Lecture 7 Flashcards
chromosomes are organized in…. in the nucleus
territories
chromosomal territory (CT), active
genes expand in which region ….
in the inter-chromatin (IC) region
CT contains different domains for …….
arms, and the centromere
CT contains different domains for p and q
arms, and the centromere
true or false: ct have variable chromatin densities
true
Early-replicating chromatin (green) late
replicating chromatin (red) are located ……
located toward the center or the periphery of the CT
The CT–IC model predicts that the IC (green)
contains …….
complexes (orange) and larger non-
chromatin domains (aggregations of orange) for transcription, splicing, DNA replication and repair
CT chromatin domains (red) and IC (green)
expanding between these domains: top and bottom
Top: active
genes are located at the surface of these
domains, whereas silenced genes (black) are
located in the interior. Bottom: alternatively,
closed ∼100-kb chromatin domains with
silenced genes are transformed into an open
configuration before transcriptional activation
Gene-poor, mid-to-late-replicating chromatin is enriched ……
in nuclear compartments that are located at the nuclear periphery and at the perinucleolar region.
A compartment for gene-dense, early-replicating chromatin is separated from the compartments for ……
mid-to-late-replicating
chromatin
interchromatin compartment (IC) contains various types of non-chromatin domains with factors for….
transcription, splicing, DNA
replication and repair
The transcriptional status of genes correlates ….
with gene positioning in CTs
what is condensin 1 importnat for
anaphase mostly
what is condensin 2 important for
prophase, metaphase, anaphase
what is cohesin important for
g2
what is ki-67 important for
METAOHASE and anaphase
what is baf important for
g2 and telophase
wgat does wee1 do
it speeds up dna rep
what does cdc25 do
it acts as an accelerator
what does sac do
it is for proper chromosome alignment
explain sac activation H
shwhwh
EXPLAIN SAC INACTIVATION
hhjjhsjh
what is mcc
mitotic checkpoint complex
what does sac mean
spindle assembly checkpoint
what did hansemann do
examined dividing cancer cells under the
microscope, and observed the presence of bizarre chromosomal aberrations
what did boveri suggest
uggested that aberrant mitoses led to the
unequal distribution of chromosomes, which, in most cases, would be detrimental
who suggested that tumours might arise because of abnormal segregation of chromosomes to daughter cells and when
boveri in 1914
1914: The Origin of Malignant Tumours
He postulated that tumour growth is based on ‘…a particular, incorrect chromosome combination which is the cause of the abnormal growth characteristics passed on
to daughter cells.
what is leukemia due
The Philadelphia chromosome (the minute, defective chromosome 22
indicated by the right arrow) results from reciprocal translocation
between chromosomes 9 and 22
what did rowley do
A new consistent chromosomal abnormality in chronic myelogenous leukemia identified by quinacrine fluorescence and Giemsa staining. Nature. 1973;243:290–293. This is a
pivotal paper describing the identification of the recurren
what was on chromosome 9 and 22
abl1 and bcr respectivelly
A cubic millimeter of blood from a healthy person contains about ……. WBC, thesame volume of blood from a person with CML contains 40,000 to 250,000 times that amount
4,000 to 10,000
chronic phase leukemia
-5-6 years
-expansion of myeloid compartment
-10-15%
-asymptomati c
accelerated phase leukemia
-6-9 months
-new cytogenetic abnormalities
-15-30%
-increased tiredness
weight loss
eblarged slpeen
blast crisis leukemia
-3-6 months
-increased genomic instatibility
-increased blast cells in bone marrow, extramedullary disease
is imatinib a slay
yaeh it isss`
why is imatinib a slay
- No patient who had a complete cytogenetic response and a reduction in levels of BCR-ABL transcripts of at least 3
log at 12 or 18 months after starting imatinib had progression of CML by 60 months. - Only 2% of patients who had a complete cytogenetic response and a reduction in levels of BCR-ABL transcripts of
less than 3 log at 18 months had progressed to the accelerated phase or blast crisis at 60 months
why us imatinib a skay ish now
resistance
-At the time of resistance to imatinib, a proportion of patients ranging from 30% to 70%—depending on disease phase—are found to carry mutations in the BCR-ABL1
kinase domain.
Chromosomal rearrangements
that disrupt transcription factor
genes can result …….
in fusion
proteins with enhanced or
aberrant transcriptional activity
or fusion proteins that mediate
transcriptional repression
ex: fli1-ewsr1 in ewings sarcoma and pml-rara in apl
Deregulated expression of genes that confer a selective growth advantage: examples
-myc in burkitts lymphoma and erg expression in prostate cancer
what are the 3 groups of leukemias and lymphomas
-Group 1: Fusion driven sarcomas. Sarcomas with near-diploid karyotypes and translocations that lead to gene fusions.
