonary fibrosis (IPF), liver cirrhosis, and solid tumors. Patients with short telomeres also may develop immunodeficiency with low counts of T-cell receptor excision circles (TRECs), kappa-deleting excision circles (KRECs), and CD4 + T cells. The aim of the present study was to comprehensively determine the immune system changes in human patients with telomeropathies by deep-phenotyping peripheral blood mononuclear cells (PBMCs) and quantifying cytokine serum levels. We applied a 39-marker panel of metal-labeled antibodies and employed mass cytometry (CyTOF) to assess the subsets of lymphocytes, monocytes, and dendritic cells (DC) in 20 patients and 10 healthy individuals. High-dimensional analysis was conducted using automated clustering ( Flow-SOM) to identify subpopulations and cell states, whereas t-SNE was employed as a visualization tool. A total of 32 serum cytokines, chemokines and growth factors were quantified by a bead-based immunoassay (Luminex™). First, we confirmed previous findings of low CD4/CD8 ratio (0.73±0.56 vs. 1.3±0.69 in controls, p=0.05), and reduced absolute naïve (CD45RA +CCR7 +) CD4 + and CD8 + cell counts ( p<0.01), with effector memory cell accumulation in patients with telomere diseases, and the current study further showed a reduction in naïve B (CD19 +IgD +CD27 -) and in recent thymic emigrants (RTE), characterized by CD31 +CD45RA + ( p<0.01), indicating a consistent aged B and T cell profile. T H1, T H17 and T H17.1 CD4 + lymphocytes were reduced ( p<0.05), whereas the T H2/T H1 ratio was increased (1.6±0.83 vs. 0.82±0.39 in controls; p=0.013), demonstrating a dysregulated T helper cell diversity. T regs, on the other hand, did not appear to be affected. Plasmacytoid DCs (CD3 -CD141 +CD123 +CD1c -), which are known inducers of T helper differentiation, were reduced in patients ( p=0.014). A double negative T cell (DNT) population, characterized as CD3 +CD4 -CD8 -Vd2 -Tbet +Granzyme B +, was significantly increased ( p=0.0002). Activated effector memory and TEMRA CD4 + cells, also expressing exhaustion markers PD-1 and TIGIT (CD4 +CD45RA +/-CCR7 -CD38 +HLADR +Ki67 +PD-1 +TIGIT low) and proliferating switched memory B cells (CD3 -CD19 +IgD -CD27 +Ki67 +) were higher ( p=0.046 and p=0.041, respectively) suggesting the occurrence of an environment prone to immune activation, also supported by the prevalence of CD14 +CD16 +CXCR3 +CCR4 + classical monocytes ( p=0.0042). Additionally, mucosal-associated invariant T (MAIT) cells (CD3 +CD161 highVɑ7.2 +) were markedly reduced in patients ( p<0.0001), possibly due to their recruitment to other tissues as a response to inflammation. Conversely, immature NK cells (CD3 -CD19 -CD56 brightCD16 -) were more frequent in patients as compared to controls ( p=0.026), and individuals with the shortest telomere lengths had an even higher frequency of these cells. In addition to the previously described CD4 + immunodeficiency, the predominance of immature NK cells may potentially impact the immunosurveillance of malignant transformations. When an unsupervised clustering algorithm using cell subpopulations as variables was applied, patients and controls were correctly identified in 100% of cases. Telomere length positively correlated with some cytokine levels in serum. This was observed for angiopoietin-1, IL-1 superfamily, IL-3, IL-4, IL-7, IL-23, IL-27, M-CSF, MCP-1, MIP-3a and PDGF-BB. Taken together, our results reveal a distinct immunophenotype in telomeropathies, which comprises deficient or skewed maturation of certain subsets, an aged phenotype of B and T cells, aberrant lymphocyte activation and very low levels of circulating MAIT cells, which might be indicators of ongoing inflammatory processes, tied with dysregulated cytokine levels. This immune perturbance may contribute to the clinical onset of telomeropathies and increase the risk of infections, cirrhosis, IPF and cancer development.

Impact of Dkc1 Deficiency on BM Niche Function during Hematopoietic Stem Cell Transplantation in a Conditional Murine Model of X-Linked Dyskeratosis Congenita

