Charles Sande (@Charlesjsande) profile picture
Joined January 2018
Charles Sande retweeted
Neutralizing interleukin-10 autoantibodies were found in a subgroup of patients with inflammatory bowel disease and in no controls without IBD. Seropositivity was strongly associated with the IBD HLA-DRB1*01:03 risk allele. Full study results: nej.md/4dXZ3od Science behind the Study: Autoantibodies against Cytokines — From Infection to Inflammation nej.md/4e1EZ4s
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Really interesting new paper from Akbari et al. identifying a lot more selection in ancient DNA than previous approaches. I think it gets at three core challenges for this type of analysis where our understanding is still limited. 🧵
Congratulations to Ali Akbari @aliakbari23 on his amazing new work on selection in Western Eurasia that is finally released as a preprint after years of painstaking work. Accompanying it is a selection browser (beta) reich-ages.rc.hms.harvard.ed… biorxiv.org/content/10.1101/…
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Charles Sande retweeted
BREAKING NEWS The 2025 #NobelPrize in Physiology or Medicine has been awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi “for their discoveries concerning peripheral immune tolerance.”
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Charles Sande retweeted
Please check out our new manuscript extending the GREML methodology to quantify assortative mating and other forms of trait-associated genetic structures. Thanks to all our co-authors and the study participants! Here: nature.com/articles/s41588-0…
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Shingles vax appears to prevent dementia! Our Nature paper is first of many from my group to show this. We use a really neat natural experiment to provide causal (not just correlational!) evidence. Paper: nature.com/articles/s41586-0…; video (👏 @DrMayaAdam): bit.ly/4ciRfLh
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Promising news: for the first time, @WHO has prequalified a maternal RSV vaccine to protect infants. Now, we are working on how to deliver it in lower-income countries, where 99% of RSV deaths occur to protect those most at risk. rb.gy/vti4ox
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Tune in tomorrow morning to @SpiceFMKE as Dr. @george_l , Bioinformatics Lead, @KEMRI_Wellcome discusses the importance of Genomic Surveillance in response to outbreaks.
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Replying to @WehliyeMohamed
GREAT 👏🏽👏🏽 They should even be MORE. We can’t have people living in SLUMS in 2023 while some live in OPULENCE. The BUBBLE should BURST. Prices DROP, people MOVE UP respective to incomes so that SLUMS stop making sense as an OPTION
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Excited to share the pre-print describing our efforts to stabilize the HCMV gB ectodomain in a prefusion-like conformation. We and others have now routinely stabilized class I viral fusion proteins, but class III viral fusogens have been more difficult.
Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation biorxiv.org/cgi/content/shor… #bioRxiv
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Congratulations, DR. Alex Macharia. Incredible defence of your PhD thesis to pass WITHOUT CORRECTIONS! And to your supervisors led by Prof Tom Williams! @alexwaiganjo @Tom_WilliamsN @IDeAL_KEMRI_WT @KEMRI_Wellcome
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A fascinating work is published today @Nature by Zhang & Zhang et al. on a serendipitous discovery of haemoglobin expression outside the RBC cells--in chondrocytes--and their critical role in keeping our cartilage alive under an oxygen-deprived environment. nature.com/articles/s41586-0… Our school teachers taught that haemoglobin (Hb) is an oxygen-transporting protein expressed exclusively in the red blood cells. Although there exist occasional sporadic reports of Hb expression outside the RBCs (e.g. neurons, retinal cells etc.), no one would have guessed Hb would play a critical role (required for survival) outside the RBCs. The discovery When studying the cartilage growth plate of neonatal mice, the authors noticed eosin-positive structures in the chondrocytes (cartilage cells) that resembled structures seen in RBCs. Out of curiosity, the researchers went on to stain and examine the chondrocytes of different cartilage tissue types both from mice and humans. They realized that no matter the source or species, the cells always displayed eosin-positive structures under the microscope. The curious researchers were determined to find out what these structures are made of. They carefully dissected these structures out and studied the protein components using mass spectrometry and were surprised to learn the results: the top hits were Hb proteins. Unable to believe the results, they went on to study the proteins using different methods--western blotting, immunohistochemistry--and every time they ended up with the same results: the cytoplasm of cells was loaded with organelles-like bodies made of haemoglobin proteins. Finally, they came to the realization that Hb is abundantly produced in chondrocytes. They named these cytoplasmic Hb bodies as "Hedy". Structure of Hedy The authors studied the structure and formation of Hb bodies floating in the cytoplasm. Are they like an organelle? Do they have a membrane? Through various experiments, the researchers found that the Hedy structures do not have a membrane. The Hb proteins condense together by phase separation to form organelle-like structures in the cytoplasm. This condensation is itself an evolved process, requiring specific sequence structures of the Hb protein. Globin switching We know that there are different forms of Hb each expressed during different developmental stages: embryonic, fetal and adult Hb. There exists a sophisticated molecular machinery (which