Abnormal biomarkers predict complex FAS or FADD defects missed by exome sequencing

BACKGROUND

Elevated TCRαβ+CD4-CD8- double-negative T cells (DNT) and serum biomarkers help identify FAS mutant patients with autoimmune lymphoproliferative syndrome (ALPS). However, in some patients with clinical features and biomarkers consistent with ALPS, germline or somatic FAS mutations cannot be identified on standard exon sequencing (ALPS-undetermined: ALPS-U).

OBJECTIVE

We sought to explore whether complex genetic alterations in the FAS gene escaping standard sequencing or mutations in other FAS pathway-related genes could explain these cases.

METHODS

Genetic analysis included whole FAS gene sequencing, copy number variation analysis, and sequencing of FAS cDNA and other FAS pathway-related genes. It was guided by FAS expression analysis on CD57+DNT, which can predict somatic loss of heterozygosity (sLOH).

RESULTS

Nine of 16 patients with ALPS-U lacked FAS expression on CD57+DNT predicting heterozygous "loss-of-expression" FAS mutations plus acquired somatic second hits in the FAS gene, enriched in DNT. Indeed, 7 of 9 analyzed patients carried deep intronic mutations or large deletions in the FAS gene combined with sLOH detectable in DNT; 1 patient showed a FAS exon duplication. Three patients had reduced FAS expression, and 2 of them harbored mutations in the FAS promoter, which reduced FAS expression in reporter assays. Three of the 4 ALPS-U patients with normal FAS expression carried heterozygous FADD mutations with sLOH.

CONCLUSION

A combination of serum biomarkers and DNT phenotyping is an accurate means to identify patients with ALPS who are missed by routine exome sequencing.

Revisiting autoimmune lymphoproliferative syndrome caused by Fas ligand mutations

BACKGROUND

Fas ligand (FasL) is expressed by activated T cells and induces death in target cells upon binding to Fas. Loss-of-function FAS or FASLG mutations cause autoimmune-lymphoproliferative syndrome (ALPS) characterized by expanded double-negative T cells (DNT) and elevated serum biomarkers. While most ALPS patients carry heterozygous FAS mutations, FASLG mutations are rare and usually biallelic. Only 2 heterozygous variants were reported, associated with an atypical clinical phenotype.

OBJECTIVE

We revisited the significance of heterozygous FASLG mutations as a cause of ALPS.

METHODS

Clinical features and biomarkers were analyzed in 24 individuals with homozygous or heterozygous FASLG variants predicted to be deleterious. Cytotoxicity assays were performed with patient T cells and biochemical assays with recombinant FasL.

RESULTS

Homozygous FASLG variants abrogated cytotoxicity and resulted in early-onset severe ALPS with elevated DNT, raised vitamin B₁₂, and usually no soluble FasL. In contrast, heterozygous variants affected FasL function by reducing expression, impairing trimerization, or preventing Fas binding. However, they were not associated with elevated DNT and vitamin B₁₂, and they did not affect FasL-mediated cytotoxicity. The dominant-negative effects of previously published variants could not be confirmed. Even Y166C, causing loss of Fas binding with a dominant-negative effect in biochemical assays, did not impair cellular cytotoxicity or cause vitamin B₁₂ and DNT elevation.

CONCLUSION

Heterozygous loss-of-function mutations are better tolerated for FASLG than for FAS, which may explain the low frequency of ALPS-FASLG.

A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS

The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune lymphoproliferative syndrome to identify a population of FAS-controlled TCRαβ⁺ T cells. They include CD4⁺, CD8⁺, and double-negative T cells and can be defined by a CD38⁺CD45RA⁺T-BET⁻ expression pattern. These unconventional T cells are present in healthy individuals, are generated before birth, are enriched in lymphoid tissue, and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative, noncytotoxic T cells with an IL-10 cytokine bias. Mechanistically, regulation of this physiological population is mediated by FAS and CTLA4 signaling, and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease.

Long-term robustness of a T-cell system emerging from somatic rescue of a genetic block in T-cell development

BACKGOUND

The potential of a single progenitor cell to establish and maintain long-term protective T-cell immunity in humans is unknown. For genetic disorders disabling T-cell immunity, somatic reversion was shown to support limited T-cell development attenuating the clinical phenotype. However, the cases reported so far deteriorated over time leaving unanswered the important question of long-term activity of revertant precursors and the robustness of the resulting T-cell system.

METHODS

We applied TCRβ-CDR3 sequencing and mass cytometry on serial samples of a now 18 year-old SCIDX1 patient with somatic reversion to analyse the longitudinal diversification and stability of a T-cell system emerging from somatic gene rescue.

FINDINGS

We detected close to 105 individual CDR3β sequences in the patient. Blood samples of equal size contained about 10-fold fewer unique CDR3β sequences compared to healthy donors, indicating a surprisingly broad repertoire. Despite dramatic expansions and contractions of individual clonotypes representing up to 30% of the repertoire, stable diversity indices revealed that these transient clonal distortions did not cause long-term repertoire imbalance. Phenotypically, the T-cell system did not show evidence for progressive exhaustion. Combined with immunoglobulin substitution, the limited T-cell system in this patient supported an unremarkable clinical course over 18 years.

INTERPRETATION

Genetic correction in the appropriate cell type, in our patient most likely in a T-cell biased self-renewing hematopoietic progenitor, can yield a diverse T-cell system that provides long-term repertoire stability, does not show evidence for progressive exhaustion and is capable of providing protective and regulated T-cell immunity for at least two decades.

FUNDING

DFG EH 145/9-1, DFG SCHW 432/4-1 and the German Research Foundation under Germany's Excellence Strategy-EXC-2189-Project ID: 390939984.

Domain sensitive contrast in photoelectron emission microscopy

We have investigated the adsorption of cesium on the Si(100) surface with photoelectron emission microscopy using linearly polarized green laser light. We observe a polarization dependent contrast between the (2 x 1) or (1 x 2) reconstructed terraces. Density-functional calculations reveal the geometric and electronic structure of the Cs/Si(100) surface. The contrast between the (2 x 1) or (1 x 2) reconstructed domains is explained on the basis of dipole selection rules for the photoemission matrix elements.

Less strain energy despite fewer misfit dislocations: the impact of ordering

The average strain state of Ge films grown on Si(111) by surfactant mediated epitaxy has been compared to the ordering of the interfacial misfit dislocation network. Surprisingly, a smaller degree of average lattice relaxation was found in films grown at higher temperature. On the other hand, these films exhibit a better ordered dislocation network. This effect energetically compensates the higher strain at higher growth temperature, leading to the conclusion that, apart from the formation of misfit dislocations, their ordering represents an important channel for lattice-strain energy relaxation.

Characterizing single crystal surfaces using high resolution electron diffraction

Characterization and controlled manipulation of surfaces is a crucial factor in modern processing of the technologically relevant Si(100) surface. Using spot profile analyzing low energy electron diffraction, the morphological changes from a single stepped vicinal Si(100) surface to a single-domain (2x1) reconstructed surface have been investigated in situ during Si deposition. The temperature range for formation of this kinetically-stabilized single-domain surface was found to be 400-500 degrees C. This single-domain surface could be preserved for further characterization and experiments after quenching to room temperature.

Direct observation of reconstruction induced changes of surface stress for Sb on Si(111)

With the combination of high resolution low energy electron diffraction and a bending sample technique we have simultaneously studied surface stress and surface structure during adsorption and desorption of antimony on the Si(111) surface. During desorption, several surface reconstructions with significantly different effects on the stress signal evolve. The surface stress of all observed structures has been obtained.