Obesity in humans is associated with a region around FTO, a "fat mass and obesity-associated” gene on chromosome 16. Although this is the strongest genetic association, it accounts for only a 1-2% difference in Body Mass Index (BMI) and the mechanism was unknown. Here, the investigators looked at regulator proteins binding to variants DNA sequences within the FTO region, particularly those binding to sites with single nucleotide polymorphisms (SNPs), in 100 healthy Europeans -- 52 subjects were homozygous for 3 risk-variant SNPs (both alleles, all 3 loci) and the remaining 48 were homozygous for the non-risk variants.
They found that the change of a T-to-C at one SNP within a risk allele of FTO prevented the binding of the repressor protein ARID5B. For want of this binding site, the repressor is lost. For want of this repressor, the expression of 2 linked genes doubles: IRX3, located about half a million base pairs (~0.5 Mbp) away, and IRX5, ~1 Mbp away. IRX3 repression made mice
thinner by “increased energy dissipation without a change in physical activity or appetite”, i.e. not changing eating or exercise but rather elevating ‘metabolism’. The doubled expression of IRX3 led to a 5-fold reduction in mitochondrial thermogenesis and a 7-fold difference in brown/white adipose tissue development. (Brown fat is brown because it holds more
mitochondria, little furnaces that burn fat and produce heat.)
The risk alleles are causative, and mediate through IRX3 and IRX5, because mimicking the repression of IRX3 or IRX5 in 8 carriers of the risk alleles, but not 10 carriers of the non-risk
allele increased stimulated metabolism (Fig 3D, shown, left panel). And overexpression of IRX3 or IRX5 reduced stimulated metabolism in non-risk allele carriers (because their endogenous genes are repressed) but not in risk allele carriers
(Fig 3D, right panel).
Figure 3D. Oxygen consumption rate (OCR), basal and stimulated, in cells with risk or non-risk alleles.
The take-home messages are that the causative SNP can be kilobases away from the genes that mediate the effect (not a huge surprise) and that small risks might develop from relatively big differences in particular developmental and cell biological pathways (reverse butterfly effect: not small-change-to-big-effect but big effect leads to small change (1-2%
BMI)).
N Engl J Med. 2015 Sep 3;373(10):895-907. “FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.” Claussnitzer M, Dankel SN, Kim KH, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson PA, Hsu YH, Drucker DJ, Mellgren G, Hui CC, Hauner H, Kellis M
Sunday, February 21, 2016
Skinny Genes: Human Warming and the Reverse Butterfly Effect
Sunday, November 22, 2015
Normalizing T lymphocyte metabolism treats lupus autoimmunity
Glucose is metabolized in two pathways to fuel cellular
functions: glycolysis, which splits glucose, yielding little energy but providing pyruvate
and other materials for synthesis, and oxidative phosphorylation, which degrades glucose in the mitochondria and produces ~15-fold
more energy. Glucose uptake is a limiting in activated T lymphocytes through CD28 costimulation. Glucose metabolism is dysregulated in T lymphocytes of
patients with the autoimmune disease Systemic Lupus Erythematosus (SLE, lupus, review).

