YouTube2Text

Sarah Teichmann — Transcript

by Fragile Nucleosome · 4,686 words · 765 segments · language en · Watch on YouTube

Full transcript

  1. 0:00my um great pleasure to introduce our
  2. 0:02second speaker um Dr. Sarah um Techman.
  3. 0:06So Sarah did her PhD at the MRC
  4. 0:09laboratory of molecular biology in
  5. 0:11Cambridge, UK and he uh she was a belt
  6. 0:15memorial fellow at University College
  7. 0:17London. In 2001, she started her own
  8. 0:20research group in MRC laboratory of
  9. 0:23molecular biology and moved to the
  10. 0:25Walcon genome campus in 2013.
  11. 0:29And in 2016, she was appointed head of
  12. 0:32the cellular genetics program, Ali
  13. 0:34Sanger. And in 2024, she then took
  14. 0:38another leadership role as a chair in
  15. 0:40Stanell medicine at the University of
  16. 0:42Cambridge. She's co-founder and also
  17. 0:44co-leader of the international human
  18. 0:47cell atlas consortium which aims to
  19. 0:49create reference maps for cells across
  20. 0:52all human tissues and has grown to
  21. 0:54include over 3,000 members across the
  22. 0:56world. Her laboratory develops as well
  23. 0:59as um applies cell atlas techniques to
  24. 1:02understand human tissue architecture
  25. 1:05with a particular focus on how cellular
  26. 1:07diversity is generated in the immune
  27. 1:10system and also throughout development.
  28. 1:12Her work has been recognized by numerous
  29. 1:15award including the amble gold medal
  30. 1:17genetic society Mary lines award among
  31. 1:20many many other awards and today um it's
  32. 1:24our great pleasure to have her
  33. 1:26presenting about multiomic Atlas of
  34. 1:28human skeleton development. Welcome
  35. 1:31Sarah. Thank you so much Sky for that
  36. 1:33kind introduction and it's a pleasure to
  37. 1:36to present this work um which we
  38. 1:38published at the end of last year um and
  39. 1:42it's slightly different from the title
  40. 1:44that I indicated but I want to kind of
  41. 1:46dig into this work because it had a um a
  42. 1:50a a component of of the epiggenome
  43. 1:54which we leveraged for gene regulatory
  44. 1:56network inference and genetics. I want
  45. 1:58to just sort of give a a very quick
  46. 2:00introduction into the the technologies
  47. 2:02that we use in the human cellless
  48. 2:04community and in projects like this and
  49. 2:06they're obviously single cell and
  50. 2:08spatial genomics and you know you're all
  51. 2:10aware of this resolution revolution that
  52. 2:12we've lived through for the past 15 plus
  53. 2:15years um where we are we are now able to
  54. 2:20map the nucleic acid content and um
  55. 2:24multimodal
  56. 2:26um features of individual cells and
  57. 2:29nuclei. And of course, combining that
  58. 2:32with spatial transcrytoics, with highly
  59. 2:35multiplex spatial mapping methods and
  60. 2:36tissue sections is a really powerful way
  61. 2:40to map human cells. And I'm really
  62. 2:42delighted that Ishtak who who preceded
  63. 2:45this talk kind of was also talking about
  64. 2:47human developmental samples, which is
  65. 2:49exactly what I'll be speaking about too.
