Cell lines are key tools for preclinical cancer research, but it remains unclear how well they represent patient tumor samples. Direct comparisons of tumor and cell line trannoscriptional profiles are complicated by several factors, including the variable presence of normal cells in tumor samples. We thus develop an unsupervised alignment method (Celligner) and apply it to integrate several large-scale cell line and tumor RNA-Seq datasets. Although our method aligns the majority of cell lines with tumor samples of the same cancer type, it also reveals large differences in tumor similarity across cell lines. Using this approach, we identify several hundred cell lines from diverse lineages that present a more mesenchymal and undifferentiated trannoscriptional state and that exhibit distinct chemical and genetic dependencies. Celligner could be used to guide the selection of cell lines that more closely resemble patient tumors and improve the clinical translation of insights gained from cell lines.
https://www.nature.com/articles/s41467-020-20294-x
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https://www.nature.com/articles/s41467-020-20294-x
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Nature
Global computational alignment of tumor and cell line trannoscriptional profiles
Nature Communications - The determination of whether cancer cell lines recapitulate the molecular features of corresponding patient tumours remains essential for the selection of appropriate cell...
Vaginal Transmission of Cancer from Mothers with Cervical Cancer to Infants
Matthew Meyerson:
"Inheritance of cancer from mother to child during the birth process! Extraordinary findings from elegant genomic analysis by Takashi Kohno, Chitose Ogawa and colleagues.
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"
https://www.nejm.org/doi/full/10.1056/NEJMoa2030391
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Matthew Meyerson:
"Inheritance of cancer from mother to child during the birth process! Extraordinary findings from elegant genomic analysis by Takashi Kohno, Chitose Ogawa and colleagues.
Quote Tweet
"
https://www.nejm.org/doi/full/10.1056/NEJMoa2030391
🆔@BioUT
Method of the Year: spatially resolved trannoscriptomics 💣🧨💣🧨
Understanding the organization of cells and tissues and how this organization influences function is a fundamental pursuit in life sciences research. Over the years, technological advances have shed much light on these aspects of biology. Sequencing approaches have allowed us to learn about cell types and their heterogeneity in complex tissues, and methodological advances in microscopy, including super-resolution and single-molecule imaging, have transformed our understanding of cell and tissue structure and function. Our Method of the Year, spatially resolved trannoscriptomics, highlights how these technologies have matured and expanded to give biologists exceptional views of the biology of single cells while retaining information on spatial context.
https://www.nature.com/articles/s41592-020-01033-y
🆔@BioUT
Understanding the organization of cells and tissues and how this organization influences function is a fundamental pursuit in life sciences research. Over the years, technological advances have shed much light on these aspects of biology. Sequencing approaches have allowed us to learn about cell types and their heterogeneity in complex tissues, and methodological advances in microscopy, including super-resolution and single-molecule imaging, have transformed our understanding of cell and tissue structure and function. Our Method of the Year, spatially resolved trannoscriptomics, highlights how these technologies have matured and expanded to give biologists exceptional views of the biology of single cells while retaining information on spatial context.
https://www.nature.com/articles/s41592-020-01033-y
🆔@BioUT
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
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A systematic inventory of HNSCC-associated proteins, phosphosites, and pathways
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Three multi-omic subtypes linked to targeted treatment approaches and immunotherapy
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Widespread deletion of immune modulatory genes accounts for loss of immunogenicity
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Two modes of EGFR activation inform response to anti-EGFR monoclonal antibodies
https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30655-3?rss=yes&utm_source=dlvr.it&utm_medium=twitter
🆔@BioUT
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A systematic inventory of HNSCC-associated proteins, phosphosites, and pathways
•
Three multi-omic subtypes linked to targeted treatment approaches and immunotherapy
•
Widespread deletion of immune modulatory genes accounts for loss of immunogenicity
•
Two modes of EGFR activation inform response to anti-EGFR monoclonal antibodies
https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30655-3?rss=yes&utm_source=dlvr.it&utm_medium=twitter
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Summary
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors ...
🆔@BioUT
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors ...
🆔@BioUT
General Information About Chronic Myelogenous Leukemia
KEY POINTS
Chronic myelogenous leukemia is a disease in which the bone marrow makes too many white blood cells.
Leukemia may affect red blood cells, white blood cells, and platelets.
Signs and symptoms of chronic myelogenous leukemia include weight loss and tiredness.
Most people with CML have a gene mutation (change) called the Philadelphia chromosome.
Tests that examine the blood and bone marrow are used to diagnose chronic myelogenous leukemia.
Certain factors affect prognosis (chance of recovery) and treatment options.
Chronic myelogenous leukemia is a disease in which the bone marrow makes too many white blood cells.
Chronic myelogenous leukemia (also called CML or chronic granulocytic leukemia) is a slowly progressing blood and bone marrow disease that usually occurs during or after middle age, and rarely occurs in children.
https://www.cancer.gov/types/leukemia/patient/cml-treatment-pdq#_1
🆔@BioUT
KEY POINTS
Chronic myelogenous leukemia is a disease in which the bone marrow makes too many white blood cells.