Sunday, March 15, 2015
Stem Cells: Unstable in Culture
Stem Cells
(SC) can differentiate into many different cell types, offering the potential
of replacing failing cells, tissues, or even entire organs with new ones
generated from the patient’s own or related donor SC (National Academy of
Sciences Workshop summary). To be useful for
therapy in the clinic, it would be necessary to grow and expand SCs in culture.
The authors explored the proliferation of human embryonic SC
(HESC), which are prepared from disrupted embryos, and the less-controversial human
inducible pluripotent stem cells (hiPSCs), which can be prepared from several
adult tissues, including blood, skin, and fat. They obtained 1 HESC line, WA09, from the
WiCell Research Institute and they generated 3 hiPSC lines from fetal dermal
fibroblasts by over-expressing the ‘standard reprogramming factors’ (pluripotency-conferring
genes, transduced OCT4/POU5F1, SOX2, KLF4, and MYC).
They compared four standard SC culture conditions: with or
without a feeder cell layer and enzymatic or “mechanical” (dissection)
disruption, with 6 replicate cultures per condition, for over 100 “passages”
(transfers to fresh cultures). Previous studies cited here revealed genomic
changes (small duplications) that are not detectable by karyotyping,
particularly on chromosome 12, where the pluripotency-related gene NANOG is
encoded, and chromosome 20, where the survival gene Bcl-xL is encoded. In addition to measuring proliferation, telomere
length, pluripotency by teratoma formation, they also analyzed over a million
reference SNPs around the genome and used those SNPs to assess copy number
variation (CNV).
Not surprisingly, genomic changes increased with time in culture, both in aberration number (A) and total length (B) (Figure 2, shown, WA09 HESC: left duplications and right deletions). The number of aberrations was lowest in “EcmMech” condition, i.e. cultures without feeder cells (only extracellular matrix, ECM), and disrupted mechanically (blue line). The number and length of aberrations was worst with MefEnz (green line), cultured with feeder cells (mouse embryo fibroblasts, Mef) and disrupted enzymatically. They conclude that there is a “need for careful assessment of the effects of culture conditions on cells intended for clinical therapies”.
“Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions” Garitaonandia et al. PLoS One 10(2), February 25, 2015
Saturday, January 24, 2015
Nurture Immunity: Immune system influenced more by environment than by genes
Differences in immune protection presumably explain why some
people exposed to infection resist disease or recover while others
succumb. These authors sought to distinguish the influences
of genes and environment on immunity. They compared the cellular and molecular components
of the immune system among 210 twins: 78 monozygotic (MZ, “identical”) and 27
dizygotic (DZ, fraternal) pairs. They measured
43 serum proteins and 72 immune cell populations repeatedly and longitudinally
(over time) to assess actual variations and account for technical
variations. MZ twins, who have
practically identical genomes, and DZ twins, who share half their genes, are
especially valuable for assessing the relative contributions of “nature or nurture” (genes or environment) to phenotype. Their analysis allowed them to detect as
little as 20% heritability.
The levels of few proteins and cell populations are under
strong genetic control, such as interleukin-6 and CD4+ “central memory” T
cells, but most are only weakly heritable or not at all (Fig 1). They found
that a common, chronic infection, by cytomegalovirus (CMV), influences the levels of most (58%) cell populations and
proteins (Fig 5). Variation
between twins increased as they age, probably reflecting different
environmental stimuli and epigenetic changes (Fig 4). Most intriguing, they correlate the
heritability of response to vaccines to the age of immunization, whereby early childhood vaccines
are highly heritable while vaccines after early adolescence have no detectable heritability
(Table 1, shown below).
Sunday, December 8, 2013
Levels of a common, chronic virus (TTV) reflects the immune competence of transplant recipients
Successful organ transplantation requires careful immune
suppression: enough to block the rejection of transplant while permitting host defense
against infectious microbes. Viruses
that are not cleared by our immune systems, are common in healthy people, and can
complicate transplantation include cytomegalovirus (CMV) and Torque
teno virus (TTV), which was first described in 1997 [review]. TTV
is a small (3.8 kb), single-stranded, transfusion transmitted DNA virus,
representative of a highly diverse family of anelloviruses.
The authors examined the influence of immune-suppressive
drugs (e.g., tacrolimus, mycophenolate mofitil, cyclosporine) and the anti-CMV
drug valgancyclovir on chronic, endogenous microbes. From 96 heart or lung transplant recipients
they collected 656 blood samples over time, some up to a year post-transplant, removed
the cells, and identified remaining DNA by sequencing. They found that 0.12% matched viral or
bacterial or fungal sequences. They
validated some ‘hits’ with quantitative PCR.
Control preparations using water or bacteriophage demonstrated no
relevant artifacts or contamination.