Dyskeratosis congenita (DC) is a telomere biology disorder associated with bone marrow failure (BMF) and the triad of dystrophic nails, skin rashes, and leukoplakia. X-linked DC (XDC) is caused by mutations in DKC1, which encodes dyskerin, a nucleolar protein associated with rRNA processing and telomerase complex formation. Hematopoietic stem cell transplantation (HSCT) is currently the only definitive curative treatment for BMF in XDC patients, though many patients exhibit only partial restoration of hematopoietic function. Our previous studies demonstrated that molecular and cellular defects in BM niches contribute to poor donor HSC engraftment in murine models of other BMF syndromes, including Shwachman-Diamond Syndrome (SDS), a disease whose pathogenesis intersects with the role of dyskerin in ribosome biogenesis. These studies led us to hypothesize that BM niche dysfunction contribute to poor graft function in DC patients post-HSCT. Defining specific deficits would enable development of novel targeting strategies to improve HSCT outcomes for patients with XDC. Here, we report that in a novel murine model of XDC driven by conditional Dkc1 deletion, Dkc1 deficiency within mesenchymal BM niche cells causes significant impairment of healthy donor HSC engraftment after HSCT. We have identified defects in multiple pathways within Dkc1-deficient BM niche in response to myeloablative conditioning that may drive this reduction in HSC supportive capacity. To generate a murine model with conditional Dkc1 deletion in BM niche, we crossed Dkc1l/lmice with Mx1 Cre+mice, inducing Cre expression in hematopoietic cells and Mx1-inducible niche cells by polyinosinic-polycytidylic acid administration. At baseline, the resulting Mx1 CreDkc1 Exc mice exhibit mild hematopoietic abnormalities versus Dkc1 l/l controls, including variable thrombocytopenia, increased blood monocytes, and reduced BM lymphoid progenitors. To assess capacity of BM niches from Mx1 CreDkc1 Exc mice to efficiently engraft donor HSC, we transplanted Mx1 CreDkc1 Exc mice and Dkc1 l/l controls with healthy GFP + wild-type donor BM and assessed efficiency of donor HSC engraftment at 2 weeks following HSCT using competitive secondary HSCT. The Mx1 CreDkc1 Exc recipients exhibited significantly impaired efficiency of donor HSC engraftment compared with controls, as indicated by a 25-30% reduction of long-term GFP + cell reconstitution in mature blood lineages in secondary recipients (Figure 1). We next sought to identify molecular and cellular defects in BM niche that contribute to the engraftment deficits in Mx1 CreDkc1 Exc mice. Flow cytometry analysis of BM niche cells 48 hours after total body irradiation (TBI) showed Mx1 CreDkc1 Exc mice exhibited a 20% reduction of CD11b+F4/80+ osteomacs compared to Dkc1 l/l controls. In contrast to our published findings in a model of SDS, the frequencies of osteoprogenitors, mesenchymal stem cell, endothelial cells and megakaryocytes in BM niche were similar between irradiated Dkc1-deficient and control mice. We then performed multiplex ELISA and RNA-seq analyses on isolated BM niche cells from Mx1 CreDkc1 Exc versus control BM at 48 hours post-TBI. Irradiated Mx1 CreDkc1 Exc BM niche demonstrated lower expression of multiple chemokines, including CXCL1, CXCL12, CCL1, CCL11 and CCL12, known to be critical for recruiting HSC and many leukocyte subsets. Dkc1 deficiency in post-TBI BM niche cells also led to lower expression of genes that regulate production of IFN-γ and IL-1, resulting in reduced expression level of both cytokines that may drive decreased osteomacs seen in Dkc1-deficient BM niches. Moreover, Gene Ontology analysis indicates that after TBI, Dkc1 deficiency within BM niches resulted in downregulation of gene expression involved in cell-cell adhesion and extracellular matrix, both of which are critical for HSC enlodgement and engraftment after HSCT. Taken together, our results demonstrated that Dkc1 deficiency in BM niche cells that are not replaced by HSCT impairs the ability of these niches to engraft donor HSC efficiently. Disruptions of molecular and cellular pathways implicated in the niche dysfunction of this XDC model are distinct from our previous findings with SDS model. Ongoing and future studies are needed to define which of these pathways have the highest potential to serve as translational targets to improve HSCT success rate to treat BMF in patients with XDC.

Implementation of a prospective screening strategy to identify adults with a telomere biology disorder among those undergoing lung transplant evaluation for interstitial lung disease

IntroductionPatients with interstitial lung disease (ILD) secondary to telomere biology disorders (TBD) experience increased morbidity after lung transplantation. Identifying patients with TBD may allow for personalized management to facilitate better outcomes. However, establishing a TBD diagnosis in adults is challenging. MethodsA TBD screening questionnaire was introduced prospectively into the lung transplant evaluation. Patients with ILD screening positive were referred for comprehensive TBD phenotyping and concurrent telomere length measurement and germline genetic testing. ResultsOf 98 patients, 32 (33%) screened positive. Eight patients (8% of total; 25% of patients with a positive screen) met strict TBD diagnostic criteria, requiring either critically short lymphocyte telomeres (<1st percentile) (n = 4), a pathogenic variant in a TBD-associated gene (n = 1), or both (n = 3) along with a TBD clinical phenotype. Additional patients not meeting strict diagnostic criteria had histories consistent with TBD along with telomere lengths <10th percentile and/or rare variants in TBD-associated genes, highlighting a critical need to refine TBD diagnostic criteria for this patient population. ConclusionA TBD phenotype screening questionnaire in patients with ILD undergoing lung transplant evaluation has a diagnostic yield of 25%. Additional gene discovery, rare variant functional testing, and refined TBD diagnostic criteria are needed to realize the maximum benefit of testing for TBD in patients undergoing lung transplantation.