  66. 2:52Um, and and these methods really sort of
  67. 2:54open up our ability to understand the
  68. 2:57molecular and cellular composition of
  69. 3:00human tissues in ways that weren't
  70. 3:03possible previously um because of the
  71. 3:06the limitations of of um you know
  72. 3:09modulating genetics and and manipulating
  73. 3:12human tissues. And it's really these
  74. 3:14technologies together with the data
  75. 3:16science that stitches them together that
  76. 3:18buoyed the launch of the human cell
  77. 3:20atlas almost 10 years ago now. And of
  78. 3:22course, this is
  79. 3:24our community grassrootsled project um
  80. 3:28that that that's an open project where
  81. 3:30we invite any anyone interested in this
  82. 3:33this this endeavor to join and the link
  83. 3:36is down at the bottom where our aim is
  84. 3:38to create a reference map of ourselves
  85. 3:42kind of from a basic understanding
  86. 3:44and discovery science point of view. And
  87. 3:48of course studying the human there's
  88. 3:50also immediately a diagnostics and and
  89. 3:53treatment implication and sort of
  90. 3:56translational relevance and and just to
  91. 3:59sort of um say this is a slide that's
  92. 4:01out of date but we're now at over 4,000
  93. 4:04members from over 100 countries around
  94. 4:06the world and you see sort of Europe and
  95. 4:09and North America and also um Latin
  96. 4:12America, Africa, Asia and so on has
  97. 4:15increasing kind of members and repres
  98. 4:17representation that uh contributing to
  99. 4:20the project. [snorts] The phase that
  100. 4:22we're in right now is really important
  101. 4:24and I want to highlight this this draft
  102. 4:27atlas assembly phase. And what this
  103. 4:30means is that we are integrating data
  104. 4:32sets and releasing reference data
  105. 4:34objects at data.humansellatlas.org
  106. 4:36the human cellless data portal. And so
  107. 4:39these are uh objects that are put
  108. 4:41together by the 12 postocs that are
  109. 4:43funded by the trans Zuckerberg
  110. 4:44initiative to integrate these data sets
  111. 4:47and work with the bio networks. We have
  112. 4:5018 biological networks that have PIs
  113. 4:53that are experts in the different organs
  114. 4:55and systems and curate do a careful
  115. 4:57curation of cell states. And so I want
  116. 5:00to emphasize that and encourage people
  117. 5:01to go and look there are now more
  118. 5:04approved atlases that we released. And
  119. 5:06this morning we approved the pancreas
  120. 5:07and the uh the the oral cranial facial
  121. 5:11atlas, the m the oral cavity basically.
  122. 5:14Uh and so that you know this is a really
  123. 5:15exciting time. We're obviously kind of
  124. 5:18still actively extending the human cell.
  125. 5:20This is far from complete with
  126. 5:22multimodal data with spatial data with
  127. 5:24more tissues pushing towards a more
  128. 5:27comprehensive mapping. We we we do have
  129. 5:31um on the data portal over 100 million
  130. 5:33cells from the 18 different biological
  131. 5:36networks and you can see the organs and
  132. 5:37systems sort of indicated around here.
  133. 5:40My story today is going to be related to
  134. 5:43muscularkeeletal
  135. 5:45network as well as
  136. 5:49human development embryionic [snorts]
  137. 5:51and and fetal development kind of along
  138. 5:53the lines that that Ishtak mentioned.
  139. 5:56And and so what I'll be what I'll be
  140. 5:58presenting is um human skeletal
  141. 6:01development where we set out to
  142. 6:03characterize osteogenesis and
  143. 6:05condrogenesis and gain insights into
  144. 6:07bone and joint conditions. And we have
  145. 6:08already worked on limb development
  146. 6:11previously and published um kind of
  147. 6:15insights into
  148. 6:17the the the condraittes. So the
  149. 6:18cartilage um that makes our tendons and
  150. 6:21and ligaments as well as osteoccytes
  151. 6:24that contribute to bone. And in terms of
  152. 6:27um oh just a sec
  153. 6:31need to change the pointer to to show
  154. 6:35these videos. So in in first trimester
  155. 6:40um embryionic osteogenesis the the bones
  156. 6:43and cartilage develop. And here what we
  157. 6:46have is a light sheet imaging from um
  158. 6:49Rafa Blan Alan Shadow's lab in Paris
  159. 6:52marking a collagen that's a marker of
  160. 6:55condrogenesis and a transcription factor
  161. 6:57SB7 that's a marker of osteoggenesis.
  162. 6:59So these are two lineages cartilage and
  163. 7:02bone that develop from the same meenal
  164. 7:05progenitors and there are two different
  165. 7:07processes um uh intra intromemebranous
  166. 7:10oification that makes our skull cap the
  167. 7:13the the top of our head and um
  168. 7:17endocchondrial oification that
  169. 7:18contributes to the other bones in the
  170. 7:20body and the the skull base. And you can
  171. 7:23see this sort of development kind of in
  172. 7:26a
  173. 7:28in this translucent um you know
  174. 7:30stunningly beautiful image of of the
  175. 7:32embryo here where [snorts]
  176. 7:34Raphael and allow then zooming in
  177. 7:36showing the skull cap has a different
  178. 7:38developmental origin to the skull base.
  179. 7:41[snorts] So, as I said, the SP7
  180. 7:44transcription factor is marking the
  181. 7:45skull cap and the
  182. 7:47specific collagen is marking the skull
  183. 7:49base because they're they're obviously a
  184. 7:51single sort of anatomical structure
  185. 7:53together, but have different origins and
  186. 7:56different
  187. 7:58mechanisms for making the bones. And if
  188. 8:00we look a couple of weeks later in in in
  189. 8:02pregnancy and in human development, we
  190. 8:04see these [snorts]
  191. 8:07um kind of more mature um
  192. 8:12um ex more extensive
  193. 8:15uh coverage of of the skull cap and the
  194. 8:17skull base through these um these two
  195. 8:21different processes.
