Summary Bacteria that cause disease rely on their ability to counteract and overcome host defenses. Here we present a genome-scale study of Mycobacterium tuberculosis (Mtb) that uncovers the bacterial determinants of surviving host immunity, sets of genes we term “counteractomes.” Through this, we find that CD4 T cells attempt to starve Mtb of tryptophan through a mechanism that limits Chlamydia and Leishmania infections. In those cases, tryptophan starvation works well, since those pathogens are natural tryptophan auxotrophs. Mtb, however, can synthesize tryptophan, and thus starvation fails as an Mtb-killing mechanism. We then describe a small molecule inhibitor of Mtb tryptophan synthesis, which turns Mtb into a tryptophan auxotroph and restores the efficacy of a failed host defense. Together, our findings demonstrate that the Mtb determinants for surviving host immunity—Mtb’s immune counteractomes—serve as probes of host immunity, uncovering immune-mediated stresses that can be leveraged for therapeutic discovery.

Gfi1 was first identified as causing interleukin 2-independent growth in T cells and lymphomagenesis in mice. Much work has shown thatGfi1 and Gfi1b, a second mouse homolog, play pivotal roles in blood cell lineage differentiation. However, neither Gfi1 norGfi1b has been implicated in nervous system development, even though their invertebrate homologues, senseless in Drosophila andpag-3 in C. elegans are expressed and required in the nervous system. We show that Gfi1 mRNA is expressed in many areas that give rise to neuronal cells during embryonic development in mouse, and that Gfi1 protein has a more restricted expression pattern. By E12.5Gfi1 mRNA is expressed in both the CNS and PNS as well as in many sensory epithelia including the developing inner ear epithelia. At later developmental stages, Gfi1 expression in the ear is refined to the hair cells and neurons throughout the inner ear. Gfi1 protein is expressed in a more restricted pattern in specialized sensory cells of the PNS, including the eye, presumptive Merkel cells, the lung and hair cells of the inner ear.Gfi1 mutant mice display behavioral defects that are consistent with inner ear anomalies, as they are ataxic, circle, display head tilting behavior and do not respond to noise. They have a unique inner ear phenotype in that the vestibular and ccchlear hair cells are differentially affected. AlthoughGfi1-deficient mice initially specify inner ear hair cells, these hair cells are disorganized in both the vestibule and cochlea. The outer hair cells of the cochlea are improperly innervated and express neuronal markers that are not normally expressed in these cells. Furthermore, Gfi1mutant mice lose all cochlear hair cells just prior to and soon after birth through apoptosis. Finally, by five months of age there is also a dramatic reduction in the number of cochlear neurons. Hence, Gfi1 is expressed in the developing nervous system, is required for inner ear hair cell differentiation, and its loss causes programmed cell death.

Attention-Deficit/Hyperactivity Disorder (ADHD) has a very high heritability (0.8), suggesting that about 80% of phenotypic variance is due to genetic factors. We used the integration of statistical and functional approaches to discover a novel gene that contributes to ADHD. For our statistical approach, we started with a linkage study based on large multigenerational families in a population isolate, followed by fine mapping of targeted regions using a familybased design. Family-and population-based association studies in five samples from disparate regions of the world were used for replication. Brain imaging studies were performed to evaluate gene function. The linkage study discovered a genome region harbored in the Latrophilin 3 gene (LPHN3). In the world-wide samples (total n = 6360, with 2627 ADHD cases and 2531 controls) statistical association of LPHN3 and ADHD was confirmed. Functional studies revealed that LPHN3 variants are expressed in key brain regions related to attention and activity, affect metabolism in neural circuits implicated in ADHD, and are associated with response to stimulant medication. Linkage and replicated association of ADHD with a novel non-candidate gene (LPHN3) provide new insights into the genetics, neurobiology, and treatment of ADHD.

Gfi1 is a transcriptional repressor implicated in lymphomagenesis, neutropenia, and hematopoietic development, as well as ear and lung development. Here, we demonstrate that Gfi1 functions downstream of Math1 in intestinal secretory lineage differentiation. The epithelium of the small intestine is a highly proliferative tissue composed of four distinct cell types: absorptive enterocytes and three secretory lineages consisting of mucus-secreting goblet cells, hormone-secreting enteroendocrine cells, and antimicrobial peptide-secreting Paneth cells. All of these cell types derive from multipotent stem cells residing near the base of the Crypts of Liberkühn, the proliferative compartment of the intestinal epithelium (Madara and Trier 1994).Differentiation within the crypts follows a spatial distribution: The stem cells are located near the base of the crypts and give rise to daughter cells that migrate up as they proliferate. Near the top of the crypt, these daughter cells terminally differentiate into the four main cell types of the intestinal epithelium. Absorptive enterocytes, goblet, and enteroendocrine cells migrate up the villus, whereas Paneth cells migrate down to reside at the crypt base.The molecular mechanisms that underlie crypt formation and intestinal cell fate specification remain incompletely defined. Several genes have been implicated in crypt morphogenesis and proliferation, including Wnt/␤-catenin pathway members and target genes such as Cdx1 and Cdx2 (Korinek et al. 1998;Beck et al. 1999;Soubeyran et al. 1999). ␤-Catenin signaling is also necessary for stem cell renewal, proliferation, and differentiation (Pinto et al. 2003). The current model of intestinal epithelial differentiation suggests that ␤-catenin drives production of a pool of multipotent progenitors that use Notch signaling to select between Math1 or Hes1 expression (Yang et al. 2001;Sancho et al. 2004). Progenitors that express Hes1 will differentiate into absorptive enterocytes, whereas progenitors that express Math1 are committed to the secretory lineage and thus fated to become goblet, Paneth, or enteroendocrine cells. Additional transcription factors such as Ngn3, Pdx1, and Neurod1 are required for terminal differentiation of enteroendocrine cells (Schonhoff et al. 2004). The mechanism of selection between enteroendocrine, goblet, and Paneth cells remains unclear, and additional factors are hypothesized to direct differentiation of goblet and Paneth cells.Math1 is a basic helix-loop-helix (bHLH) transcription factor important in cell fate determination (Akazawa et al. 1995;Ben-Arie et al. 1997). Math1-null embryos die at birth due to respiratory failure and lack many specific cell lineages, including cerebellar granule neurons, spinal cord interneurons, inner ear hair cells, and intestinal secretory cells (Ben-Arie et al. 1997;Bermingham et al. 1999Bermingham et al. , 2001Yang et al. 2001).Gfi1 is a zinc-finger transcriptional repressor essential for hematopoietic stem cell function and differentiation of immune cells and a prot...