# Inborn errors of human transcription factors governing IFN-γ antimycobacterial immunity

Masato Ogishi, Rui Yang, Jérémie Rosain, Jacinta Bustamante, Jean-Laurent

Casanova, Stéphanie Boisson-Dupuis

► To cite this version:

Masato Ogishi, Rui Yang, Jérémie Rosain, Jacinta Bustamante, Jean-Laurent Casanova, et al. Inborn errors of human transcription factors governing IFN-γ antimycobacterial immunity. Current Opinion in Immunology, 2023, 81, pp.102296. 10.1016/j.coi.2023.102296. hal-04088516

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Review

# Inborn errors of human transcription factors governing IFN-γ antimycobacterial immunity

Masato Ogishi<fnref n="1" />,<fnref n="2" />, Rui Yang<fnref n="1" />, Jérémie Rosain<fnref n="3" />,<fnref n="4" />,<fnref n="5" />,
Jacinta Bustamante<fnref n="1" />,<fnref n="3" />,<fnref n="4" />,<fnref n="5" />, Jean-Laurent Casanova<fnref n="1" />,<fnref n="3" />,<fnref n="4" />,<fnref n="6" />,<fnref n="7" /> and
Stéphanie Boisson-Dupuis<fnref n="1" />,<fnref n="3" />,<fnref n="4" />

<figure><img src="image_2.png" /></figure>

Inborn errors of immunity (IEI) delineate redundant and essential
defense mechanisms in humans. We review 15 autosomal-
dominant (AD) or -recessive (AR) IEI involving 11 transcription
factors (TFs) and impairing interferon-gamma (IFN-γ) immunity,
conferring a predisposition to mycobacterial diseases. We
consider three mechanism-based categories: 1) IEI mainly
affecting myeloid compartment development (AD GATA2 and
AR and AD IRF8 deficiencies), 2) IEI mainly affecting lymphoid
compartment development (AR FOXN1, AR PAX1, AR RORγ/
RORγT, AR T-bet, AR c-Rel, AD STAT3 gain-of-function (GOF),
and loss-of-function (LOF) deficiencies), and 3) IEI mainly
affecting myeloid and/or lymphoid function (AR and AD STAT1
LOF, AD STAT1 GOF, AR IRF1, and AD NFKB1 deficiencies).
We discuss the contribution of the discovery and study of
inborn errors of TFs essential for host defense against
mycobacteria to molecular and cellular analyses of human IFN-
γ immunity.

### Addresses

### Current Opinion in Immunology 2023, 81:102296

This review comes from a themed issue on **Lymphocyte development and activation**

Edited by Stuart G Tangye and Carolyn King

For complete overview of the section, please refer to the article
collection, "Lymphocyte development and activation (April 2023)"

Available online 1 March 2023

https://doi.org/10.1016/j.coi.2023.102296

0952-7915/© 2023 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

## Introduction

Since 2010, the rate of discovery of new inborn errors of
immunity (IEI) has massively increased, thanks largely
to the high-throughput sequencing of human exomes.
Almost 500 IEI are now recognized by the International
Union of Immunological Societies [7,47]. Disease-
causing loss-of-function (LOF) variants are more fre-
quent than disease-causing gain-of-function (GOF) var-
ants. However, remarkably, 13 genes are known to
harbor both LOF and GOF variants, in patients with
different, but sometimes overlapping clinical pheno-
types [47]. Neomorphic variants, which encode mutant
proteins with a new function, are rarer. Autosomal-re-
ccessive (AR) inheritance is also more common than au-
tosomal-dominant (AD) and X-linked recessive (XR) or
dominant (XD) inheritance. The three principal

<footnote n="1">¹St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA</footnote>

<footnote n="2">²The David Rockefeller Graduate Program, Rockefeller University, New York, NY, USA</footnote>

<footnote n="3">³Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France</footnote>

<footnote n="4">⁴Paris Cité University, Imagine Institute, Paris, France</footnote>

<footnote n="5">⁵Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France</footnote>

<footnote n="6">⁶Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France</footnote>