  196. 8:22Intramebran intramebranous ocification
  197. 8:25and endocchondrial ocification.
  198. 8:29um in in the skull cap the introme
  199. 8:32intramebranous ocification is the main
  200. 8:34mechanism. So here again just to um
  201. 8:37emphasize that
  202. 8:40the the different um plates effectively
  203. 8:44that that um contribute to our skull are
  204. 8:49uh anterior regions of the skull cap and
  205. 8:51skull base. And you have these uh
  206. 8:53sutures and um [snorts] um the coronal
  207. 8:58suture and sagittal sutures that uh are
  208. 9:01at the the interfaces between the the
  209. 9:03the the plates. Um there's ocification
  210. 9:07across regions during development and
  211. 9:09the the skull cap is formed by
  212. 9:12intramebranous ocification and Ken toe
  213. 9:15who was an incredibly talented um
  214. 9:18clinical PhD student traininee in the
  215. 9:20lab and has now gone back to surgical
  216. 9:23training dissected these regions
  217. 9:25extremely carefully for then paired
  218. 9:28single nuclear and single single nuclear
  219. 9:31RNA and attack sequencing. So multi ohm
  220. 9:33analysis of the nuclei which you can
  221. 9:37it's the tissue soft enough that you can
  222. 9:38extract it basically from this first
  223. 9:40trimester samples and um and then also
  224. 9:45analyze uh the sections by vizium
  225. 9:49spatial transcrytoics and this is shown
  226. 9:51here um [snorts] uh sort of indicating
  227. 9:55the skull the the skull cap the skull
  228. 9:57base and then also the appendicular
  229. 9:59skeleton joints in the shoulder the hip
  230. 10:01and the knee
  231. 10:03um that were dissected at different time
  232. 10:05points in in first trimester development
  233. 10:08year 5 6 7 8 9 10 11 12 postconception
  234. 10:11weeks and then analyzed by um
  235. 10:15multi ohm so RNA plus attack sequencing
  236. 10:18at these different time points for the
  237. 10:19different um bone and joints and then um
  238. 10:23also by vizium and incite 155th fiveplex
  239. 10:27incitu sequencing which we carried out
  240. 10:28with with Kenny White um in in Omar
  241. 10:32Batra's lab um and the the the process
  242. 10:38of um intramebranous oification sort of
  243. 10:42takes place throughout where the onset
  244. 10:45of oification is kicked off in the skull
  245. 10:47cap throughout this period. Whereas in
  246. 10:50the other um bone and and joint regions
  247. 10:54there's this misenal condensation
  248. 10:56interzone formation and then formation
  249. 10:59of of cartilage primordia and
  250. 11:01paricchondrium and and then finally
  251. 11:04oification through endocchondrial
  252. 11:06oification which is sort of a different
  253. 11:08developmental process.
  254. 11:11If we kind of look at the the cell
  255. 11:13states of these 300,000 um nuclei that
  256. 11:17we profiled by Multium, the meseno
  257. 11:20states are shown on the right hand side
  258. 11:21and you can see a lot of different um uh
  259. 11:24progenitor and um
  260. 11:28developmental states kind of um all
  261. 11:32projected together from from the
  262. 11:34different regions. Over on the right
  263. 11:35hand side here, um
  264. 11:39you've got condondraite progenitors of
  265. 11:41different at different stages. Um
  266. 11:44hypertrophic condraittes
  267. 11:46uh and and articular condondraittes. If
  268. 11:49we focus on the the the the the skull
  269. 11:52cap and craniogenesis,
  270. 11:54we describe these previously unreported
  271. 11:56human cell states of the cranium misim,
  272. 11:59the suture misenheime, and then a
  273. 12:02pre-ostoblast progenitor prior to the
  274. 12:04osteoblast and osteoccy differentiation.
  275. 12:06And because we have um [snorts] we we
  276. 12:10can sort of plot this in in this pseudo
  277. 12:13time um developmental cell cell pseudo
  278. 12:17time here um and and and plot the
  279. 12:20markers that are differentially the
  280. 12:22genes that are differentially expressed
  281. 12:24along this this trajectory.
