Category Archives: Cell Biology

RNA Molecules Are Masters of Their Own Destiny Regulating Their Own Production Through a Feedback Loop – SciTechDaily

A collaboration between biologists and physicists suggests that RNA is a feedback regulator of its own production. Low concentrations of RNA lead to the formation of transcriptional condensates (represented here as bubbles), and high levels lead to the dissolution of those condensates. Credit: Jennifer Cook-Chrysos/Whitehead Institute

Research suggests the products of transcription RNA molecules regulate their own production through a feedback loop.

At any given moment in the human body, in about 30 trillion cells, DNA is being read into molecules of messenger RNA, the intermediary step between DNA and proteins, in a process called transcription.

Scientists have a pretty good idea of how transcription gets started: Proteins called RNA polymerases are recruited to specific regions of the DNA molecules and begin skimming their way down the strand, synthesizing mRNA molecules as they go. But part of this process is less-well understood: How does the cell know when to stop transcribing?

Now, new work from the labs of Richard Young, Whitehead Institute for Biomedical Research member and MIT professor of biology, and Arup K. Chakraborty, professor of chemical engineering, physics, and chemistry at MIT, suggests that RNA molecules themselves are responsible for regulating their formation through a feedback loop. Too few RNA molecules, and the cell initiates transcription to create more. Then, at a certain threshold, too many RNA molecules cause transcription to draw to a halt.

The research, published in Cell, represents a collaboration between biologists and physicists, and provides some insight into the potential roles of the thousands of RNAs that are not translated into any proteins, called noncoding RNAs, which are common in mammals and have mystified scientists for decades.

Researchers formed these droplets in the lab to investigate the role of RNA in their formation and dissolution. Credit: Jon Henninger

Previous work in Youngs lab has focused on transcriptional condensates, small cellular droplets that bring together the molecules needed to transcribe DNA to RNA. Scientists in the lab discovered the transcriptional droplets in 2018, noticing that they typically formed when transcription began and dissolved a few seconds or minutes later, when the process was finished.

The researchers wondered if the force that governed the dissolution of the transcriptional condensates could be related to the chemical properties of the RNA they produced specifically, its highly negative charge. If this were the case, it would be the latest example of cellular processes being regulated via a feedback mechanism an elegant, efficient system used in the cell to control biological functions such as red blood cell production and DNA repair.

As an initial test, the researchers used an in vitro experiment to test whether the amount of RNA had an effect on condensate formation. They found that within the range of physiological levels observed in cells, low levels of RNA encouraged droplet formation and high levels of RNA discouraged it.

With these results in mind, Young lab postdocs and co-first authors Ozgur Oksuz and Jon Henninger teamed up with physicist and co-first author Krishna Shrinivas, a graduate student in Arup Chakrabortys lab, to investigate what physical forces were at play.

Shrinivas proposed that the team build a computational model to study the physical and chemical interactions between actively transcribed RNA and condensates formed by transcriptional proteins. The goal of the model was not to simply reproduce existing results, but to create a platform with which to test a variety of situations.

The way most people study these kinds of problems is to take mixtures of molecules in a test tube, shake it and see what happens, Shrinivas says. That is as far away from what happens in a cell as one can imagine. Our thought was, Can we try to study this problem in its biological context, which is this out-of-equilibrium, complex process?

Studying the problem from a physics perspective allowed the researchers to take a step back from traditional biology methods. As a biologist, its difficult to come up with new hypotheses, new approaches to understanding how things work from available data, Henninger says. You can do screens, you can identify new players, new proteins, new RNAs that may be involved in a process, but youre still limited by our classical understanding of how all these things interact. Whereas when talking with a physicist, youre in this theoretical space extending beyond what the data can currently give you. Physicists love to think about how something would behave, given certain parameters.

Once the model was complete, the researchers could ask it questions about situations that may arise in cells for instance, what happens to condensates when RNAs of different lengths are produced at different rates as time ensues? and then follow it up with an experiment at the lab bench. We ended up with a very nice convergence of model and experiment, Henninger says. To me, its like the model helps distill the simplest features of this type of system, and then you can do more predictive experiments in cells to see if it fits that model.