-Group 2:non- translocation-associated
sarcomas of intermediate genomic complexity
-Group 3: Sarcomas with sarcomas highly unbalanced karyotypes.
example of group 1
ewing sarcoma and synovial sarcoma
-example of grpup 2
-embryonal rhabdomyosarcoma and malignant peripheral nerve sheath sarcoma
example of group 3
-osteosarcoma and undifferenciated pleomorphic sarcoma
which group is tthe most mutation burden
GROUP 3
What are the 2 types of chromosomal abnormalities
-balanced chromosomal rearrangement
-chromosomal imbalances
types if balanced chromosomal rearrangement
-formation or chimeric fusion gene
-deregulated expression of structurally normal gene
what are the 2 types of chromosomal imbalances
-genomic gain
-genomic loss
what are the 2 types of chimeric fusion genes
-involving tyrosine kinases
-involving transcription factors
what does the myc expression in burkitts lymphoma
it affects b cells since they make immunoglobin
fusion driven sarcomas tend to arise how
-de novo
-in some cases, harbor a single defining cytogenic abnormality that is present at initiation and is retained throughput their clonal evolution
-this is called a driver event
the majority og gene fusions resu;ting from the translcons encode what
-chimeric transcriptional factors that cause the tranbscriptional dysregulation of target genes
true or false: fusions encode chimeric protein tyrosine kinases or autocrine growth factors
false; it is in rare cases
-the DNA binding domain of one transcription factor
is fused with …… leading to large changes in gene
expression of the target genes.
-b) The fusion gene creates a ……form of an RTK activating proliferation/survival pathways.
c) The fusion gene creates a ….. chromatin
regulator
d) The fusion gene enables an autocrine mechanism
that feeds the tumor through specific growth
factors
-the transactivation domain of another
transcription factor
-constitutively active
-chimeric
whayt is pax3
PAX3 is a member of the paired-box family of transcription factors. Directs various developmental processes and has distinct functions in the developing muscle
what is foxo1a
ubiquitously expressed member of the
forkhead family of transcription factors. Its normal function is regulated through phosphorylation by AKT
what is the pax3-foxo1a`
DNA-binding domain of
FOXO1 is lost, and therefore any DNA-binding specificity of the fusion gene is directed by the PAX3 sequences
-strong activating domain
true or false: pax3 is important for genomic expansion
true
what are transcription factors
are master regulators of cell identity and, on other hand, given a cell type it is possible to infer what signaling pathways and transcription factors are
active
In poorly differentiated sarcomas, such as
….. it is somewhat complex to
make hypothesis about the role of the
chimeric transcription factor and it is harder
to understand the molecular mechanism
that underlies transformation
Ewing’s sarcomas
Experimental approaches to assess the molecular mechanism of fusion mediated transformation in Ewing sarcoma
-overexpressionb if a fusion protein
-silencing a gene like ews-fli1
Silencing of EWS-FLi1 fusion in EWS cell lines followed by transcriptomic profiling and ChIP-seq of EWS-Fli1 fusion
EWS/FLI1 gene is turned off, the cells exhibit gene expression patterns that are most similar to mesenchymal progenitor cells. Despite being blocked in their ability to differentiate into fat and bone cells, Ewing sarcoma cells regain their potential to develop into various cell types when EWS/FLI1 expression is inhibited for an extended period
Overexpression of the fusion in human and mouse cells followed by expression profiling -> variable results depending on the cell type
-tolerant->Fibroblast, hMSC, NSC
-transformed->mMSC, NIH3T3
-A common observation in these studies was that
ectopic EWS/FLI1 imposed neuronal and endothelial
features of gene expression on non-Ewing sarcoma
cells
Well-differentiated and dedifferentiated liposarcomas, driven by chromosome 12 amplifications, often manifesting ……
manifesting as double minute
chromosomes and ring chromosomes
These 12q gains have high prevalence
(80–90%), and the co-amplified
oncogenes ……. can
serve as confirmatory diagnostic
markers
CDK4 and MDM2
sarcomas with complex karyotypes usually show… and complex cytogenetic changes that lack specificity
aneuploidy
what is the most common bone cancer
-osteosarcoma
-most common primary bone sarcoma
-20% of all bone tumor
-
what is osteosarcoma defined as
-is defined as a tumor forming an immature bone matrix called an osteoid
Approximately half of the osteosarcomas had a pattern of hypermutation associated with SVs, called……
kataegis
-The regions of the genome with kataegis were not recurrent, and
none of the most recurrently mutated genes were found in regions
of kataegis
Chromosomal lesions, rather than SNVs, were the major mechanism of recurrent mutations, and many of the most significant chromosomal lesions were found in known cancer genes, including …………..