  282. 12:27And then what I'd like to um you know
  283. 12:29what's really beautiful is that this
  284. 12:31also maps kind of onto onto um
  285. 12:37different locations in in space in the
  286. 12:40skull cap. And just to orient ourselves
  287. 12:43this is 50 micron vizium spatial
  288. 12:45transcripttoics where each voxil you
  289. 12:47know is a group of cells. We can
  290. 12:49deconvolute the cells with
  291. 12:50celltolocation which is a probabistic
  292. 12:53model um that gives us the individual
  293. 12:56states in the voxels and um the suture
  294. 12:59the coronal
  295. 13:01sutures basically along along in this
  296. 13:04region you've got der the dermal layer
  297. 13:06the skin on the top and then mining
  298. 13:10um along the bottom then then the brain
  299. 13:12basically below that and
  300. 13:16um in fact the the different uh the the
  301. 13:20different cell types that I just
  302. 13:21mentioned are organized in um in a
  303. 13:26zonated way basically along the skull
  304. 13:28cap and we can use our organ access um
  305. 13:32modeling framework that's on GitHub that
  306. 13:35we published as part of a a whole thymus
  307. 13:38cell atlas model um in order to
  308. 13:40calculate kind of the different uh the
  309. 13:43different zones in a progressive way
  310. 13:46that represent the different cell uh
  311. 13:48cell states or the different sort of
  312. 13:51tissue niches if you like kind of um
  313. 13:55along the um along the skull cap. So
  314. 13:58you've got suture zones and then
  315. 14:01different osteogenic zones um sort of in
  316. 14:04a progressive way and the the the the
  317. 14:08[snorts] osteoccytes are are basically
  318. 14:10enriched in the um
  319. 14:13in the osteogenic zones and and the
  320. 14:15progenitors basically earlier on
  321. 14:19um because this is multi ohm data so we
  322. 14:22don't have the the the beautiful histone
  323. 14:23modifications that you saw in Ishtiaak's
  324. 14:25talk what we have is is open versus
  325. 14:27closed chromatin And so we can define
  326. 14:30um combinations of of enhancers and and
  327. 14:33and actively transcribed genes using the
  328. 14:36scenic plus um gene reguy network
  329. 14:39inference pipeline and and [snorts]
  330. 14:41calculate these enhancer
  331. 14:44gene transcription factor active gene
  332. 14:47sort of modules and that's what you see
  333. 14:49over here on the right hand side where
  334. 14:51we quantify the activity of these
  335. 14:52different transcription factors in the
  336. 14:55different um in [snorts] the different
  337. 14:57cell compon compartments, the different
  338. 14:58cell lineages. And you so you can see a
  339. 15:01set of transcription factors that's um
  340. 15:05um sort of more active in the in the
  341. 15:08earlier cell compartments and and and
  342. 15:11then this SP7 transcription factor that
  343. 15:13I meant that I mentioned marking the
  344. 15:16intromebrinous oification and the
  345. 15:18osteoblast and osteoccytes is coming up
  346. 15:20here in these more mature compartments
  347. 15:23and we can you know represent these
  348. 15:25regulons
  349. 15:26with their their dominant transcription
  350. 15:29factor. factor basically in and and
  351. 15:32correlate different modules kind of
  352. 15:34together within cells. And so there's
  353. 15:37sort of [snorts] modules that are
  354. 15:39essentially activating or pushing
  355. 15:41forwards osteogenesis versus modules
  356. 15:44that are kind of inhibiting osteogenesis
  357. 15:48if you like and and they're shown here
  358. 15:49in the red and the blue.
  359. 15:52Um so so using that sort of um network
  360. 15:56approach
  361. 15:58um we we can
  362. 16:01essentially [snorts]
  363. 16:03um calculate a a hierarchy of
  364. 16:05transcription factors that are
  365. 16:07maintaining the progenitor pool and um
  366. 16:10versus ones that are activating
  367. 16:13um activating uh the osteogenic
  368. 16:17phenotype essentially in in both
  369. 16:20intramebranous and in um um
  370. 16:24endocchondrial
  371. 16:25uh ocification.
  372. 16:30and and and then if we if we again sort
  373. 16:33of zoom in and map uh the locations of
  374. 16:36the transcription factors and their
  375. 16:38activity onto the the skull cap in space
  376. 16:41in the spatial transcripttoics, what we
  377. 16:44can see is the um
  378. 16:47um transcription factors that are kind
  379. 16:50of poisoning for osteogenesis in the
  380. 16:52sutra misanky versus transcription
  381. 16:55factors that are that are um maintaining
  382. 16:57patency like twist one and lmx1b.
  383. 17:00And then also um you know correlate how
  384. 17:05these transcription factors how these
  385. 17:07key transcription factors link to
  386. 17:09genetic conditions like cranioinostosis
  387. 17:12where you have fusion of the sutures.