Leukemia may affect red blood cells, white blood cells, and platelets.
Signs and symptoms of chronic myelogenous leukemia include weight loss and tiredness.
Most people with CML have a gene mutation (change) called the Philadelphia chromosome.
Tests that examine the blood and bone marrow are used to diagnose chronic myelogenous leukemia.
Certain factors affect prognosis (chance of recovery) and treatment options.
Chronic myelogenous leukemia is a disease in which the bone marrow makes too many white blood cells.
Chronic myelogenous leukemia (also called CML or chronic granulocytic leukemia) is a slowly progressing blood and bone marrow disease that usually occurs during or after middle age, and rarely occurs in children.
https://www.cancer.gov/types/leukemia/patient/cml-treatment-pdq#_1
🆔@BioUT
Anatomy of the bone. The bone is made up of compact bone, spongy bone, and bone marrow. Compact bone makes up the outer layer of the bone. Spongy bone is found mostly at the ends of bones and contains red marrow. Bone marrow is found in the center of most bones and has many blood vessels. There are two types of bone marrow: red and yellow. Red marrow contains blood stem cells that can become red blood cells, white blood cells, or platelets. Yellow marrow is made mostly of fat.
🆔@BioUT
🆔@BioUT
Leukemia may affect red blood cells, white blood cells, and platelets.
Normally, the bone marrow makes blood stem cells (immature cells) that become mature blood cells over time. A blood stem cell may become a myeloid stem cell or a lymphoid stem cell. A lymphoid stem cell becomes a white blood cell.
A myeloid stem cell becomes one of three types of mature blood cells:
Red blood cells that carry oxygen and other substances to all tissues of the body.
Platelets that form blood clots to stop bleeding.
Granulocytes (white blood cells) that fight infection and disease.
In CML, too many blood stem cells become a type of white blood cell called granulocytes. These granulocytes are abnormal and do not become healthy white blood cells. They are also called leukemia cells. The leukemia cells can build up in the blood and bone marrow so there is less room for healthy white blood cells, red blood cells, and platelets. When this happens, infection, anemia, or easy bleeding may occur.
🆔@BioUT
Normally, the bone marrow makes blood stem cells (immature cells) that become mature blood cells over time. A blood stem cell may become a myeloid stem cell or a lymphoid stem cell. A lymphoid stem cell becomes a white blood cell.
A myeloid stem cell becomes one of three types of mature blood cells:
Red blood cells that carry oxygen and other substances to all tissues of the body.
Platelets that form blood clots to stop bleeding.
Granulocytes (white blood cells) that fight infection and disease.
In CML, too many blood stem cells become a type of white blood cell called granulocytes. These granulocytes are abnormal and do not become healthy white blood cells. They are also called leukemia cells. The leukemia cells can build up in the blood and bone marrow so there is less room for healthy white blood cells, red blood cells, and platelets. When this happens, infection, anemia, or easy bleeding may occur.
🆔@BioUT
Complete blood count (CBC). Blood is collected by inserting a needle into a vein and allowing the blood to flow into a tube. The blood sample is sent to the laboratory and the red blood cells, white blood cells, and platelets are counted. The CBC is used to test for, diagnose, and monitor many different conditions.
🆔@BioUT
🆔@BioUT
Bone marrow aspiration and biopsy. After a small area of skin is numbed, a bone marrow needle is inserted into the patient’s hip bone. Samples of blood, bone, and bone marrow are removed for examination under a microscope.
🆔@BioUT
🆔@BioUT
Stem cell transplant. (Step 1): Blood is taken from a vein in the arm of the donor. The patient or another person may be the donor. The blood flows through a machine that removes the stem cells. Then the blood is returned to the donor through a vein in the other arm. (Step 2): The patient receives chemotherapy to kill blood-forming cells. The patient may receive radiation therapy (not shown). (Step 3): The patient receives stem cells through a catheter placed into a blood vessel in the chest.
🆔@BioUT
🆔@BioUT
Curious about the EBRAINS Collaboratory?
Learn more about our secure work environment for #researchers and developers in our #SfNConnectome21 session on Monday!
Rightwards arrow Register your interest here: https://humanbrainproject.eu/en/sfn-gc-2021/
🆔@BioUT
Learn more about our secure work environment for #researchers and developers in our #SfNConnectome21 session on Monday!
Rightwards arrow Register your interest here: https://humanbrainproject.eu/en/sfn-gc-2021/
🆔@BioUT
Send your answers to admin, 1st correct answer will get a gift, tomorrow night we will inform you about frequency of answers.
have fun 😊
🆔@BioUT
have fun 😊
🆔@BioUT
Send your answers to admin, 1st correct answer will get a gift, tomorrow night we will inform you about all answer frequencies of both tests.
have fun 😊
🆔@BioUT
have fun 😊
🆔@BioUT