Through a series of modeling and experiments at the lab bench, the researchers were able to confirm their hypothesis that the effect of RNA on transcription is due to RNAs molecules highly negative charge. Furthermore, it was predicted that initial low levels of RNA enhance and subsequent higher levels dissolve condensates formed by transcriptional proteins. Because the charge is carried by the RNAs phosphate backbone, the effective charge of a given RNA molecule is directly proportional to its length.

In order to test this finding in a living cell, the researchers engineered mouse embryonic stem cells to have glowing condensates, then treated them with a chemical to disrupt the elongation phase of transcription. Consistent with the models predictions, the resulting dearth of condensate-dissolving RNA molecules increased the size and lifetime of condensates in the cell. Conversely, when the researchers engineered cells to induce the production of extra RNAs, transcriptional condensates at these sites dissolved. These results highlight the importance of understanding how non-equilibrium feedback mechanisms regulate the functions of the biomolecular condensates present in cells, says Chakraborty.

Confirmation of this feedback mechanism might help answer a longstanding mystery of the mammalian genome: the purpose of non-coding RNAs, which make up a large portion of genetic material. While we know a lot about how proteins work, there are tens of thousands of noncoding RNA species, and we dont know the functions of most of these molecules, says Young. The finding that RNA molecules can regulate transcriptional condensates makes us wonder if many of the noncoding species just function locally to tune gene expression throughout the genome. Then this giant mystery of what all these RNAs do has a potential solution.

The researchers are optimistic that understanding this new role for RNA in the cell could inform therapies for a wide range of diseases. Some diseases are actually caused by increased or decreased expression of a single gene, says Oksuz, a co-first author. We now know that if you modulate the levels of RNA, you have a predictable effect on condensates. So you could hypothetically tune up or down the expression of a disease gene to restore the expression and possibly restore the phenotype that you want, in order to treat a disease.

Young adds that a deeper understanding of RNA behavior could inform therapeutics more generally. In the past 10 years, a variety of drugs have been developed that directly target RNA successfully. RNA is an important target, Young says. Understanding mechanistically how RNA molecules regulate gene expression bridges the gap between gene dysregulation in disease and new therapeutic approaches that target RNA.

Reference: RNA-Mediated Feedback Control of Transcriptional Condensates by Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Ido Sagi, Gary LeRoy, Ming M. Zheng, J. Owen Andrews, Alicia V. Zamudio, Charalampos Lazaris, Nancy M. Hannett, Tong Ihn Lee, Phillip A. Sharp, Ibrahim I. Ciss, Arup K. Chakraborty and Richard A. Young, 16 December 2020, Cell.DOI: 10.1016/j.cell.2020.11.030

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RNA Molecules Are Masters of Their Own Destiny Regulating Their Own Production Through a Feedback Loop - SciTechDaily

HistoIndex Explores the Clinical Utility of Stain-free AI Digital Pathology Platform in 388 Patients with Triple-Negative Breast Cancer (TNBC) – The…

Assessing Collagen Features at a Finer Level of Detail

In a collaborative study involving scientists from the Institute of Molecular and Cell Biology (IMCB) in Singapore and TNBC pathologists from the Singapore General Hospital (SGH), unstained biopsies from 388 TNBC patients were scanned using HistoIndex's AI-based SHG platform and analyzed to extract different collagen features from the SHG images at a finer level of detail. Findings published in the leading peer-reviewed oncology journal, Breast Cancer Research [3], showed a strong correlation between several imaging features and clinicopathological characteristics. Aggregation of collagen fibers, collagen fiber density and the length of dispersed thin collagen fibers were key collagen-associated parameters revealed to be of prognostic value based on the patient cohort and clinical outcomes. Furthermore, analyzing the aggregated thick collagen (ATC) fibers and dispersed thin collagen (DTC) fibers (as shown in Figure 1) provided a novel understanding of collagen remodeling during cancer progression.

Says Professor Tan Puay Hoon, Chairman, Division of Pathology, and Senior Consultant, Department of Anatomical Pathology, SGH, and lead pathologist of the study, "Critical biomarkers in TNBC are needed to stratify patients and predict clinical outcomes. Technological advances in pathology such as SHG assessment may improve the characterization of detailed and minute changes in important collagen features within the tumor stromal microenvironment such as the collagen structure, density and length. These are important parameters that could possibly enhance pathological assessment and allow for a clearer understanding of the relationship between collagen features and tumor progression."