  388. 17:15And so this um you know twist one is
  389. 17:18expressed in this region maintaining the
  390. 17:21the the separation of the the the skull
  391. 17:25plates. Um and if there if that's
  392. 17:28mutated then then there's fusion
  393. 17:30cranioinistosis of the the skull plates
  394. 17:32which is a bad thing. Um in similarly uh
  395. 17:36when we look at um
  396. 17:39[snorts] at at other um other other
  397. 17:43signaling or factors or receptors or
  398. 17:46transcription factors involved in in for
  399. 17:48instance um digit you know the the
  400. 17:51development of the bones and the digits.
  401. 17:53We can plot basically where these genes
  402. 17:57are active or penetrating during first
  403. 18:00trimester development in the the not
  404. 18:03only the skull cap but also the other um
  405. 18:06you know the other parts of other bones
  406. 18:08for instance in digit development and
  407. 18:09relate essentially the the the phenotype
  408. 18:13from proximal digit only distal digit
  409. 18:15only and so on to the the location where
  410. 18:18the genes are acting during development.
  411. 18:21And so this is um you know it's it's
  412. 18:24giving us a very high resolution fine
  413. 18:26grained insight into the
  414. 18:29>> [snorts]
  415. 18:29>> um the mechanisms of these genetic
  416. 18:31conditions
  417. 18:33and you know including the sort of
  418. 18:35cranioacial cleft which is enriched in
  419. 18:37cranial bone
  420. 18:39pytorranial disostois enriched in
  421. 18:42cranial bone and limb paricchondrium and
  422. 18:44so on.
  423. 18:46um we collaborated with the Zen group in
  424. 18:48also linking um expression of of G-W was
  425. 18:53fine mapping of of G-W was signals so
  426. 18:56where you've got a genetic association
  427. 18:58with with adult diseases such as
  428. 19:00osteoarthritis and rheumatoid arthritis
  429. 19:04into the the developmental cell states
  430. 19:06and you know we were discussing this in
  431. 19:08my lab this morning uh whether this
  432. 19:10makes sense and you know I would I would
  433. 19:13argue there are two there are two well
  434. 19:16not only did the the reviewers kind of
  435. 19:19accept this but you know beyond that I
  436. 19:22would argue that it it is likely and
  437. 19:26there is evidence that that some of the
  438. 19:28conditions that we experience as adults
  439. 19:30and that are late onset are actually
  440. 19:32sort of already poised um in in terms of
  441. 19:37uh you know subtle variations during
  442. 19:39pregnancy in in our embryionic and fetal
  443. 19:41developmental stages and and So, you
  444. 19:44know, understanding the genetic variants
  445. 19:47that increase our risk of various adult
  446. 19:50diseases during development,
  447. 19:53I would argue is is relevant and is of
  448. 19:56interest. And obviously, you know, if we
  449. 19:58find map variants and then understand
  450. 20:00how they're modulating binding of
  451. 20:03transcription factors and influencing
  452. 20:05changes in gene expression in cells
  453. 20:07during development, that can give us
  454. 20:10mechanistic insights. And so this
  455. 20:12exercise, you know, this is this is one
  456. 20:14example
  457. 20:15um uh where we're relating adult risk
  458. 20:19genetic risk factors that are mostly
  459. 20:21non-coding by the way into um you know
  460. 20:24they're they're acting through distal
  461. 20:26enhancers and repressors and so on into
  462. 20:29um the the developmental data is is is
  463. 20:32is kind of you know one example. And um
  464. 20:37the way we went about this was using a
  465. 20:40new method called snip to cell which we
  466. 20:41published in this in this paper um that
  467. 20:44was led by Ken toe with Lee Jang Feay
  468. 20:46and Patrick Pet uh who who worked
  469. 20:49together to develop this method. And the
  470. 20:51the the principle is that you take the
  471. 20:53G-W was summary statistics, map them
  472. 20:55into the um the multi ohm data uh into
  473. 20:58the the enhancers and the gene regulator
  474. 21:00network and look for enrichment of
  475. 21:03modules of of genetic variance in cell
  476. 21:06types through as they sort of percolate
  477. 21:10through the gene reguary network that's
  478. 21:12calculated from um from the scenic plus
  479. 21:16data. And so you can kind of propagate
  480. 21:18variance through uh modules and
  481. 21:20calculate subn networks that are that
  482. 21:22are affected. And and indeed when we do
  483. 21:25this this this when we use this snip to
  484. 21:29cell pipeline that uses fine mapping of
  485. 21:31GW was and FGW was uh package with the
  486. 21:35single single nuclear multiom data. We
  487. 21:37can identify enrichment of osteogenic
  488. 21:40cell types uh in in HIP.