<footnote n="7">⁷Howard Hughes Medical Institute, New York, NY, USA</footnote>
molecular mechanisms underlying AD or XD diseases include haploinsufficiency (the normal function of the product of a single wild-type (WT) allele is insufficient to ensure good health), negative dominance (the product of the mutant allele impairs the function of the product of the WT allele), and GOF. The proteins encoded by the genes mutated in patients with IEI include cytokines, surface receptors, cytoplasmic adaptors, and transcription factors (TFs). The appropriate regulation of gene expression by TFs, which dictate how specific mRNAs and proteins are made by appropriate cells at appropriate times (e.g. in response to specific signals), is an essential feature of living organisms. Inborn errors of TFs can have a detrimental impact on the development and function of lymphoid cells, including purely adaptive cells (T and B cells and their respective subsets), innate-like adaptive cells ($\gamma\delta$ T cells, mucosal-associated invariant T [MAIT] cells, and natural killer T (NKT) cells), and purely innate cells (natural killer cells [NKs] and innate lymphoid cells). They can also have an impact on myeloid cells, including granulocytes (neutrophils, eosinophils, and basophils), monocytes (classical, intermediate, and nonclassical), myeloid dendritic cells (mDC, including conventional dendritic cells type 1 and 2 [cDC1 and cDC2]), plasmacytoid dendritic cells, and the diverse tissue-resident macrophages (Kupffer cells, osteoclasts, microglia, etc.).

Mendelian susceptibility to mycobacterial disease (MSMD) is a collection of IEI characterized by an unusual vulnerability to weakly virulent mycobacterial species, including environmental mycobacteria (EM) and *Mycobacterium bovis* bacille Calmette–Guérin (BCG) vaccines, in otherwise healthy individuals. MSMD is described as isolated if such infections are the only clinical phenotype, and syndromic if there are two or more clinical phenotypes (infectious or otherwise). Twenty-five years of human genetic studies have revealed the existence of 20 causal genes, defining 36 disease entities [8]. Affected patients are also susceptible to *M. tuberculosis* (*M.th*), the causal pathogen of tuberculosis (TB), which is ~1000 times more virulent than *M. bovis* BCG [5,8]. Some IEI are weakly penetrant for, or do not cause MSMD but are highly penetrant for TB [6,21,33–35]. The extent to which interferon-gamma (IFN-$\gamma$)-mediated immunity (IFN-$\gamma$ production, response to IFN-$\gamma$, or both) is impaired determines the nature, penetrance, and severity of mycobacterial diseases. In this review, we revisit mycobacterial diseases from the angle of IEI involving TFs. The > 500 IEI reported to date include 15 IEI due to mutations of 11 TF-encoding genes underlying mycobacterial diseases with variable penetrance (Tables 1 and 2). We will not deal with inborn errors of NF-$\kappa$B2 or AIOLOS deficiencies here due to their low penetrance and uncertainties concerning the mechanisms underlying mycobacterial disease [22,24]. We classify the inborn errors of TFs

underlying mycobacterial diseases into three categories on the basis of their impact on the development or function of the myeloid and lymphoid compartments. We also summarize the nonredundant roles of these TFs in antimycobacterial immunity in humans.

## Impaired development of myeloid cell subsets

AD GATA2 deficiency underlies various clinical and hematological phenotypes, including monoMAC syndrome, characterized by a progressive loss of monocytes, DCs, B cells, and NK cells. Patients with monoMAC syndrome develop severe recurrent infections due to EM (particularly *M. avium* and *M. kansasii*), and *M.th* [38], and other opportunistic viral and fungal infections. However, they rarely suffer from BCG disease. Importantly, monoMAC patients with residual circulating mononuclear myeloid cells (monocytes or DCs) are not susceptible to mycobacterial infections [38]. *Gata2*-heterozygous mutant mice have low levels of inflammatory cytokines, including Interleukin (IL)-12p40 and IFN-$\gamma$ in particular, and impaired bacterial clearance [46]. The susceptibility to mycobacterial infection associated with GATA2 deficiency therefore results from insufficient IFN-$\gamma$ production due to the impaired production of myeloid cell-derived IL-12.

AR complete IRF8 deficiency results in the depletion of circulating monocytes and DCs and neutrophilia [4,10,17,41]. Three unrelated patients with early-onset disseminated BCG disease (BCG-osis) following BCG vaccination have been reported [4,17,41]. The whole-blood leukocytes of these patients fail to produce IL-12p70 and produce insufficient IFN-$\gamma$. Consistently, IRF8-deficient mice harboring a hypomorphic variant are susceptible to mycobacteria [50]. Furthermore, AD IRF8 deficiency due to a *de novo* dominant-negative (DN) IRF8 mutation was found to cause isolated MSMD in two unrelated patients by impairing the development of cDC2 and the production of IL-12p70 by peripheral blood mononuclear cells [17,23]. Thus, impaired IFN-$\gamma$ production due to the defective production of IL-12p70 by myeloid cells leads to unrestricted mycobacterial infection in AR and AD IRF8 deficiency, a situation reminiscent of that observed for AD GATA2 deficiency. Overall, these IEI involving the TFs governing the development and function of myeloid cells demonstrate that myeloid cells protect humans from mycobacterial infections by fueling IL-12 production to ensure the production of sufficient IFN-$\gamma$.