was believed to be RBC-specific) that switches one Hb type to the other at appropriate times. Using gene silencing experiments, the authors were further awestruck to find that the chondrocytes too switched their Hb types from embryonic to fetal to adult stages, just like RBCs! Regulation of chondrocyte Hb production It is well known that hypoxia induces Hb production via upregulating hypoxia-inducible factors (HIFs), an evolutionarily conserved molecular mechanism (Nobel Prize 2019; nobelprize.org/prizes/medici…). But it turned out that chondrocytes have evolved to increase their Hb expression not via HIF proteins, but through a different protein, the same protein that is required for fetal to adult Hb switching: KLF1 (nature.com/articles/ng0910-7…). How important is Hb for chondrocytes? Such a high Hb expression in chondrocytes with similar globin switching behaviour as RBCs would mean that this Hb is critical for chondrocytes' survival. By deleting the Hbb gene specifically in the chondrocytes, the authors found that without Hb the chondrocytes die killing the animal a few days after birth. Conclusion Continuous oxygen supply is a prerequisite for the survival of cells in all tissues. The only way the cells can receive oxygen is through RBCs in the blood, which requires the tissue to be highly vascularized. When demand exceeds the supply, the cells evolve to survive an oxygen-depriving environment. Muscles evolved to produce their own globin--myoglobin which has a higher affinity to oxygen than Hb thereby withholding O2 during oxygen excess states and releasing it back during oxygen-deprived state (during exercise). Likewise, the brain has its own globin: neuroglobin (nature.com/articles/35035181). Today, we are learning that cartilage (an avascular tissue), too, has its own globin. But unlike muscle and brain, have evolved to store oxygen not by making a new type of globin but by making just the same type as the ones in RBCs, but with a higher affinity than RBC Hb. When it comes to fundamental biology, we often assume that we have found everything and then one day a discovery like this drops, hitting us on the head to make us realize that there is a whole universe of hidden biological secrets waiting to be discovered. Some recent posts: 1. Gene x sex interaction of PNPLA3 I148M variant (xitter.cf/doctorveera/status/170…) 2. Effect of consanguineous marriage on the risk of common diseases in offsprings (xitter.cf/doctorveera/status/170…) 3. Whole genome vs. Whole exome sequencing. Which is more cost-effective for genetic association studies? (xitter.cf/doctorveera/status/170…)
Whole genome sequencing (WGS) vs. whole exome sequencing plus array genotyping and imputation (WES+IMP), which one is more cost-effective for population-scale genetic association studies? My colleagues at Regeneron Genetics Center (Gaynor et al.) answer this question using a systematic comparison of genetic discovery yield between the two approaches. I guess most of you might have guessed it already. Yes, the winner is clearly WES+IMP. WES captures most of the variants, across the full allele frequency spectrum, that sit within the coding region, which comprises merely 1% of the genome. Genotyping+imputation captures common variants (MAF > 1%) and, to some extent, low-frequency variants (0.1-1%) across the entire genome. So, the extra thing we capture using WGS is the rare variants from the noncoding genome. For example, in a sample size of ~150k UK Biobank participants, WES+IMP yielded ~125M variants (SNVs and indels) and WGS yielded ~600M variants. But does this ~5-fold increase in variant discovery using WGS translate into genetic discovery? Nope. When running a genetic association analysis for 100 phenotypes using WGS and WES+IMP, the authors found an almost similar number of discoveries using both approaches with a mere ~1% more genetic associations using WGS. This is because a majority of the extra variants that WGS captures are singletons i.e., seen in only one individual. The ~5-fold increase in variant count translates to just ~0.3% per individual. So, this doesn't help with the sample size that you'll need to make a genetic discovery. Comparing WGS against WES+IMP in a fixed sample size is not fair as WGS is more expensive than WES+IMP. So, what happens if we invest the extra money to boost the sample size of WES+IMP? When increasing the sample size by 3-fold, the genetic discoveries rise by 4-fold. If we increase the sample size by 10-fold, the genetic discoveries are likely to rise by 20-fold. The authors conclude that "prioritizing WES+IMP and large sample sizes, rather than current short-read WGS alternatives, will maximize the number of discoveries in genetic association studies." medrxiv.org/content/10.1101/…
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I'm a Professor!!!!!! (thought about more mature ways of saying it, but this worked) Thanks to everyone @imperialcollege @ImperialMed @ImperialInfect for all the support along the way: mentors, team, colleagues And of course @DrCharlieWeller
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Biggest thing to ever come out of my little group. Pls help spread this finding! We found clean, CAUSAL evidence that the shingles vaccine prevents a good chunk of dementia cases. So, could a virus cause Alzheimer’s->YES! Hear me out & see preprint: bit.ly/3MVqXU9 🧵1/
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Remarkable insights into the immunology of severe COVID from these incredible genetic studies - humbling to have been a very small part. So mechanisms to be understood!
Delighted to share biggest paper yet from GenOMICC study. Our first report found 5 genes underlying critical covid, one of which pointed to an effective new treatment (baricitinib). Now we report 49 genes & multiple new drug options nature.com/articles/s41586-0…
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