Telomere biology disorders may manifest as common variable immunodeficiency (CVID)

Telomere biology disorders (TBD) are caused by germline pathogenic variants in genes related to telomere maintenance and are characterized by critically short telomeres. In contrast to classical dyskeratosis congenita (DC), which is typically diagnosed in infancy, adult or late onset TBD frequently lack the typical DC triad and rather show variable organ manifestations and a cryptic disease course, thus complicating its diagnosis. Common variable immunodeficiency (CVID), on the other hand, is a primary antibody deficiency (PAD) syndrome. PADs are a heterogenous group of diseases characterized by hypogammaglobulinemia which occurs due to dysfunctional B lymphocytes and additional autoimmune and autoinflammatory complications. Genetic screening reveals a monogenic cause in a subset of CVID patients (15–35%). In our study, we screened the exomes of 491 CVID patients for the occurrence of TBD-related variants in 13 genes encoding for telomere/telomerase-associated proteins, which had previously been linked to the disease. We found 110/491 patients (22%) carrying 91 rare candidate variants in these 13 genes. Following the American College of Medical Genetics and Genomics (ACMG) guidelines, we classified two variants as benign, two as likely benign, 64 as variants of uncertain significance (VUS), four as likely pathogenic, and one heterozygous variant in an autosomal recessive disease gene as pathogenic. We performed telomere length measurement in 42 of the 110 patients with candidate variants and CVID. Two of these 42 patients showed significantly shorter telomeres compared to controls in both lymphocytes and granulocytes. Following the evaluation of the published literature and the patient's manifestations, we re-classified two VUS as likely pathogenic variants. Thus, 0.5–1% of all CVID patients in our study carry possibly pathogenic variants in telomere/telomerase-associated genes. Our data adds CVID to the broad clinical spectrum of cryptic adult-onset TBD. As the molecular diagnosis greatly impacts patient management and treatment strategies, we advise inclusion of all TBD-associated genes—despite their low prevalence—into the molecular screening of patients with antibody deficiencies.

Telomere Length Testing of Lymphocytes Alone By Flow-FISH Is a Highly Sensitive and Specific Test to Screen for a Telomere Biology Disorder in a Cohort of Children and Very Young Adults with Bone Marrow Failure

Background Uncovering an underlying telomere biology disorder (TBD) in patients with bone marrow failure (BMF) has crucial implications for treatment and outcomes, including hematopoietic cell transplantation and malignancy risk. Telomere length (TL) testing of peripheral blood leukocytes by clinical Flow-FISH has become an important test in diagnosing TBDs. In seminal studies, Alter et al. compared age-adjusted TL lengths (&amp;lt; or ≥1 st percentile) in lymphocytes (lymphs), granulocytes (grans), and four lymph subsets in individuals with a known TBD and their unaffected relatives. They found that very low (VL) TL (&amp;lt;1 st percentile) in lymphs had a sensitivity (Sens) of 97%, specificity (Spec) of 91%, and positive predictive value (PPV) of 85% for a TBD diagnosis. VL TL in 3 or 4 lymph subsets had slightly better test performance with a Sens of 98%, Spec of 94%, and PPV of 89%. We hypothesized that test performance characteristics of flow FISH would be different if applied to a ‘real-world’ cohort, which could inform the use of TL in lymphs alone versus in the four lymph subsets for different clinical indications. Methods We performed a search of the electronic medical record to identify all individuals who had Flow-FISH performed at Texas Children's Hospital from 2007 - 2022 (Figure 1). We excluded those who had the 2-panel test (lymphs and grans) or family TL cascade testing. We collected the indication for and results of Flow-FISH, demographic and clinical characteristics, and genetic testing information via chart review. A composite score (Comp Score) was created to define TBD (Comp Score of 1 or 2) vs. Not TBD (Comp Score &amp;lt;1). Performance of lymph TL alone and TL in 3 or 4 lymph subsets in predicting TBD was evaluated using Sens, Spec, PPV, NPV, area under ROC curve (AUC), and Cohen's Kappa statistic (k). Results Our final cohort included 433 individuals who received the 6-panel test (lymphs, grans, and four lymph subsets) with a median age of 9.7 years, range 0.06-22.6. Top indications for Flow-FISH were severe aplastic anemia (SAA) (n=106), mild aplastic anemia (AA) (i.e., not fulfilling criteria for MAA or SAA) (103), cytopenias without known or documented bone marrow hypoplasia or dysplasia (70), moderate aplastic anemia (MAA) (37), non-therapy-related myelodysplastic syndrome (26), and an incidental TBD gene variant identified through comprehensive sequencing (17). Twenty-two subjects (5.1%) had a TBD, 17 (3.9%) of which had a pathogenic/likely pathogenic variant (P/LPV) in a known TBD gene (Figure 1). Seven of those with SAA (6.6%) had VL TL in lymphs, 5 (4.7%) of which also had VL TL in 3 or 4 of the lymph subsets, and only 1 (0.9%) had a TBD based on Comp Score. Importantly, none had VL TL in 3 or 4 of the lymph subsets without VL TL in lymphs. Five of those with MAA (13.5%) had VL TL in lymphs, all of which had VL TL in 3 or 4 lymph subsets. Three had a TBD based on Comp Score, and each had a PV in a TBD gene; a TBD variant was not identified in two despite exome sequencing and chromosomal microarray testing. Eighteen of those with mild AA (17.5%) had VL TL in lymphs, 15 (14.6%) also had VL TL in 3 or 4 lymph subsets, 9 (8.7%) had a TBD based on Comp Score, and 7 (6.8%) had a P/LPV in a TBD gene. The Sens of TL in lymphs &amp;lt; vs. ≥ 1 st percentile and TL &amp;lt; 1 st percentile in 3 or 4 vs. &amp;lt; 3 lymph subsets against TBD based on Comp Score in those with AA regardless of severity was 100%, and the Spec ranged from 90.4% (lymph TL testing alone in mild AA) to 96.2% (lymph subsets testing in SAA) (Table 1). The PPV for both test approaches was low (≤20%) in SAA due to the low prevalence of TBD in this population. PPV was between 50-60% in the other AA groups. The AUC for detecting a TBD in the various AA groups was comparably high for both test approaches (0.95-0.98). The two tests had a substantial to almost perfect agreement (k=0.82, p&amp;lt;0.001). Conclusions This single institutional cohort demonstrates that the prevalence of TBD in young patients presenting with SAA is remarkably low, and the Sens and Spec of TL testing in lymphs alone are sufficiently high to detect the rare TBD patient and prompt additional testing (e.g., genetics) in few patients due to false positive testing. The prevalence of TBD is higher in those with MAA or mild AA, yet both test approaches detect all TBD patients. Spec level in mild AA is marginally higher with lymph subset TL testing but, at ~94%, underscores the need for other clinical parameters (e.g., genetics) to establish a TBD diagnosis in a small percentage of patients.