  489. 21:44um but um
  490. 21:47condondrogenic cell types in in knee
  491. 21:51osteoarthritis. And so what it's what
  492. 21:53it's suggesting is that knee
  493. 21:54osteoarthritis is more um you know
  494. 21:57associated with cartilage and and cart
  495. 22:00and and sort of poised through cartilage
  496. 22:02development and hip osteoarthritis is
  497. 22:04more connected to osteogenic bone cell
  498. 22:07types in in in the hip. [snorts] Um
  499. 22:14so basically that sort of takes me to
  500. 22:16the end of this story and um just to
  501. 22:20summarize what we've um discovered are
  502. 22:23are cell types and tissue niches in in
  503. 22:26skeletal development that were
  504. 22:28previously unappreciated
  505. 22:30in in in mammals. So not just in humans.
  506. 22:34Um
  507. 22:36that uh uh uh also we use scenic plus to
  508. 22:41uh identify gene regu network triads
  509. 22:44using the multiome data and and define
  510. 22:46transcription factors, regulatory
  511. 22:48regions and genes that are linked
  512. 22:50basically in in in these uh different
  513. 22:54cartilage and bone developmental
  514. 22:57processes that occur in the different
  515. 22:58regions of our skeleton and then connect
  516. 23:01to rare disease and common disease
  517. 23:03genetics.
  518. 23:04and and gain more detailed insights into
  519. 23:06the mechanisms of these genetic
  520. 23:08conditions.
  521. 23:10Basically, by mapping the rare disease
  522. 23:12genes in terms of their locations and
  523. 23:13where they're penetrating during
  524. 23:15pregnancy and then also gaining insight
  525. 23:17into where adult onset disease uh risk
  526. 23:22factors may be acting during
  527. 23:24development.
  528. 23:26So I've mentioned Ken who um
  529. 23:30worked closely with Lee Shang and
  530. 23:32Patrick who are two incredibly talented
  531. 23:34um uh computational [snorts]
  532. 23:37data science and AI postocs in the
  533. 23:39group. Patrick has now gone to uh
  534. 23:42relation a biotech company. Our
  535. 23:44collaborators um were Mosh Hanifa, Roger
  536. 23:47Barker and I've also mentioned Omar
  537. 23:49Bactctor already and also Alan Shadowal
  538. 23:52for the beautiful light sheet imaging
  539. 23:54and Chris Buckley who co-supervised Ken
  540. 23:56for his PhD and is an an expert
  541. 23:59rheumatologist in Oxford and this is a
  542. 24:01picture of our lab and um these are my
  543. 24:05disclosures.
  544. 24:07Thank you for your attention and I'd
  545. 24:08[clears throat] be delighted to take
  546. 24:09questions.
  547. 24:12Thank you Sarah for the uh wonderful
  548. 24:14presentations. Um if you have any
  549. 24:16questions you can raise your hand or you
  550. 24:18can type your questions um in the Q&A
  551. 24:21box so that um Sarah can answer it
  552. 24:24directly.
  553. 24:29Let me just make sure
  554. 24:43So the first question is um
  555. 24:47[clears throat and laughter]
  556. 24:48[gasps]
  557. 24:48um it's a praise.
  558. 24:59How easy is it um to collect a lot of
  559. 25:02samples for your like this single cell
  560. 25:06experiment?
  561. 25:14Sorry, I'm just answering the question.
  562. 25:16Um so, so sample access is a crucial
  563. 25:19point and thank you so much for that
  564. 25:21question which I kind of skipped over.
  565. 25:24um you know all this data was enabled by
  566. 25:26the the generosity of the women who are
  567. 25:28donating their tissue um in a a social
  568. 25:32termination.