## Impaired development of T-lymphoid cell subsets

FOXN1 (forkhead box N1) is a TF expressed in non-hematopoietic cells. Patients with biallelic deleterious variants of *FOXN1* present complete athymia and the equivalent of T$^+$B$^+$NK$^+$ severe combined immunodeficiency (SCID) with or without congenital alopecia and nail
<table><caption>**Table 1**
Immunological characteristics of patients with inborn errors of transcription factors underlying mycobacterial disease.</caption><thead><tr><th>Disorder/disease</th><th>MIM#</th><th>Inheritance</th><th>Gene</th><th>Protein</th><th>Defects in leukocyte development</th><th>Defects in IFN-γ immunity</th><th>Mechanism of vulnerability to Mycobacterium</th></tr></thead><tbody><tr><td colspan="8"><strong>Impaired development of myeloid cell subsets</strong></td></tr><tr><td>MonoMAC</td><td>614172</td><td>AD (HI)</td><td>GATA2</td><td>GATA2</td><td>↓Ø monocytes and DC; ↓NK lymphocytes; ↓B lymphocytes</td><td>Unknown</td><td>↓Ø IFN-γ-responsive mononuclear myeloid cells</td></tr><tr><td>AR IRF8 deficiency</td><td>226990</td><td>AR</td><td>IRF8</td><td>IRF8</td><td>Ø monocytes and DC</td><td>N/A (absence of circulating mononuclear myeloid cells)</td><td>Ø IFN-γ-responsive mononuclear myeloid cells</td></tr><tr><td>AD IRF8 deficiency</td><td>614893</td><td>AD (DN)</td><td>IRF8</td><td>IRF8</td><td>↓cDC2</td><td>↓IFN-γ production</td><td>↓Ø IFN-γ-responsive mononuclear myeloid cells ↓IFN-γ production by Mycobacterium-specific memory TH1+ cells; ↓IL-12p70 production</td></tr><tr><td colspan="8"><strong>Impaired development of T-lymphoid cell subsets</strong></td></tr><tr><td>Otofaciocervical syndrome 2</td><td>615560</td><td>AR</td><td>PAX1</td><td>PAX1</td><td>↓CD4+ T lymphocytes</td><td>↓IFN-γ production</td><td>↓IFN-γ-producing CD4+ lymphocytes</td></tr><tr><td>T-cell immunodeficiency, congenital alopecia, and nail dystrophy</td><td>601705</td><td>AR</td><td>FOXN1</td><td>FOXN1</td><td>↓CD4+ T lymphocytes</td><td>↓IFN-γ production</td><td>↓IFN-γ-producing CD4+ lymphocytes</td></tr><tr><td>RORγ/RORγT deficiency</td><td>616622</td><td>AR</td><td>RORC</td><td>RORγ/ RORγT</td><td>Ø MAIT lymphocytes; Ø iNKT lymphocytes; ↓CD4+ (↓TH17, ↓TH1') and ↓CD8+ T lymphocytes</td><td>↓IFN-γ production</td><td>↓IFN-γ production by γδT and TH1+ CD4+ αβ T lymphocytes; Ø IFN-γ-producing MAIT and iNKT lymphocytes</td></tr><tr><td>T-bet deficiency</td><td>619630</td><td>AR</td><td>TBX21</td><td>T-bet</td><td>↓NK, Vδ2+ γδT, MAIT, and iNKT lymphocytes; ↓TH1 CD4+ T lymphocytes; ↓CD11c high CD21-low B lymphocytes</td><td>↓IFN-γ production</td><td>↓IFN-γ-producing lymphocytes (NK, Vδ2+ γδT, MAIT, and iNKT lymphocytes); ↓IFN-γ production by the remaining NK, Vδ2+ γδT, MAIT, and iNKT lymphocytes</td></tr><tr><td>c-Rel deficiency</td><td>619652</td><td>AR</td><td>REL</td><td>c-Rel</td><td>↓NK, effector CD8+, memory CD4+ T (↓TH1 and TH1'), Treg, memory B lymphocytes</td><td>↓IFN-γ production</td><td>↓IL-12 and IL-23 production by cDC1 and monocytes</td></tr><tr><td>Autoimmune disease, multisystem, infantile-onset, 1; ADMIO1</td><td>615952</td><td>AD (GOF)</td><td>STAT3</td><td>STAT3</td><td>↓B lymphocytes; ↓NK, TH17, Treg; ↓intermediate, nonclassical monocytes, cDC1; ↓Vδ2+ γδT and MAIT lymphocytes</td><td>Unknown</td><td>↓IFN-γ-producing lymphocytes (Vδ2+ γδT, MAIT, and NK lymphocytes) and ↓ of IL-12/IL-23- producing cells</td></tr><tr><td>AD STAT3 deficiency; hyper-IgE syndrome (HIES)</td><td>147060</td><td>AD (DN)</td><td>STAT3</td><td>STAT3</td><td>↓γδT and MAIT lymphocytes; ↓TH17 and memory CD8+ T lymphocytes</td><td>Unknown</td><td>↓Barrier function and mucociliary clearance in late-stage HIES; ↓IFN-γ-producing lymphocytes (γδT and MAIT lymphocytes)</td></tr><tr><td colspan="8"><strong>Impaired function, but not development of lymphoid or myeloid cell subsets</strong></td></tr><tr><td>AR STAT1 deficiency</td><td>613796</td><td>AR</td><td>STAT1</td><td>STAT1</td><td>NA</td><td>↓IFN-γ response</td><td>↓IFN-γ downstream signaling</td></tr><tr><td>AD STAT1 deficiency</td><td>614892</td><td>AD (DN)</td><td>STAT1</td><td>STAT1</td><td>NA</td><td>↓IFN-γ response</td><td>↓IFN-γ downstream signaling</td></tr><tr><td>AD STAT1 GOF disease</td><td>614162</td><td>AD (GOF)</td><td>STAT1</td><td>STAT1</td><td>Variable</td><td>Unknown</td><td>Likely due to ↓IFN-γ downstream signaling secondary to negative feedback loop secondary to prolonged STAT1 phosphorylation</td></tr><tr><td>AR IRF1 deficiency</td><td>NA</td><td>AR</td><td>IRF1</td><td>IRF1</td><td>↓cDC1; ↓NK cells; ↓CD4+ T lymphocytes; ↓CD8+ T lymphocytes</td><td>↓IFN-γ response</td><td>Ø IFN-γ cell- intrinsic immunity in monocyte-derived macrophages</td></tr><tr><td>AD NF-kB1 deficiency</td><td>616576</td><td>AD (DN)</td><td>NFKB1</td><td>NFKB1</td><td>NA</td><td>Unknown</td><td>Likely due to ↓IL-12 and IL-23 production by cDC- and monocytes</td></tr></tbody></table>