Prevalence and Spectrum of Autoimmune Diseases Among Patients with Telomere Biology Disorder

Introduction Telomeres are the protective ends of linear chromosomes that prevent DNA degradation with each replication. Premature attrition or dysfunction of telomeres due to an inherited defect in a telomere maintenance gene results in a spectrum of phenotypes collectively known as telomere biology disorders (TBD). To date, 18 genes have been implicated in TBD. Disease phenotypes are variable including bone marrow failure, immunodeficiency, myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), idiopathic pulmonary fibrosis (IPF), liver cirrhosis, nail dystrophy, and premature graying of hair. Short telomeres have been observed in patients with autoimmune disorders (AID) and have been shown to increase the risk of AID. Furthermore, TBD have been associated with T cell dysfunction and exhaustion, mechanisms which may predispose to autoimmune phenotypes. Given the potential relationship between short telomeres and immune dysregulation, we hypothesize that the prevalence of AID may be increased in patients with a diagnosis of TBD. The aim of this study is to describe the prevalence and spectrum of AID in a cohort of patients with TBD. Methods Health record data were reviewed for 34 adult patients with confirmed TBD treated at the University of Wisconsin-Madison. A TBD diagnosis was established for patients who had a compatible clinical history plus either critically short lymphocyte telomere lengths (&amp;lt;1 st percentile for age as measured by FlowFISH) or one or more pathogenic/likely pathogenic variant(s) in a gene known to cause TBD. Demographics, rheumatologic history, serologies, and family history were collected. AID were included if diagnoses were made by a rheumatologist or other appropriate specialist with clinical features, physical exam findings, and/or serologies meeting diagnostic criteria per subspecialty guidelines. Results Eight of 34 patients (23.5%) with TBD had a concomitant diagnosis of a primary autoimmune condition. Specific AID included inflammatory bowel disease, Graves' disease, Hashimoto's thyroiditis, rheumatoid arthritis, scleroderma, and Sjogren's syndrome (Table 1). Two patients had autoimmune cytopenias, including steroid-responsive immune thrombocytopenic purpura and pure red cell aplasia (PRCA). Patient 8 was diagnosed with PRCA mixed with spur cell anemia prior to transplant, and bone marrow biopsy showed pure erythroid hypoplasia without evidence of malignancy. He responded to treatment with steroids and immunosuppression. Of the eight patients with a primary autoimmune condition, two had pathogenic/like pathogenic variants, two had rare variants of uncertain significance, and four had no detectable variants in a telomere associated gene. Twenty-three patients (67.6%) had a first- or second-degree relative with an autoimmune disorder. Conclusions An AID, as defined by strict diagnostic criteria per subspecialty guidelines, was present in 23.5% of patients with TBD defined by conservative diagnostic criteria. The spectrum of AID was diverse, including two patients with autoimmune hematologic disorders, and the majority had a family history of various AID. Thus, TBD may be associated with an increased prevalence of AID, though confirmation in a larger cohort of genetically defined TBD patients is needed. In the absence of a causative genetic lesion, diagnosis of a TBD based on critically short telomeres in those with multisystem autoimmune disorders with features that overlap TBD phenotypes can be challenging. Screening for AID as part of routine TBD comprehensive assessments as well as offering germline genetic testing for individuals with primary autoimmune disease with a compatible TBD phenotypes and studies to determine the mechanistic relationship between telomere length and autoimmunity are warranted.