Evaluating Therapeutic Efficacy with Key Collagen Parameters

The advantages of these novel collagen parameters make the platform a valuable asset in existing and future TNBC studies that are currently monitoring therapeutic responses in their exploration of targeted treatments. For instance, an ongoing collaboration between HistoIndex and a team at the Memorial Sloan Kettering Cancer Center (MSK), led by Professor Linda Vahdat, Chief of Medical Oncology and Clinical Director of Cancer Services at the MSK Physicians at Norwalk Hospital, is currently investigating influencing the tumor microenvironment with anti-copper therapy (copper depletion) for patients with breast cancer who are at a high risk of a relapse.

Copper encourages the growth of the blood vessels that feed dormant, and later active, cancer cells, and is also needed by certain cancer molecules to communicate with and influence the tumor microenvironment. Subsequently, this element is a necessary resource to build a collagen scaffolding that cancer cells populate as they become aggressive. Having spent many years examining copper depletion in TNBC studies, Prof. Vahdat has previously explained the role of copper in triggering metastasis, and how the collagen scaffolding that houses the tumor breaks down once copper is pulled out of the system [4].

Says Prof. Vahdat, "Collagen within the tumor microenvironment represents an under-explored predictor of treatment outcome. Preliminary data from our group suggests that we can normalize the collagen microenvironment with a copper depletion strategy rendering an inhospitable environment for metastases. With this collaboration with HistoIndex, we hope to be able to predict those primary tumors that are amenable to this treatment strategy."

About TNBC

The term Triple-Negative Breast Cancer refers to the fact that the cancer cells do not possess estrogen or progesterone receptors and also do not overexpress the protein called HER2. A patient is diagnosed with this form of breast cancer when the cells test "negative" for all three receptors. TNBC differs from other types of invasive breast cancer as they progress faster, have limited targeted treatments, and a generally bleak prognosis. According to the American Cancer Society, TNBC accounts for about 10-15% of all breast cancers and is more common in women younger than the age 40, who are African-American, or women who have a BRCA1 mutation [5].

References

SOURCE Histoindex Pte. Ltd.

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HistoIndex Explores the Clinical Utility of Stain-free AI Digital Pathology Platform in 388 Patients with Triple-Negative Breast Cancer (TNBC) - The...

Organoids give insight into the development of cervical cancer – BioNews

25 January 2021

Molecular changes that give rise to cervical cancer have been identified using novel 'organoid' models.

Published in Nature Cell Biology, researchers in Germany have developed an organoid model of the cervix, providing them with a unique way to study its normal biology and better understand why cancers develop.

'These fundamental findings form a basis for further understanding of the mechanisms involved in carcinogenesis at these metaplastic sites. To study how human papillomavirus (HPV), together with superseding bacterial infections, plays a key role in transforming cells to malignancy,' said Dr Cindrilla Chumduri from the Biocentre at the University of Wrzburg, who led the study.

Organoids are tiny 3D structures made of cells just a few millimetres in size that are artificially developed to closely resemble whole organs. They are increasingly used in medical research to allow scientists to study life processes and the effect of drugs.

Prior to this new study, it was known that the cervix has two regions covered by two different types of epithelial cells so called 'squamous epithelia' and 'columnar epithelia'. The boundaries between these two different cell types are called transition zones, and 90 perecent of cervical cancers originate at these sites. However, it was not known exactly how these two cell populations and their boundaries are ordinarily kept distinct in a healthy cervix, or why this is a hotspot for cancer development.

Using the organoid structures, the researchers discovered that instead of the two different epithelial cell types developing from the same stem cells, they are in fact derived from two discrete stem cell populations.

Complex interactions between these stem cells and their surrounding microenvironment were found to be important for keeping the two types of cells separate and for ensuring a healthy cervical architecture. This is achieved using the Wnt signaling pathway proteins known for their role in cellular differentiation, among other processes.

The researchers also showed that disrupting Wnt signalling can alter the homeostasis seen in the cervix, allowing one type of epithelium cell to replace the other an early event in cancer development termed metaplasia. Different types of cervical cancers can develop depending on which epithelial cell population is displaced.

It is hoped that this improved understanding of the fundamental biology of the cervix and the molecular changes seen in cervical metaplasia will help improve our understanding of how certain viral and bacterial infections principally HPV cause cervical cancer.

Dr Chumduri also added, 'these critical insights can help to develop diagnostics for the early detection of these two tumour forms and new therapeutic strategies'.