NA: not applicable, AR: autosomal recessive, AD: autosomal dominant, DC: dendritic cells, DN: dominant negative, GOF: gain-of-function, HI: haploinsufficiency.
<table><caption>**Table 2**

Clinical characteristics of patients with inborn errors of transcription factor underlying mycobacterial disease.</caption><thead><tr><th rowspan="2">Disorder/disease</th><th rowspan="2">Inheritance</th><th rowspan="2">Gene</th><th colspan="2">Mycobacterial phenotypes (localized/disseminated)<sup>a</sup></th><th rowspan="2">Penetrance of EM/BCG</th><th rowspan="2">Associated clinical features</th></tr><tr><th>BCG/EM</th><th>TB</th></tr></thead><tbody><tr><td>MonoMAC</td><td>AD (HI)</td><td>GATA2</td><td>BCG/EM localized/disseminated</td><td>Localized (pulmonary)</td><td>High<sup>a</sup></td><td>Myelodysplastic syndrome/acute myelogenous leukemia, lymphedema, pulmonary alveolar proteinosis, HPV, and histoplasmosis</td></tr><tr><td>AR IRF8 deficiency</td><td>AR</td><td>IRF8</td><td>BCG disseminated</td><td>NA</td><td>Complete<sup>b</sup></td><td>Viral infections, invasive candidiasis</td></tr><tr><td>AD IRF8 deficiency</td><td>AD (DN)</td><td>IRF8</td><td>BCG disseminated</td><td>NA</td><td>Complete<sup>b</sup></td><td>None</td></tr><tr><td>Otofaciocervical syndrome 2</td><td>AR</td><td>PAX1</td><td>BCG localized</td><td>NA</td><td>Low</td><td>Omnenn-like syndrome, athymia, otofaciocervical syndrome type 2, and ear abnormalities</td></tr><tr><td>T-cell immunodeficiency, congenital alopecia, and nail dystrophy</td><td>AR</td><td>FOXN1</td><td>BCG/TB localized</td><td>Localized</td><td>Low</td><td>Abnormal thymic epithelium, congenital alopecia, nail dystrophy, neural tube defect, and recurrent viral and bacterial respiratory tract infections</td></tr><tr><td>RORγ/RORYT deficiency</td><td>AR</td><td>RORC</td><td>BCG disseminated</td><td>Localized</td><td>Complete<sup>b</sup></td><td>Chronic mucocutaneous candidiasis (CMC)</td></tr><tr><td>T-bet deficiency</td><td>AR</td><td>TBX21</td><td>BCG disseminated</td><td>NA</td><td>Complete<sup>b</sup></td><td>Upper airway inflammation, eosinophilia</td></tr><tr><td>c-Rel deficiency</td><td>AR</td><td>REL</td><td>BCG disseminated</td><td>Disseminated</td><td>Complete<sup>b</sup></td><td>Recurrent infections with pyogenic bacteria, mycobacteria, Salmonella, and opportunistic organisms</td></tr><tr><td>Autoimmune disease, multisystem, infantile-onset, 1; ADMIO1</td><td>AD (GOF)</td><td>STAT3</td><td>EM localized (pulmonary)</td><td>Localized (pulmonary)</td><td>Low</td><td>Autoimmunity, lymphoproliferation, interstitial lung disease, growth failure, and bacterial, viral, fungal, and opportunistic infections</td></tr><tr><td>AD STAT3 deficiency; hyper-IgE syndrome</td><td>AD (DN)</td><td>STAT3</td><td>BCG/EM localized/disseminated</td><td>Localized/disseminated</td><td>Low</td><td>Distinctive facial features (broad nasal bridge), bacterial respiratory tract infections, CMC, eczema, hyperextensible joints, osteoporosis and bone fractures, scoliosis, retained primary teeth, and coronary and cerebral aneurysms</td></tr><tr><td>AR STAT1 deficiency</td><td>AR</td><td>STAT1</td><td>BCG/EM disseminated</td><td>NA</td><td>High</td><td>Severe viral infections</td></tr><tr><td>AD STAT1 deficiency</td><td>AD (DN)</td><td>STAT1</td><td>BCG/EM localized/disseminated (cutaneous lesions, osteomyelitis)</td><td>Localized/disseminated (pulmonary, osteomyelitis)</td><td>High</td><td>None</td></tr><tr><td>AD STAT1 GOF disease</td><td>AD (GOF)</td><td>STAT1</td><td>BCG/EM localized/disseminated</td><td>Localized/disseminated</td><td>Low</td><td>CMC, histoplasmosis, coccidioidomycosis, autoimmunity, and enteropathy</td></tr><tr><td>AR IRF1 deficiency</td><td>AR</td><td>IRF1</td><td>BCG/EM disseminated</td><td>NA</td><td>Complete<sup>b</sup></td><td>Histoplasmosis</td></tr></tbody></table>