Distribution of Chromosome-Arm Specific Telomere Length in Patients with Telomere Biology Disorders

Introduction: Telomere biology disorders (TBD) are multisystem diseases often associated with bone marrow failure (BMF) and pulmonary fibrosis. TBD are clinically diagnosed when mean telomere lengths (TL) in blood cells measured by clinical flowFISH assays fall &amp;lt;1 st percentile, in comparison to age-matched reference controls. This information has limitations, e.g. TL in blood cells may not represent TL in other organs (e.g. lung, liver) and moreover, individuals with high clinical suspicion of TBD can show borderline average TL which complicates their diagnosis. The likely reason for this is that cell senescence can be triggered by shortening of a subset, or even a single chromosome arm telomere, a situation that may be missed when measuring average TL. Previous approaches to measure individual chromosome-arm telomere length (CA-TL) are only available for a small number of chromosome arms or can only estimate the number of shortened telomeres without matching them to specific chromosome arms. Taking advantage of recent developments in long-read next generation sequencing (NGS) and the availability of the recently published telomere-to-telomere (T2T) reference human genome, our group developed Telogator, (Stephens Z. et al, 2022) a bioinformatic tool that estimates CA-TL for most chromosome arms using long-read NGS data. Here we use Telogator to describe for the first time the CA-TL pattern in TBD patients in comparison with a control non-TBD cohort. Methods: TBD patients were identified through the Pre-Myeloid and Bone Marrow Failure Specialty Clinic at Mayo Clinic. All patients underwent flowFISH and genetic testing. Age-matched non-TBD patients identified at the Center for Individualized Medicine (Mayo Clinic) were used as reference controls. Informed consent was obtained from all individuals with approval from the Mayo Clinic Institutional Review Board. DNA from peripheral blood mononuclear cells was sequenced using PacBio Sequel II following the manufacturer indications for HiFi sequencing. BAM files were aligned to the T2T reference and CA-TL was calculated using Telogator as described in Stephens Z. et al. 2022. Average TL, CA-TL, and percent of short telomeres (both defined as &amp;lt;5 kb and &amp;lt;3.2 kb) were calculated. Comparisons of average TL and percent of short telomeres were performed using t-test, while Wilcoxon rank-sum test was used to compare CA-TL. Results: Four TBD patients [median age = 58.5 (52-60), 50% female] and 6 non-TBD controls [Median age = 56 (50-63), 33% female] were included in the analysis. All TBD patients presented average TL below the 1 st centile in both lymphocytes and granulocytes, and TBD-related phenotype (100% with pulmonary fibrosis, 50% with BMF, 25% with liver fibrosis). Three had a pathogenic variant in a TBD related genes [2 in TERT (NM_198253.3: c.2030G&amp;gt;A, p.(Gly677Asp) and c.2515_2533del, p.(Thr839Alafs*29)) and 1 in NHP2 (NM_017838.3: c.459_460delAT; p.(X154Argext29))]. The average TL calculated by Telogator showed high correlation with flowFISH values (r 2 = 0.9883, p = 0.0059) and was lower in TBD patients than controls (p = 0.0012). Next, when comparing individual CA-TL between groups, only half of CA-TL was statistically different in the TBD group compared to controls (1p, 3q, 4p, 5p, 5q, 6q, 7p, 7q, 8q, 9p, 9q, 10q, 11p, 12q, 12q, 16p, 16q, 18q, 19p, 19q, 20p, 20q, 21q - Figure 1). The percentage of telomeres &amp;lt;5kb and &amp;lt;3 kb was significantly increased in TBD patients compared to controls (p= 0.014 and 0.0333, respectively). Discussion: Using a novel informatic tool, we replicate previous results obtained using classic approaches and were able to expand on these studies by measuring specific CA-TL in TBD patients. We identified statistically significant differences at the CA-TL level in these patients when compared to age-matched controls, while other CA-TL were not statistically different. Future studies and the inclusion of additional TBD patients will help define the clinical relevance of the differential CA-TL shortening and its prevalence among TBD patients. While limited by the small number of samples in the study, we show the feasibility of using this approach to study TL with unprecedented resolution and show that Telogator offers important advantages compared to classic methods to study telomere biology that can be used in other relevant fields like aging and/or cancer. Our results pave the way to advance the mechanistic understanding of TBD.

