Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Senior Smile

Oil on canvas | 20 x 24https://digitalcommons.imsa.edu/art_sw/1000/thumbnail.jp

11: Stem Cell Therapy for Cancer Patients

Currently, the most common methods of fighting cancer are chemotherapy and radiation, which destroy tumor cells. However, both of these methods also kill healthy cells, cause organ damage, and destroy the stem cells necessary for cell regeneration.https://digitalcommons.imsa.edu/stem_posters/1007/thumbnail.jp

Peripheral deletional tolerance of alloreactive CD8 but not CD4 T cells is dependent on the PD-1/PD-L1 pathway

Although interaction between programmed death-1 (PD-1) and the ligand PD-L1 has been shown to mediate CD8 cell exhaustion in the setting of chronic infection or the absence of CD4 help, a role for this pathway in attenuating early alloreactive CD8 cell responses has not been identified. We demonstrate that the PD-1/PD-L1 pathway is needed to rapidly tolerize alloreactive CD8 cells in a model that requires CD4 cells and culminates in CD8 cell deletion. This protocol involves allogeneic bone marrow transplantation (BMT) following conditioning with low-dose total body irradiation and anti-CD154 antibody. Tolerized donor-reactive T-cell receptor transgenic CD8 cells are shown to be in an abortive activation state prior to their deletion, showing early and prolonged expression of activation markers (compared with rejecting CD8 cells) while being functionally silenced by day 4 after transplantation. Although both tolerized and rejecting alloreactive CD8 cells up-regulate PD-1, CD8 cell tolerance is dependent on the PD-1/PD-L1 pathway. In contrast, CD4 cells are tolerized independently of this pathway following BMT with anti-CD154. These studies demonstrate a dichotomy between the requirements for CD4 and CD8 tolerance and identify a role for PD-1 in the rapid tolerization of an alloreactive T-cell population via a deletional mechanism

Follicular Helper T Cells Promote Liver Pathology in Mice during <i>Schistosoma japonicum</i> Infection

<div><p>Following <i>Schistosoma japonicum</i> (<i>S. japonicum</i>) infection, granulomatous responses are induced by parasite eggs trapped in host organs, particular in the liver, during the acute stage of disease. While excessive liver granulomatous responses can lead to more severe fibrosis and circulatory impairment in chronically infected host. However, the exact mechanism of hepatic granuloma formation has remained obscure. In this study, we for the first time showed that follicular helper T (Tfh) cells are recruited to the liver to upregulate hepatic granuloma formation and liver injury in <i>S. japonicum</i>-infected mice, and identified a novel function of macrophages in Tfh cell induction. In addition, our results showed that the generation of Tfh cells driven by macrophages is dependent on cell–cell contact and the level of inducible costimulator ligand (ICOSL) on macrophages which is regulated by CD40–CD40L signaling. Our findings uncovered a previously unappreciated role for Tfh cells in liver pathology caused by <i>S. japonicum</i> infection in mice.</p></div

LAG-3, TGF-β, and cell-intrinsic PD-1 inhibitory pathways contribute to CD8 but not CD4 T-cell tolerance induced by allogeneic BMT with anti-CD40L

Administration of a single dose of anti-CD40L mAb at the time of allogeneic BM transplantation tolerizes peripheral alloreactive T cells and permits establishment of mixed hematopoietic chimerism in mice. Once engrafted, mixed chimeras are systemically tolerant to donor Ags through a central deletion mechanism and will accept any donor organ indefinitely. We previously found that the PD-1/PD-L1 pathway is required for CD8 T-cell tolerance in this model. However, the cell population that must express PD-1 and the role of other inhibitory molecules were unknown. Here, we report that LAG-3 is required for long-term peripheral CD8 but not CD4 T-cell tolerance and that this requirement is CD8 cell-extrinsic. In contrast, adoptive transfer studies revealed a CD8 T cell–intrinsic requirement for CTLA4/B7.1/B7.2 and for PD-1 for CD8 T-cell tolerance induction. We also observed that both PD-L1 and PD-L2 are independently required on donor cells to achieve T-cell tolerance. Finally, we uncovered a requirement for TGF-β signaling into T cells to achieve peripheral CD8 but not CD4 T-cell tolerance in this in vivo system

Macrophages drive Tfh cell generation.

<p>Expression of CXCR5 versus PD-1 on CD4⁺ T cells (gated as CD3⁺CD4⁺) after co-culture of normal mice derived CD4⁺ T cells with macrophages (A, B), B cells (E, F), and DCs (G, H) from normal or infected mice in the presence or absence of SEA. Numbers represent the frequency of the boxed population within the CD4⁺ T cell population; (C) Quantitative RT-PCR analysis of the expression of <i>BCL-6</i> mRNA in CD4⁺ T cells cultured with or without macrophage from infected mice. ***, P<0.001; **, P<0.01; *, P<0.05 (Student's <i>t</i>-test); (D) The expression of Bcl6 and ICOS was evaluated as previous described in CXCR5^lowPD-1^lowCD4⁺ T cells and CXCR5^highPD-1^highCD4⁺ T cells directly isolated from <i>S. japonicum</i>-infected mice or <i>in vitro</i> induced by macrophages from <i>S. japonicum</i>-infected.</p

Tfh cells promote liver pathology.

<p>(A) Mouse spleens, mesenteric LN, and livers from WT and ICOSL KO mice infected with or without <i>S. japonicum</i> were harvested, and cells were stained with CD3-percpcy5.5, CD4-FITC, CXCR5-APC, and PD-1-PE antibodies. Data shown are gated on CD3⁺CD4⁺ cells. Numbers represent the frequency of the boxed population within the CD4⁺ T cell population; (B) Data are expressed as the mean ± SD of 18 mice from three independent experiments, ***, P<0.001 (Student's <i>t</i>-test); (C) The absolute numbers of CXCR5^highPD-1^high cells in spleens, mesenteric LN, and livers from WT and ICOSL KO mice infected with or without <i>S. japonicum</i> were calculated. Data are expressed as the mean ± SD of 18 mice from three independent experiments, ***, P<0.001 (Student's <i>t</i>-test); (D) Three weeks after adoptive transfer of none, PBS, non-Tfh CD4⁺ T cells, Tfh cells, or Th2 as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004097#s4" target="_blank">Materials and Methods</a>, liver sections from <i>S. japonicum</i>-infected ICOSL KO recipient mice were Paraffin-embedded, formalin fixed and stained with H&E. Images shown are representative of two independent experiments. Original magnification, ×100; (E) For each mouse, the sizes of 30 granulomas around single eggs were quantified with AxioVision Rel 4.7. Data are expressed in area units. Values are given as mean ± SD of 12 mice from two independent experiments, ***, P<0.001 (Student's <i>t</i>-test), compared with control mice; (F) Serum samples were collected from mice three weeks after adoptive transfer of none, PBS, Tfh cells, non-Tfh CD4⁺ T cells, or Th2 cells. Levels of serum ALT/AST were determined. Data are expressed as the mean ± SD of 12 mice from two independent experiments, **, P<0.01; *, P<0.05 (Student's <i>t</i>-test); (G) Paraffin-embedded sections were stained with sirius red. Images shown are representative of two independent experiments. Original magnification, ×100; (H) The mean optical density of collagen fibers by sirius red staining was digitized and analyzed on Image-Pro Plus software. Values are given as mean ± SD of 12 mice from two independent experiments, ***, P<0.001 (Student's <i>t</i>-test), compared with control mice.</p