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Organoids give insight into the development of cervical cancer - BioNews

Assistant Professor in Stem Cell Biology or Regenerative Biology job with University of California, Irvine | 312638 – The Chronicle of Higher…

Assistant Professor in Stem Cell Biology or RegenerativeBiology

Applications are invited for a tenure-track faculty position at thelevel of Assistant Professor in the Department of Developmental andCell Biology. We seek candidates with an interest in stem cell orregeneration biology, broadly defined. Applicants should pursueresearch in the major areas of interest of the department,including, but not limited to developmental biology, stem celland/or niche biology, regeneration and cancer stem cells. Prioritywill be given to candidates whose research will benefit frominterdisciplinary collaborations, interactions with members of thedepartment (http://devcell.bio.uci.edu), andfrom affiliation with campus centers and institutes.

The successful applicant is expected to conduct a vibrant researchprogram, contribute to the teaching and service missions of theUniversity of California, and share our commitment to diversity,equity and inclusion. Please send a curriculum vitae, 3-pagesummary of research accomplishments and goals, 1-page statement ofteaching and mentoring experience and philosophy, 1-page statementhighlighting past and/or potential contributions to diversity,equity and inclusion, and at least three letters of reference viathe online recruitment URL: https://recruit.ap.uci.edu/apply/JPF06561. Evaluation criteria for the research, teaching, and diversitystatements are provided at the online recruitment URL. Applicationscompleted by March 7, 2021 will be granted full consideration. Anyquestions about the suitability of an applicant for thisopportunity can be directed to the search chair, Peter Donovanpdonovan@uci.edu.

The UCI School of Biological Sciences is recognized as a nationalleader in the development of programs designed to increase theparticipation of underrepresented groups in the biomedical sciencesand is firmly committed to the ideals of equity, diversity, andinclusion (https://port.bio.uci.edu/about/,https://equity.bio.uci.edu). UCIis an Hispanic-Serving Institution, an Asian American and NativeAmerican Pacific Islander Serving Institution, and a chartermember of the AAAS SEA Change initiative that supportsinstitutional efforts to increase access and success for students,faculty and staff from groups marginalized in STEMM (https://www.aaas.org/news/four-new-charter-members-join-sea-change).Programs are available to meet the needs of dual-career academicpartners. Faculty are eligible for subsidized housing and aMortgage Origination Program. UC Irvine (https://uci.edu) is located 10 minutes fromthe coast (https://www.youtube.com/watch?v=82ARz3B60pU),is consistently ranked among the nations top 10 publicuniversities, and has recently been designated the #1 universitydoing the most for the American dream. The city of Irvine is hometo excellent parks, schools, entertainment opportunities, and adiverse citizenry.

The University of California, Irvine is an EqualOpportunity/Affirmative Action Employer advancing inclusiveexcellence. All qualified applicants will receive consideration foremployment without regard to race, color, religion, sex, sexualorientation, gender identity, national origin, disability, age,protected veteran status, or other protectedcategories covered by the UC nondiscrimination policy. A recipientof an NSF ADVANCE award for gender equity, UCI is responsive to theneeds of dual career couples, supports work-life balance through anarray of family-friendly policies, and is dedicated to broadeningparticipation in higher education.

The University of California is committed to creating andmaintaining a community dedicated to the advancement, application,and transmission of knowledge and creative endeavors throughacademic excellence, where all individuals who participate inUniversity programs and activities can work and learn together in asafe and secure environment, free of violence, harassment,discrimination, exploitation, or intimidation. With thiscommitment, as well as a commitment to addressing all forms ofacademic misconduct, UC Irvine conducts institutional referencechecks for candidate finalists to whom the department or otherhiring unit would like to extend a formal offer of appointment intoLadder Rank Professor or Professor of Teaching series, at all ranks(i.e., assistant, associate, and full). The institutional referencechecks involve contacting the administration of the applicantsprevious institution(s) to ask whether there have beensubstantiated findings of misconduct that would violate theUniversitys Faculty Code of Conduct. To implement this process, UCIrvine requires all candidates of Ladder Rank Professor orProfessor of Teaching series, at all ranks (i.e., assistant,associate, and full) to complete, sign, and upload the formentitled Authorization to Release Information into AP RECRUIT aspart of their application. If the candidate does not include thesigned authorization to release information with the applicationmaterials, the application will be considered incomplete. As withany incomplete application, the application will not receivefurther consideration. Although all applicants for facultyrecruitments must complete the entire application, only finalists(i.e., those to whom the department or other hiring unit would liketo extend a formal offer) considered for Ladder Rank Professor orProfessor of Teaching series, at all ranks (i.e., assistant,associate, and full) positions will be subject to institutionalreference checks.