  569. 25:33So similar to what Ishtak said and in
  570. 25:36the UK we have a wonderful tissue bank
  571. 25:38called the human developmental uh
  572. 25:40biology repository www.hdbr.org
  573. 25:45and um that that repository is based at
  574. 25:49um London and Newcastle and provides
  575. 25:52tissues uh on a bio bank basis uh to to
  576. 25:56scientists in the UK and also uh to
  577. 25:59scientists in other countries if you can
  578. 26:03uh work with them uh to show that you
  579. 26:05have the the appropriate ethics from
  580. 26:07your institution the ethical approval
  581. 26:10>> um the these samples were also uh
  582. 26:14collected under a separate ethics held
  583. 26:16by Roger Barker in Cambridge uh he's one
  584. 26:19of the PIs that I acknowledge on the
  585. 26:21last slide and Roger has run a um a
  586. 26:25research program for over 20 years on um
  587. 26:29um dopamineergic neurons in the
  588. 26:31developing brain in order to uh better
  589. 26:34understand and treat Parkinson's disease
  590. 26:36and and and [clears throat] we worked
  591. 26:38with him. I'm a co-PI on that research
  592. 26:41ethics project where we also collect
  593. 26:44samples locally from the uh tertiary
  594. 26:47teaching hospital in in the Cambridge
  595. 26:49University Clinical School.
  596. 26:52Nice. I think Jackson has a question
  597. 26:54that um he's going to ask himself.
  598. 27:00>> Got that closing camera. Yeah. Uh that
  599. 27:03was really fascinating, Sarah. And I'm
  600. 27:06wondering um how much information you
  601. 27:09can kind of glean or infer from these uh
  602. 27:12networks about like the
  603. 27:16origin of all of these different cell
  604. 27:18types in the skeletal system. um like
  605. 27:22from like the transcription factors that
  606. 27:24you're pulling out or anything else
  607. 27:26about the chromatin accessibility, can
  608. 27:28you identify subsets of cells that might
  609. 27:31be like neural crest derived versus the
  610. 27:34cells that come from other ectoermal
  611. 27:36lineages? Yeah. So the this is all
  612. 27:39mezeno lineage and um sorry let me just
  613. 27:43go back.
  614. 27:46Um
  615. 27:53yeah so these lineages are derived from
  616. 27:55different condensates essentially in the
  617. 27:59um in the developing embryo that are
  618. 28:02meenal
  619. 28:03um meenal derived. um there are the the
  620. 28:08anterior part so the anterior plates
  621. 28:12are are are neural crest derived and
  622. 28:16have
  623. 28:17um so I didn't I didn't kind of go into
  624. 28:21this actually here
  625. 28:23um
  626. 28:26yeah so so it's a great question so
  627. 28:28basically these parts are are neural
  628. 28:30crest derived and these parts are mezenl
  629. 28:33derived and the neural crest test
  630. 28:35derived
  631. 28:36um
  632. 28:38do have a kind of um
  633. 28:42scar or like remnants of transcription
  634. 28:45factors that give us the clue that
  635. 28:46they're neuro crest arrived in um
  636. 28:51and and and
  637. 28:52the um the dissection also
  638. 28:57um kind of has a you know there the
  639. 29:00dissection is is um is kind of
  640. 29:04platebased and we can also um trace that
  641. 29:08basically from the spatial
  642. 29:09transcripttoics
  643. 29:12in terms of
  644. 29:15non-coding kind of regatory elements
  645. 29:19you know and epigenetics there should
  646. 29:21also be kind of a scar or like a a
  647. 29:24memory but I I can't remember exactly
  648. 29:27whether we dug into that but you know
  649. 29:29the I I should say that the data you
  650. 29:31know all of this data is publicly
  651. 29:32available for deeper
  652. 29:34or reanalysis,
  653. 29:36further analysis, reuse and so on so
  654. 29:38forth and um both on the human cell data
  655. 29:43portal and also from our own
  656. 29:44supplementary website.
  657. 29:50>> Yeah, that's thanks so much. Looks
  658. 29:52[clears throat] like there is another
  659. 29:52question in the Q&A.
  660. 29:56Um
  661. 29:57>> okay, let's see. Um sorry,
  662. 30:01>> two more questions now. Yeah, two more
  663. 30:03questions. You suggested that the embryo
  664. 30:06marks adult disease. How did you uh in
  665. 30:10amber lease mark being activated in the
  666. 30:13adult?
  667. 30:17Yeah. So, so the way I'm thinking about
  668. 30:19this and and this is kind of, you know,
  669. 30:22I sort of welcome critical feedback and
  670. 30:25input and kind of conversation around
  671. 30:27this, but the way I think about this is
  672. 30:29that, you know, our DNA is kind of the
  673. 30:31blueprint
  674. 30:32um of of ourselves. And remember, a lot
  675. 30:35of these variants that are risk factors
  676. 30:37for adult onset diseases are in
  677. 30:39non-coding regions. And so that that
  678. 30:42molecular variant [snorts] that you know
  679. 30:45is different in different people is
  680. 30:47going to have you know a mechanistic
  681. 30:50impact on transcription factor binding
  682. 30:52affinity on gene expression levels
  683. 30:55whether it's in [snorts] you know
  684. 30:57whether it's it's it's active I'll say
  685. 31:00in in development in in a certain
  686. 31:03context and certain cell compartment
  687. 31:07equally as in adult if it becomes comes
  688. 31:11sort [snorts] of unleashed if you like
  689. 31:12in disease
  690. 31:15and but the the specific
  691. 31:18like the the the the specific cell type
  692. 31:20or location in the body may not be
  693. 31:22identical.