Telomere dysfunction promotes cholangiocyte senescence and biliary fibrosis in Primary Sclerosing Cholangitis.

Cellular senescence and biliary fibrosis are prototypical features of obliterative cholangiopathies, such as Primary Sclerosing Cholangitis (PSC). Telomere dysfunction can lead to senescence either through telomere erosion or damaged telomeres. Our goal was to investigate a mechanistic relationship between telomere damage and biliary fibrosis in PSC. Telomere attrition was observed in the bile ducts of PSC patients along with a reduction in telomerase reverse transcriptase (TERT) expression compared to normal livers. Similarly, liver tissue from mice models of biliary fibrosis showed telomere attrition with increased damage at telomeres measured as telomere-associated foci (TAF). Cellular models of senescence induction increased the TAFs in cholangiocytes. This coincided with decreased TERT expression and increased senescence, which was rescued by modulating TERT levels. Epigenetic analysis revealed increased acquisition of repressive histone methylation at the TERT promoter which correlated with decreased TERT transcription. Cholangiocyte-selective deletion of TERT in mice exacerbated fibrosis whereas androgen therapy towards telomerase rescued liver fibrosis and liver function in genetic mouse model of PSC. Our results demonstrate a mechanistic role for telomere dysfunction in cellular senescence and fibrosis that characterize PSC. This suggests that PSC may be, in part, a telomere biology disorder, and identifies TERT as a potential therapeutic target.

Telomeric repeat-containing RNA is dysregulated in acute myeloid leukemia

AbstractTERRA (telomeric repeat-containing RNA) is a class of long noncoding RNAs transcribed from subtelomeric and telomeric regions. TERRA binds to the subtelomeric and telomeric DNA–forming R-loops (DNA-RNA hybrids), which are involved in telomere maintenance and telomerase function, but the role of TERRA in human cells is not well characterized. Here, we comprehensively investigated for the first time TERRA expression in primary human hematopoietic cells from an exploratory cohort of patients with acute myeloid leukemia (AML), patients with acute lymphoblastic leukemia (ALL), patients with telomere biology disorder (TBD), and healthy subjects. TERRA expression was repressed in primary human hematopoietic cells, including healthy donors, patients with ALL, and patients with TBD, irrespective of their telomere length, except for AML. A second cohort comprising 88 patients with AML showed that TERRA was overexpressed in an AML subgroup also characterized by higher R-loop formation, low TERT and RNAseH2 expression, and a paucity of somatic splicing factor mutations. Telomere length did not correlate with TERRA expression levels. To assess the role of TERRA R-loops in AML, we induced R-loop depletion by increasing RNAseH1 expression in 2 AML cell lines. Decreased TERRA R-loops in AML cell lines resulted in increased chemosensitivity to cytarabine. Our findings indicate that TERRA is uniformly repressed in primary human hematopoietic cells but abnormally expressed in an AML subset with low telomerase.

Germline landscape of RPA1, RPA2 and RPA3 variants in pediatric malignancies: identification of RPA1 as a novel cancer predisposition candidate gene.

Replication Protein A (RPA) is single-strand DNA binding protein that plays a key role in the replication and repair of DNA. RPA is a heterotrimer made of 3 subunits - RPA1, RPA2, and RPA3. Germline pathogenic variants affecting RPA1 were recently described in patients with Telomere Biology Disorders (TBD), also known as dyskeratosis congenita or short telomere syndrome. Premature telomere shortening is a hallmark of TBD and results in bone marrow failure and predisposition to hematologic malignancies. Building on the finding that somatic mutations in RPA subunit genes occur in ~1% of cancers, we hypothesized that germline RPA alterations might be enriched in human cancers. Because germline RPA1 mutations are linked to early onset TBD with predisposition to myelodysplastic syndromes, we interrogated pediatric cancer cohorts to define the prevalence and spectrum of rare/novel and putative damaging germline RPA1, RPA2, and RPA3 variants. In this study of 5,993 children with cancer, 75 (1.25%) harbored heterozygous rare (non-cancer population allele frequency (AF) < 0.1%) variants in the RPA heterotrimer genes, of which 51 cases (0.85%) had ultra-rare (AF < 0.005%) or novel variants. Compared with Genome Aggregation Database (gnomAD) non-cancer controls, there was significant enrichment of ultra-rare and novel RPA1, but not RPA2 or RPA3, germline variants in our cohort (adjusted p-value < 0.05). Taken together, these findings suggest that germline putative damaging variants affecting RPA1 are found in excess in children with cancer, warranting further investigation into the functional role of these variants in oncogenesis.

Genetic Counseling and Family Screening Recommendations in Patients with Telomere Biology Disorders.