Incomplete penetrance is arbitrarily categorized into low, intermediate, and high.

NA: not applicable, AR: autosomal recessive, AD: autosomal dominant, DN: dominant negative, EM: environmental mycobacteria, GOF: gain-of-function, HI: haploinsufficiency

<footnote>a Penetrance of EM is high in MonoMAC. However, the penetrance for BCG infection is low (very rare).</footnote>

<footnote>b Too few kindreds to draw firm conclusions.</footnote>
dystrophy [14], resulting in a phenotype similar to that of nude mice. Immunologically, all these patients present a severe impairment of T-cell development and function, affecting CD4⁺ T cells in particular, whereas their B and NK cells remain unaffected (Tβ'NK⁺ SCID). They suffer severe, recurrent, life-threatening diseases caused by diverse pathogens in the first few months of life [9]. Two of the 13 FOXN1-deficient patients identified to date suffered from mycobacterial diseases (one case of localized or regional BCG disease (BCG-itis) and one case of pneumonia due to *M. bovis*) [14]. Monoallelic *FOXN1* mutations have recently been shown to be associated with nonmycobacterial infections [9].

PAX1 (paired box 1) is a member of the paired box (PAX) family of TFs expressed in the pharyngeal pouches during embryogenesis and fetal development and involved in thymus organogenesis [9]. AR PAX1 deficiency leads to otofaciocervical syndrome 2, characterized by short stature, facial dysmorphism, shoulder girdle abnormalities, hearing loss, mild intellectual disability, severe thymic hypoplasia, and severe T-cell immunodeficiency [53]. Patients with PAX1 deficiency have a phenotype mimicking Tβ'NK⁺ SCID. Two of the 15 known PAX1-deficient patients suffered from BCG-itis [53]. The surprisingly low penetrance for mycobacterial diseases in these T⁻/lo SCID patients probably results from 1) early death from other infectious diseases and 2) protection conferred by hematopoietic stem cell transplantation. A severe impairment of T-cell development underlies the susceptibility to weakly virulent mycobacteria with incomplete penetrance in the patients with AR FOXN1 and PAX1 deficiency.