  694. 31:25So
  695. 31:27my feeling is basically that that it's
  696. 31:29you know from a it's worth tracing the
  697. 31:33impact of these variants that we know
  698. 31:35from G-W was associations
  699. 31:38are risk factors for disease. It's worth
  700. 31:40understanding also how they are
  701. 31:42influencing you know or whether they're
  702. 31:45they're
  703. 31:47they're active
  704. 31:50in influencing subtle changes in in
  705. 31:52human development.
  706. 31:54So that that's how I think about it. And
  707. 31:56I don't know if that makes sense to
  708. 31:58everyone, but I'
  709. 32:00um [snorts] you know that's that's
  710. 32:02basically
  711. 32:04um why I think it's useful to actually
  712. 32:07do this this analysis.
  713. 32:14>> The second question is how about
  714. 32:16sinosis? Anything special with regards
  715. 32:19to the rest of the skull?
  716. 32:22>> Sinuses. Okay.
  717. 32:26Um,
  718. 32:28yeah, they cause a lot of pain kind of
  719. 32:30when you've got a an infection. Um,
  720. 32:35so I'm not sure when
  721. 32:39Yeah, I'm just going back to the the
  722. 32:42video. Um,
  723. 32:46so we didn't
  724. 32:49dissect the sinuses specifically. So we
  725. 32:51didn't sort of we didn't although you
  726. 32:54can see the the the regions that we that
  727. 32:57we focused on as I said were sort of
  728. 32:59skull cup skull base and then you know
  729. 33:01the knee
  730. 33:03um [snorts]
  731. 33:05um um the the shoulder the hip and the
  732. 33:07knee
  733. 33:10the dissections what what I should
  734. 33:12emphasize is that the surge the surgical
  735. 33:15trainee who did this can tow you know
  736. 33:18this is really like micro micro surgery
  737. 33:21and dissection or dissection.
  738. 33:25I think it would be super interesting to
  739. 33:27look at the different the you know the
  740. 33:29other the sort of oral cranial facial
  741. 33:33anatomical components
  742. 33:36um and and and maybe the way to tackle
  743. 33:39that is not by dissection but by you
  744. 33:42know getting the right sections for
  745. 33:44spatial transcrytoics
  746. 33:47and and sort of serial sectioning to
  747. 33:49kind of reconstruct in three dimensions.
  748. 33:52Um,
  749. 33:55so I think, you know, things like the
  750. 33:56sinuses, the inner ear,
  751. 33:59even the dental kind of development are
  752. 34:02super interesting, but we didn't we
  753. 34:04didn't tackle that part kind of in this
  754. 34:06study, but [snorts] it would be it would
  755. 34:08be a really interesting project for the
  756. 34:10future.
  757. 34:14>> Right, I think um that's pretty much all
  758. 34:17the questions we have for your talk and
  759. 34:18it's a lot of questions and thank you
  760. 34:20for answering. Um we are actually right
  761. 34:22on time. Thank you again um for both
  762. 34:24speakers for the wonderful presentations
  763. 34:26and also for everyone for participating.
  764. 34:29Yeah, with that we are going to end this
  765. 34:31um seminar.

About this transcript

This page contains the full transcript of Sarah Teichmann by Fragile Nucleosome, generated from the public captions YouTube serves with the video. The transcript has 4,686 words across 765 segments, with the original timestamps preserved so you can click any line to jump to that moment in the embedded player.

What you can do with it

Use the transcript to take notes, quote the speaker, build a study guide, generate a summary with ChatGPT or Claude via the YouTube Summary tool, or export it as a timed subtitle file with YouTube to SRT. You can also re-open it in the transcriber to translate the transcript into 100+ languages.

Free YouTube transcript tool

YouTube2Text is a free YouTube transcript generator — no signup, no daily limit. Paste any YouTube link and get the full transcript instantly, with timestamps, click-to-jump, translation to 100+ languages, AI prompts for ChatGPT, Claude, and Gemini, and exports to TXT, SRT, VTT, or Markdown.