Telomere biology disorders (TBDs) encompass a spectrum of genetic diseases with a common pathogenesis of defects in telomerase function and telomere maintenance causing extremely short telomere lengths. Here, we review the current literature surrounding genetic testing strategies, cascade testing, reproductive implications, and the role of genetic counseling. The understanding of the genetic causes and clinical symptoms of TBDs continues to expand while genetic testing and telomere length testing are nuanced tools utilized in the diagnosis of this condition. Access to genetic counseling is becoming more abundant and is valuable in supporting patients and their families in making informed decisions. Patient resources and support groups are valuable to this community. Defining which populations should be offered genetic counseling and testing is imperative to provide proper diagnoses and medical management for not only the primary patient, but also their biological relatives.

Novel pathological variants of NHP2 affect N-terminal domain flexibility, protein stability, H/ACA RNP complex formation and telomerase activity.

Telomere biology disorders (TBDs) are characterized by short telomeres, premature aging, bone marrow failure, and cancer predisposition. Germline mutations in NHP2, encoding for one component of the telomerase cofactor H/ACA RNA binding complex together with Dyskerin, NOP10, and GAR1, have been previously reported in rare cases of TBDs. Here we report two novel NHP2 variants (NHP2-A39T and NHP2-T44M) identified in a compound heterozygous patient affected by premature aging, bone marrow failure/myelodysplastic syndrome, and gastric cancer. Although still able to support cell viability, both variants reduce the levels of hTR, the telomerase RNA component, and telomerase activity, expanding the panel of NHP2 pathological variants. Furthermore, both variants fail to be incorporated in the H/ACA RNA binding complex when in competition with wild-type endogenous NHP2, and the lack of incorporation causes their drastic proteasomal degradation. By RoseTTAFold prediction followed by molecular dynamics simulations, we reveal a dramatic distortion of residues 33-41, which normally position on top of the NHP2 core, as the main defect of NHP2-A39T. Furthermore, we predicted high flexibility and the misplacement of the N-terminal region (residues 1-24) in NHP2-T44M and, to a lower degree, in NHP2-A39T. Since deletion of amino acids 2-24 cause a reduction in NHP2 levels only in the presence of wild type NHP2, while deletion of amino acids 2-38 completely disrupts NHP2 stability, we propose that the two variants are mis-incorporated into the H/ACA binding complex due to the altered dynamics of the first 23 amino acids and/or the distortion of the residues 25-41 loop.

The distribution and accumulation of the shortest telomeres in telomere biology disorders.

Individuals with telomere biology disorders (TBDs) have very short telomeres, high risk of bone marrow failure (BMF), and reduced survival. Using data from TBD patients, a mean leukocyte Southern blot telomere length (TL) of 5 kilobases (kb) was estimated as the 'telomere brink' at which human survival is markedly reduced. However, the shortest telomere, not the mean TL, signals replicative senescence. We used the Telomere Shortest Length Assay (TeSLA) to tally TL of all 46 chromosomes in blood-derived DNA and examined its relationship with TBDs. Patients (n = 18) had much shorter mean TL (TeSmTL) (2.54 ± 0.41 kb vs. 4.48 ± 0.52 kb, p < 0.0001) and more telomeres <3 kb than controls (n = 22) (70.43 ± 8.76% vs. 33.05 ± 6.93%, p < 0.0001). The proportion of ultrashort telomeres (<1.6 kb) was also higher in patients than controls (39.29 ± 10.69% vs. 10.40 ± 4.09%, p < 0.0001). TeS <1.6 kb was associated with severe (n = 11) compared with non-severe (n = 7) BMF (p = 0.027). Patients with multi-organ manifestations (n = 10) had more telomeres <1.6 kb than those with one affected organ system (n = 8) (p = 0.029). Findings suggest that TBD clinical manifestations are associated with a disproportionately higher number of haematopoietic cell telomeres reaching a telomere brink, whose length at the single telomere level is yet to be determined.

DNA methylation variations and epigenetic aging in telomere biology disorders

Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.

Progression of liver disease and portal hypertension in dyskeratosis congenita and related telomere biology disorders.

Dyskeratosis congenita (DC) and related telomere biology disorders (TBD) are characterized by very short telomeres and multisystem organ involvement including liver disease. Our study aimed to characterize baseline hepatic abnormalities in patients with DC/TBD and determine risk factors associated with liver disease progression. A retrospective review was performed on a cohort of 58 patients (39 males) with DC/TBD who were prospectively evaluated at a single institute from 2002 to 2019. The median age at initial assessment was 18 (1.4-67.6) years, and median follow-up duration was 6 (1.4-8.2) years. Patients with autosomal or X-linked recessive inheritance and those with heterozygous TINF2 DC were significantly younger, predominantly male, and more likely to have DC-associated mucocutaneous triad features and severe bone marrow failure compared with autosomal dominant-non- TINF2 DC/TBD patients. Liver abnormality (defined at baseline assessment by laboratory and/or radiological findings) was present in 72.4% of patients with predominantly cholestatic pattern of liver enzyme elevation. Clinically significant liver disease and portal hypertension developed in 17.2% of patients during the 6-year follow-up; this progression was mainly seen in patients with recessive or TINF2 -associated DC. Significant risk factors associated with progression included the presence of pulmonary or vascular disease. Our experience shows a high prevalence of cholestatic pattern of liver abnormality with progression to portal hypertension in patients with DC/TBD. Presence of pulmonary and/or vascular disease in patients with recessive or TINF2 DC was an important predictor of liver disease progression, suggesting the need for increased vigilance and monitoring for complications in these patients.