RORγ/RORγT is a lineage-defining TF of T<sub>H</sub>17 cells in mice [19]. AR RORγ/RORγT deficiency underlies both mycobacteriosis (BCG and TB) and candidiasis [36]. Patients with biallelic *RORC* LOF variants display a complete absence of innate-like adaptive T (MAIT and iNKT) cells and very low levels of purely adaptive (CD4⁺ and CD8⁺) αβ T cells, including T<sub>H</sub>17 and T<sub>H</sub>1* cells [a memory CD4⁺ αβ T-cell subset capable of producing both IL-17A/F and IFN-γ [11]. The lack of mycobacterium-responsive T cells (MAIT and iNKT cells), combined with a profound defect of IFN-γ production by γδ T cells and T<sub>H</sub>1* CD4⁺ αβ T cells, underlies mycobacterial susceptibility in AR RORγ/RORγT deficiency.

T-bet is a lineage-defining TF of T<sub>H</sub>1 cells in mice [45] that is indispensable for antimycobacterial immunity in mice [44]. AR complete T-bet deficiency defines a new isolated form of MSMD underlying BCG-osis and refractory airway hypersensitivity with peripheral eosinophilia [54,55]. The immunophenotyping of inherited T-bet deficiency revealed not only the expected depletion

of T<sub>H</sub>1 cells, but also very low counts of purely innate NK cells, innate-like adaptive T cells (Vδ2⁺ γδ T, MAIT, and iNKT), and the absence of a distinctive subset of CD11c<sup>high</sup>CD21<sup>low</sup> B cells [54,56]. The residual population of innate lymphocytes and innate-like adaptive lymphocytes produced only small amounts of IFN-γ. To our surprise, we found that mycobacterium-responsive CD4⁺ and CD8⁺ αβ T cells produced normal amounts of IFN-γ during infection *in vitro*. Thus, human T-bet deficiency underlies mycobacterial disease by preventing (i) the development of mycobacterium-responsive NK, Vδ2⁺ γδ T, MAIT, and iNKT cells and (ii) IFN-γ production by the few remaining NK, Vδ2⁺ γδ T, MAIT, and iNKT cells [54].

AR c-Rel deficiency is a new form of CID that predisposes patients to multiple infections, including mycobacteriosis [3,26]. One of the two reported patients developed BCG-osis, whereas the other suffered from TB osteomyelitis with no adverse events following BCG vaccination. The immunophenotyping of a patient with AR c-Rel deficiency revealed low frequencies of NK cells, effector memory CD8⁺ T cells, and memory CD4⁺ T cells, including T<sub>H</sub>1 and T<sub>H</sub>1*, Tregs, and memory B cells [26]. Levels of IFN-γ production by c-Rel-deficient whole-blood leukocytes in response to BCG mycobacteria were also very low, due to a profound impairment of the production of IL-12 and IL-23 by cDC1 and monocytes. The low levels of IFN-γ, IL-12, and IL-23 production account for mycobacterial susceptibility in patients with AR c-Rel deficiency [3,26].

AD STAT3 deficiency due to monoallelic DN variants causes hyper-IgE syndrome (HIES), a condition characterized by extremely high IgE levels with severe atopic disease and recurrent pyogenic infections [2]. Several studies have shown that about 10–30% of patients with DN STAT3 HIES are susceptible to mycobacterial disease (BCG, EM, and *M.tb*) [49]. Impairments of barrier function and mucociliary clearance in late-stage HIES probably contribute to the susceptibility to mycobacterial disease in these patients, through mechanisms similar to those operating in patients with cystic fibrosis and primary ciliary dyskinesia, in whom pulmonary EM infections are prevalent (> 10%) [32,39]. Low levels of γδ T and MAIT cells and defective STAT3-dependent IL-23 signaling may make synergic contributions to mycobacterial disease in at least some AD STAT3 HIES patients [28,40,52].

AD STAT3 GOF variants cause early-onset lymphoproliferation and autoimmunity [12]. A recent report of an international cohort of 191 STAT3 GOF patients revealed that 6% of these patients suffered from mycobacterial diseases [25], with 8 EM and 2 TB cases. The
penetrance of mycobacterial disease may be under-
estimated, as many cases manifest persistent or recurrent
infections without identification of the causal microbes.
STAT3 GOF mutations impede the development of
both the lymphoid and myeloid compartments, in-
cluding NK cells, T<sub>H</sub>17 cells, regulatory T cells, inter-
mediate and nonclassical monocytes, and cDC1 [16,30].
In-depth immunophenotypic analyses of unconventional
T cells, such as γδ and MAIT cells, are lacking. The
abnormally low numbers of IL-12/IL-23-producing
myeloid cells and IFN-γ-producing lymphocytes may
make synergic contributions to mycobacterial disease in
AD STAT3 GOF disease.