REQUIREMENTS Curriculum Vitae Cover Letter Three letters of Reference Statement of Research Three pages.1. One page describing the significance and impact of your graduateand postdoctoral research.2. Two pages providing a plan for your future independent researchprogram that indicates how your research program will synergizewith the research environment at UCI (see e.g., https://www.bio.uci.edu/centers-institutes) Statement of Teaching One page.1. Describe any experience teaching/lecturing toundergraduates/graduate students or other populations and mentoringothers.2. Explain your teaching philosophy and describe how you willengage in teaching strategies that are effective in diversepopulations. Statement of Contributions to Diversity(http://www.uci.edu/diversity) One page.1. Indicate how you have demonstrated awareness of the issues facedby historically underrepresented or economically disadvantagedgroups and the benefits of a diverse and inclusive faculty.2. Provide evidence (if any) of your track record and success inactivities aimed at reducing barriers in education or research forunderrepresented or disadvantaged groups.3. Detail your specific plans (if any) to contribute through campusprograms, new activities, or through national or off-campusorganizations.

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Assistant Professor in Stem Cell Biology or Regenerative Biology job with University of California, Irvine | 312638 - The Chronicle of Higher...

RNA ties itself in knots, then unties itself in mesmerizing video – Livescience.com

Striking new videos show how RNA the genetic molecule that tells cells how to build proteins tangles up in insane knots as it forms, only to disentangle itself at the last second, and in a way that took scientists by surprise.

The high-resolution videos depict a bouncing conga line of nucleotides, the building blocks of RNA; as the single strand of RNA grows longer, these nucleotides dance and twist into different three-dimensional shapes, wiggling first into one conformation and then another. Once fully assembled, the RNA assumes its final shape, which dictates how it can interact with other molecules and proteins in the cell.

But on the way, the RNA can get trapped in "knots" that must be undone for this final shape to emerge.

"So the RNA has to get out of it," said study author Julius Lucks, an associate professor of chemical and biological engineering and a member of the Center for Synthetic Biology at Northwestern University. The RNA won't function correctly if it remains trapped in the wrong knot, meaning a knot that gets in the way of its final shape, he said. "What was surprising is how it got out of that trap. This was only discovered when we had the high-resolution videos."

Related: Genetics by the numbers: 10 tantalizing tales

In the new study, published Jan. 15 in the journal Molecular Cell, Lucks and his colleagues generated their videos of RNA using experimental data and a computer algorithm. The goal was to zoom in on how RNA forms, both to better understand basic cell biology and to pave the way to better treatments for RNA-related diseases.

In the experiments, the team used a specific kind of RNA called signal recognition particle (SNP) RNA, an evolutionarily ancient molecule found across all kingdoms of life. They used this RNA as a model since it serves a fundamental function in many kinds of cells.

To zoom in on how cells build this RNA, the team used chemicals to pause the construction process. So as new nucleotides got added to the RNA, the researchers hit pause and then recorded how those nucleotides interacted with others already in the lineup, and what shapes they all formed together. By capturing the data from many individual RNA molecules, the team developed snapshots of how RNA generally builds itself through time.

These snapshots served as individual frames in what would become their final videos of RNA formation. That's where the computer model came in. The algorithm essentially strung together the individual frames into mini-movies and filled in the gaps between frames with the most likely nucleotide interactions. In these videos, the team noticed how the RNA got tangled into complex knots that, if left tied, would render the whole molecule useless.

"It folds into this trap state, and it kind of stays there," Lucks said. SNP RNA is meant to form in a signature "hairpin-like" shape, and these traps seem to get in the way. But as more nucleotides get added to the sequence, the new nucleotides swoop in to unravel the knot by displacing the nucleotides tangled up inside.

"That last little nucleotide is like a trigger" that allows the whole RNA to pop into the correct conformation, Lucks said. Think of the last fold in an origami project, which suddenly transforms a crinkly piece of paper into a lovely butterfly. In the videos, the nucleotides highlighted in dark purple knot themselves up, and the dark pink nucleotides help free them, Lucks noted.