Identification of Adult Patients With Classical Dyskeratosis Congenita or Cryptic Telomere Biology Disorder by Telomere Length Screening Using Age-modified Criteria

Telomere biology disorders (TBD) result from premature telomere shortening due to pathogenic germline variants in telomere maintenance-associated genes. In adults, TBD are characterized by mono/oligosymptomatic clinical manifestations (cryptic TBD) contributing to severe underdiagnosis. We present a prospective multi-institutional cohort study where telomere length (TL) screening was performed in either newly diagnosed patients with aplastic anemia (AA) or if TBD was clinically suspected by the treating physician. TL of 262 samples was measured via flow-fluorescence in situ hybridization (FISH). TL was considered suspicious once below the 10th percentile of normal individuals (standard screening) or if below 6.5 kb in patients >40 years (extended screening). In cases with shortened TL, next generation sequencing (NGS) for TBD-associated genes was performed. The patients referred fell into 6 different screening categories: (1) AA/paroxysmal nocturnal hemoglobinuria, (2) unexplained cytopenia, (3) dyskeratosis congenita, (4) myelodysplastic syndrome/acute myeloid leukemia, (5) interstitial lung disease, and (6) others. Overall, TL was found to be shortened in 120 patients (n = 86 standard and n = 34 extended screening). In 17 of the 76 (22.4%) standard patients with sufficient material for NGS, a pathogenic/likely pathogenic TBD-associated gene variant was identified. Variants of uncertain significance were detected in 17 of 76 (22.4%) standard and 6 of 29 (20.7%) extended screened patients. Expectedly, mutations were mainly found in TERT and TERC. In conclusion, TL measured by flow-FISH represents a powerful functional in vivo screening for an underlying TBD and should be performed in every newly diagnosed patient with AA as well as other patients with clinical suspicion for an underlying TBD in both children and adults.

Thymidine nucleotide metabolism controls human telomere length.

Telomere length in humans is associated with lifespan and severe diseases, yet the genetic determinants of telomere length remain incompletely defined. Here we performed genome-wide CRISPR-Cas9 functional telomere length screening and identified thymidine (dT) nucleotide metabolism as a limiting factor in human telomere maintenance. Targeted genetic disruption using CRISPR-Cas9 revealed multiple telomere length control points across the thymidine nucleotide metabolism pathway: decreasing dT nucleotide salvage via deletion of the gene encoding nuclear thymidine kinase (TK1) or de novo production by knockout of the thymidylate synthase gene (TYMS) decreased telomere length, whereas inactivation of the deoxynucleoside triphosphohydrolase-encoding gene SAMHD1 lengthened telomeres. Remarkably, supplementation with dT alone drove robust telomere elongation by telomerase in cells, and thymidine triphosphate stimulated telomerase activity in a substrate-independent manner in vitro. In induced pluripotent stem cells derived from patients with genetic telomere biology disorders, dT supplementation or inhibition of SAMHD1 promoted telomere restoration. Our results demonstrate a critical role of thymidine metabolism in controlling human telomerase and telomere length, which may be therapeutically actionable in patients with fatal degenerative diseases.

Boosting NAD ameliorates hematopoietic impairment linked to short telomeres in vivo

Short telomeres are a defining feature of telomere biology disorders (TBDs), including dyskeratosis congenita (DC), for which there is no effective general cure. Patients with TBDs often experience bone marrow failure. NAD, an essential metabolic coenzyme, is decreased in models of DC. Herein, using telomerase reverse transcriptase null (Tert−/−) mice with critically short telomeres, we investigated the effect of NAD supplementation with the NAD precursor, nicotinamide riboside (NR), on features of health span disrupted by telomere impairment. Our results revealed that NR ameliorated body weight loss in Tert−/− mice and improved telomere integrity and telomere dysfunction-induced systemic inflammation. NR supplementation also mitigated myeloid skewing of Tert−/− hematopoietic stem cells. Furthermore, NR alleviated villous atrophy and inflammation in the small intestine of Tert−/− transplant recipient mice. Altogether, our findings support NAD intervention as a potential therapeutic strategy to enhance aspects of health span compromised by telomere attrition.