Impaired function, but not development of
lymphoid or myeloid cell subsets

STAT1 mediates signaling downstream from IFN-α/βR and IFN-γR, by forming a transcription-activating complex known as interferon-stimulated gamma factor 3 (ISGF3; STAT1/STAT2/IRF9 heterotrimer) and a gamma-activating factor (GAF; phosphorylated STAT1 homodimer), respectively [11]. AR complete or partial STAT1 deficiency predisposes humans to both severe mycobacterial and viral diseases due to the impairment of IFN-γ and IFN-α/β signaling, respectively [51]. By contrast, AD STAT1 deficiency due to heterozygosity for variants impairing phosphorylation, DNA binding, or both, results in vulnerability to mycobacterial, but not viral infection [31]. The penetrance of mycobacterial disease is incomplete in patients with AD STAT1 deficiency. Patients with AD STAT1 deficiency frequently develop multifocal mycobacterial osteomyelitis, a clinical manifestation also often seen in patients in AD IFN-γR1 deficiency [31]. Mycobacterial disease in these patients results from an abolition or impairment of the response to IFN-γ in myeloid cells, probably tissue-resident myeloid cells, a mechanism common to AR IRF1 deficiency [42].

Monoallelic GOF variants of *STAT1* are more common
than LOF mutations of this gene [37]. Affected patients
develop chronic mucocutaneous candidiasis (CMC) in
the presence or absence of other infectious diseases or
autoimmunity [48]. Contrary to expectations, 6% of pa-
tients heterozygous for *STAT1* GOF variants are also
susceptible to *M.tb* and weakly virulent mycobacteria
[48]. The underlying mechanism remains elusive but
might be related to impaired IFN-γ production by in-
nate-like adaptive T cells (MAIT and Vδ2+ γδ T cells) in
response to IL-23 and mycobacterium-specific antigens
[40]. More patients will need to be discovered and stu-
died before any firm conclusions can be drawn. STAT1
integrity is therefore essential for IFN-γ-mediated anti-
mycobacterial immunity.

AR complete IRF1 deficiency was recently discovered in two unrelated patients with severe recurrent infections caused by both BCG and EM [42], consistent with the findings for IRF1-deficient mice [20]. IRF1 is a TF acting downstream from STAT1. Its expression is mediated by IFN-γ in a GAF-dependent manner. When produced, the IRF1 protein enters the nucleus, where it binds to promoters containing interferon-stimulated gene element motifs. A study of macrophages derived from IRF1-deficient patients found that IRF1 controlled the expression of one-third of IFN-γ-inducible mRNAs, including numerous targets previously described as essential for cell-intrinsic immunity to intracellular pathogens [13]. IRF1-deficient mononuclear macrophages do not control mycobacteria or related intramacrophagic pathogens normally in response to IFN-γ, as observed in IFN-γR1- or STAT1-deficient macrophages [42]. Human IRF1 thus governs IFN-γ-dependent macrophage activation and resistance to intracellular pathogens.

NF-κB1 (p50) is one of the five subunits of NF-κB TFs [57]. The IKK complex (NEMO/IKKα/IKKβ heterotrimer) phosphorylates IκB to induce its proteasomal degradation, thereby releasing NF-κB heterodimers for nuclear translocation. The NF-κB pathway is indispensable for human antimycobacterial immunity, as AR IKKβ deficiency and XL NEMO deficiency result in severe mycobacterial diseases [57]. Consistent with these observations, three patients with AD NF-κB1 deficiency were reported to suffer from mycobacterial disease: disseminated *M. genavense* and disseminated MAC in two patients heterozygous for an amorphic *NFKB1* mutation [15,27,29] and *M.tb*, in a patient heterozygous for a hypomorphic *NFKB1* mutation [27]. The patients’ leukocytes displayed defective IFN-γ production *in vitro* in response to various stimuli, including phytohemagglutinin and BCG infection, due to insufficient IL-12 production by myeloid cell subsets. By contrast, immunophenotyping revealed no consistent abnormality of leukocyte development. Hence, impaired IFN-γ production due to insufficient IL-12 production is probably responsible for mycobacterial disease in patients with AD NF-κB1 deficiency.

Conclusion

TFs control constitutive features of cells and responses
to diverse stimuli. They also often control different
downstream targets in different leukocyte subsets.
Dissections of IEI for several human TFs have revealed
the essential roles of these factors at the individual cell
and whole-body levels. In MSMD, the most compre-
hensively studied inherited human infectious disease,
T-bet, RORγ/RORγT, STAT1, IRF1, and IRF8 defi-
ciencies unequivocally disrupt the production of, or
cellular responses to IFN-γ, accounting for mycobacterial diseases. Remarkably, seven of the 24 known genetic etiologies of MSMD involve the deficiency of a TF: AR T-bet, RORγ/RORγT, STAT1, IRF8, IRF1 AD IRF8, and STAT1 deficiencies. The disruption of IFN-γ-dependent immunity has also been documented experimentally, albeit less thoroughly, in AD GATA2, AR c-Rel, and AD NF-κB1 deficiencies. Despite the lack of experimental dissection for AR FOXN1, AR PAX1, AD STAT3 DN, AD STAT3 GOF, and AD STAT1 GOF variants, the mycobacterial diseases observed in the affected patients can also be explained by an impairment of IFN-γ-dependent immunity. These studies converge to implicate defective IFN-γ immunity as a core mechanism of susceptibility to *Mycobacterium* at whole-body level. It is tempting to speculate that more IEI underlying mycobacterial diseases will be discovered in the future, including IEI involving other TFs, and that these IEI will also involve impairments of IFN-γ immunity. Prime candidate TFs, based on the mouse model *in vivo* and human studies *in vitro*, include STAT4 [43] and BHLHE40 [18].