TP53, RB1, and ATRX
The most common growth-factor pathways:
1) insulin-like growth factor 1 (IGF1)-receptor pathway in rhabdomyosarcomas and leiomyosarcomas
2) PDGFR pathway in desmoplastic round-cell tumours and osteosarcomas
3) c-KIT receptor pathway in Ewing’s sarcomas and GIST
4) c-MET-receptor pathway in synovial sarcomas and rhabdomyosarcomas.
The discovery of PIK3CA mutations in ……… of myxoid/round-cell
liposarcomas raised the possibility that secondary mutations may
cooperate with the FUS–CHOP fusion protein in oncogenesis
18%
Mutations in PIK3CA clustered in the same two ‘hot spots’ that are observed in ……….
epithelial tumours that do not harbor fusions
CML-> arises in …….
CD34 + cells where BCR and ABL are in closer proximity than PML and RAR A. PML and RAR A become closer in myeloid committed
precursors->promyelocytic leukemia
MYC fuses with……
MYC fuses with the immunoglobulin
heavy chain (IGH) locus or
immunoglobulin light chain (IGL) at high
frequencies and with the
immunoglobulin kappa (IGK) locus at a
low frequency. -> MYC is in closer
proximity with its frequent
translocation partners than with its rare
translocation partner IGK or a control
locus
Independently from the mechanism by which CINis induced, …..
it leads to karyotypic diversity withinthe cancer cell population, thereby adding to intratumor heterogeneity
In endometrial, gastric, and colorectal cancer, TP53- mutant tumors present more unstable and complex
karyotypes than……
TP53-proficient tumors.
Adaptations of the cellular physiology and homeostasis to attenuate the effects of CIN.
1) APC/C dysfunction allows segregation error correction and prevents excessive CIN.
2) aneuploid cells restrict the effects of chromosome imbalances on the proteome by activating autophagy-
related protein p62.
3) transition to near-triploid karyotypes enhances cancer cell fitness.
explain the lil karyotype lil drawing
fdafsffdfd
All connective tissues originate from embryonic ……., a tissue developing
mainly from the middle layer of the embryo, the mesoderm.
mesenchyme
whatr are Mesenchymal cells
are undifferentiated and have large
nuclei, with prominent nucleoli and
fine chromatin. They are often said
to be “spindle-shaped,” with their
scant cytoplasm extended as two or
more thin cytoplasmic processes
-embryonic mesenchyme includes stem cells for other tissues such as blood, the
vascular endothelium, and muscle.
Molecular profiling for detection of chromosomal translocations in sarcomas:
-identified new entities in tumors with identical features under the microscope (Ewing and CIC-DUX4 sarcomas)
reconciled clinical findings of different response to treatment regimens
Sometimes diagnosis of sarcomas is not clear-cut:
-sarcomas do not always adhere to their morphologic categories: some sarcomas
with usually spindle cell appearances may rarely show epithelioid morphology.
Unusual clinical presentations in terms of location and patient age or sex may
further contribute to challenges
groups of sarcomas
Chromosomal abnormalities in cancer diagnostic: sarcomas
* Two major groups: soft tissue and bone sarcomas
is sarcoma more common
Overall rare tumors but more frequent in children, adolescents and young adults
Heterogeneous types of sarcoma are divided based on what ….
based on the mesenchymal differentiation lineage tumor cells are most alike.
reunite entities that were previously thought to be distinct
(1)The tumor is often large and
fast-growing, but it rarely spreads
to other parts of the body.
congenital fibroblastoma
(2)is the most common renal
tumor identified in the neonatal
period: mesoblastic nephroma
Unlike most epithelial cells tumours, which are defined by the organ of origin,
sarcomas can be defined by their…..
molecular alterations
Patients with amplification of GLI
family transcription
factors will also be resistant ……
to targeted therapies such as SMO
antagonists (shh inhibitors)
copy number of chr14q and amplification of gli2 determines what
the outcome
true or false: often in sarcomas, the DNA binding domain of one transcription factor is duplicated
and the transactivation domain of another transcription factor is deleted leading to
a chimeric protein
false