Cell. 2013 Nov 21;155(5):1178-87. Temporal response of the human virome to immunosuppression and antiviral therapy. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, BernsteinD, Valantine HA, Quake SR.
Sunday, October 27, 2013
Salt develops a taste for Th17 lymphocytes

Sunday, April 21, 2013
Recipe for Developing Th17 cells
Thymus-dependent “T” lymphocytes develop into several
effector and regulatory lineages, including the well-characterized regulatory
“helper” T (Th) cells that express the cellular differentiation marker 4 (CD4+)
and CD8+ cytotoxic T lymphocytes (CTL, or Tc) that kill virus-infected cells.
The CD4+ Th lineages further differentiate into Th1, Th2, and Treg cells that
help protect against intracellular microbes, or helminthes, or specifically
regulate immune responses, as well as Th17 cells, so-called because they make the interleukin-17 (IL17) that
is required for protecting the mucosa against infection by bacteria and
fungi.
Sunday, December 9, 2012
The peptide binding site accounts for the MHC link to Rheumatoid Arthritis
That genes within the major histocompatibility complex (MHC, human HLA) influence
susceptibility to rheumatoid arthritis (RA) has been known for over 40 years, even before HLA nomenclature was well established (e.g., Dick et al. 1975). However, the few “classical” HLA genes constitute only a small fraction of the hundreds genes within the MHC, which include the inflammatory cytokine tumor necrosis factor (TNF), a key player in RA. Which genes are responsible for the association?
The authors investigated 5,018 “cases” of RA, all with antibodies against cyclic citrullinated peptides, CCP (i.e, seropositive, accounting for 70% of RA patients [review]) and 14,974 health, ethnically matched controls.
First they tested their ability to “impute” HLA alleles from their SNP data using a
reference panel of 2,767 individuals. Conclusion, not bad: 98% accuracy for “two digit” mapping and >80% for 4 digit (allele). Then they found the most significant nucleotide (p<10^-526!) is part of a codon for amino acid 11 of the HLA-DR beta 1,
and thus not part of the “shared epitope” (a 5-amino acid sequence and antibody epitope linked to RA [review]). A valine at this position confers a 3.8-fold higher risk whereas a (polar) serine is protective (the converse of risk). Comparing cases and controls shows a clear difference (shown here, from fig 3). Adding amino acids at positions 71 and 74 improved significance slightly, and alleles with these amino acids were independently shown to confer risk.
The authors conclude “These results are consistent with a disease model in which classical HLA genes and proteins are the dominant factors in rheumatoid arthritis pathogenesis, with only a minor contribution from non-HLA loci in the MHC”. It seems that someone might also explore whether these variants bind CCP better!

Sunday, October 7, 2012
ENCODE salvages “junk” DNA
The “ENCyclopedia Of DNA Elements”, ENCODE, founded in 2003 with grants from the NIH Genome Institute, seeks to identify
all the functional parts of the human genome, assessed by DNA and histone
modifications, chromatin looping, transcription factor binding, chromatin
compaction (DNAse accessibility), and transcripts. The collaboration of ~37 groups, first developed technology. Recently they published their
first salvo of 30 research papers, several published in Nature along with a News & Views.

Saturday, March 31, 2012
Monkey’s Uncle? Your HLA might be Neanderthal
Humans’ genomes are extremely similar to those of other primates because the species diverged relatively recently, approximately 6 million years ago in the case of our nearest cousins, Chimpanzees. Modern humans and Denisovans separated 250,000 years ago (10,000 generations). With the recent sequencing of extinct, ancient hominids, such as Neanderthals and their Denisovan relatives, it was realized that up to 6% of the genomes of humans now in Europe and Asia derive from these older lineages.
HLA genes are by far the most polymorphic within the human genome, with thousands of variants (alleles). Here, investigators first identified one particular HLA allele, HLA-B*73:01, as being more similar to homologous Chimpanzee alleles than other human HLA-B alleles. This allele diverged from other HLA-B alleles 16 million years ago, before the separation of humans and Chimps, and was lost from the majority of modern humans. Its reappearance in the human genome was most likely, they reckoned, a result of “introgression”, introduction from ancient humans such as Neanderthal. An alternative model, which computer simulations indicate is 100 times less probable, is that this allele came out of Africa late