Cellularly, studies of inborn errors of TFs have highlighted the essential roles of specific leukocyte lineages in IFN-γ immunity to mycobacteria. Myeloid cells (monocytes/macrophages and mDCs) produce IL-12/IL-23, thereby enhancing IFN-γ production by lymphoid cells, leading to the IFN-γ-dependent elimination of mycobacteria. AR and AD IRF8, and AD GATA2 deficiencies result predominantly in an impairment of the development of IL-12/IL-23-producing myeloid cells, whereas AR IRF1 and AR and AD STAT1 deficiencies predominantly impair the IFN-γ-dependent upregulation of antimycobacterial effectors in macrophages. Studies of several inborn errors of TFs affecting only the lymphoid compartment have suggested that infected macrophages need lymphocyte-derived IFN-γ to eliminate mycobacteria. All reported inborn errors of TFs to date underlying mycobacterial disease and affecting the development of lymphoid compartment have an impact on multiple subsets. The essential or redundant functions of each of these lymphocyte subsets therefore remain unclear. The depletion of purely innate NK cells and innate-like adaptive T-cell subsets ($V\delta^2$, $\gamma\delta$, T, MAIT, and iNKT) has been reported in AD STAT3 DN, AD STAT3 GOF, AR RORγ/RORγT, and AR T-bet deficiencies. Conversely, the levels of *Mycobacterium*-specific adaptive CD4$^+$, $\alpha\beta$ memory T cells, known as $T_{H1}^*$ cells (CCR6$^+$CXCR3$^+$) [1], are reportedly low in both AR c-Rel and RORγ/RORγT deficiencies. Qualitative and quantitative defects of multiple IFN-γ-producing lymphocyte subsets have now been shown to predispose humans to clinical disease caused by weakly or even more virulent mycobacteria. Discovering novel

IEI that selectively deplete one or more IFN-γ-producing lymphocyte subsets will shed further light on the cellular basis of antimycobacterial immunity.

## Funding

This study was supported in part by a grant from the St. Giles Foundation, The Rockefeller University, Institut National de la Santé et de la Recherche Médicale (INSERM), University Paris Cité, Sidra Medicine, the National Institute of Allergy and Infectious Diseases (R01AI095983 to J.-L.C. and J.B.; U19AI162568 to J.-L.C. and U19AI142737 to S.B.-D.), the National Center for Research Resources, the National Center for Advancing Sciences of the National Institutes of Health (UL1TR001866), the French National Research Agency (ANR) under the "Investments for the Future" program (ANR-10IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), GENMSMD (ANR-16-CE17.0005-01, to J.B.), MAFMACRO (ANR-22-CE92-0008 to J.B.), ECOS-NORD (C19S01-63407 to J.B.) the French Foundation for Medical Research (FRM) (EQU201903007798), an ANRS project ECTZ170784-ANRS0073 grant to S.B.-D., the Square Foundation, and the SCOR Corporate Foundation for Science.

M.O. was supported by the David Rockefeller Graduate Program, the Funai Foundation for Information Technology (FFIT), the Honjo International Scholarship Foundation (HISF), the New York Hideyo Noguchi Memorial Society (HNMS), and the National Cancer Institute (NCI) F99 Award (F99CA274708). R.Y. was supported by the Immune Deficiency Foundation and the Stony Wold-Herbert Fund. J.R. was supported by the Inserm PhD program ("poste d'accueil Inserm") and the MD-PhD program of the Imagine Institute with the support of the Bettencourt-Schueller Foundation.

## Conflict of interest statement

The authors have no competing financial interests to declare.

## Data availability

No data were used for the research described in the article.

## Acknowledgements

We thank Laurent Abel, and the members of the St. Giles Laboratory of Human Genetics of Infectious Diseases, particularly the mycobacterial team members, for helpful discussions. We thank Erin Williams, Yelena Nemirovskaya, Dana Liu, Mark Woollett, Maya Chrabieh, and Lazaro Lorenzo for administrative assistance.
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