Learning how RNA tangles and untangles is key to understanding how cells function and how proteins form; the research can also help address diseases where RNA doesn't function properly or a specific protein can't form, such as spinal muscular atrophy, and infectious diseases such as COVID-19 that are caused by RNA viruses, according to a statement.

A big question is whether RNA can mostly untangle itself from these knots, or whether it sometimes needs helper proteins to ease the process. It's possible that some proteins act as so-called "RNA chaperones" and help sculpt the molecule into its final form, Lucks said. He added that it may be a combination of both, although at this point, that's speculative.

Originally published on Live Science.

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RNA ties itself in knots, then unties itself in mesmerizing video - Livescience.com

HistoIndex Explores the Clinical Utility of Stain-free AI Digital Pathology Platform in 388 Patients with Triple-Negative Breast Cancer (TNBC) -…

TNBC is an incredibly challenging and aggressive form of breast cancer compared to other subtypes and holds a relatively poor prognosis primarily due to a lack of targeted treatments. In cancer, collagen fibers play a significant role in the tumor microenvironment, with remodeling of the extracellular matrix (ECM) that is often more collagen-rich with increased 'stiffness' [1]. As a component of the ECM, collagen may also influence cancer cell behavior[2]. Particularly in TNBC, collagen remodeling is seen in the stromal compartment [3].

Assessing Collagen Features at a Finer Level of Detail

In a collaborative study involving scientists from the Institute of Molecular and Cell Biology (IMCB) in Singapore and TNBC pathologists from the Singapore General Hospital (SGH), unstained biopsies from 388 TNBC patients were scanned using HistoIndex's AI-based SHG platform and analyzed to extract different collagen features from the SHG images at a finer level of detail. Findings published in the leading peer-reviewed oncology journal, Breast Cancer Research [3], showed a strong correlation between several imaging features and clinicopathological characteristics. Aggregation of collagen fibers, collagen fiber density and the length of dispersed thin collagen fibers were key collagen-associated parameters revealed to be of prognostic value based on the patient cohort and clinical outcomes. Furthermore, analyzing the aggregated thick collagen (ATC) fibers and dispersed thin collagen (DTC) fibers (as shown in Figure 1) provided a novel understanding of collagen remodeling during cancer progression.

Says Professor Tan Puay Hoon, Chairman, Division of Pathology, and Senior Consultant, Department of Anatomical Pathology, SGH, and lead pathologist of the study, "Critical biomarkers in TNBC are needed to stratify patients and predict clinical outcomes. Technological advances in pathology such as SHG assessment may improve the characterization of detailed and minute changes in important collagen features within the tumor stromal microenvironment such as the collagen structure, density and length. These are important parameters that could possibly enhance pathological assessment and allow for a clearer understanding of the relationship between collagen features and tumor progression."

Evaluating Therapeutic Efficacy with Key Collagen Parameters

The advantages of these novel collagen parameters make the platform a valuable asset in existing and future TNBC studies that are currently monitoring therapeutic responses in their exploration of targeted treatments. For instance, an ongoing collaboration between HistoIndex and a team at the Memorial Sloan Kettering Cancer Center (MSK), led by Professor Linda Vahdat, Chief of Medical Oncology and Clinical Director of Cancer Services at the MSK Physicians at Norwalk Hospital, is currently investigating influencing the tumor microenvironment with anti-copper therapy (copper depletion) for patients with breast cancer who are at a high risk of a relapse.

Copper encourages the growth of the blood vessels that feed dormant, and later active, cancer cells, and is also needed by certain cancer molecules to communicate with and influence the tumor microenvironment. Subsequently, this element is a necessary resource to build a collagen scaffolding that cancer cells populate as they become aggressive. Having spent many years examining copper depletion in TNBC studies, Prof. Vahdat has previously explained the role of copper in triggering metastasis, and how the collagen scaffolding that houses the tumor breaks down once copper is pulled out of the system [4].

Says Prof. Vahdat, "Collagen within the tumor microenvironment represents an under-explored predictor of treatment outcome. Preliminary data from our group suggests that we can normalize the collagen microenvironment with a copper depletion strategy rendering an inhospitable environment for metastases. With this collaboration with HistoIndex, we hope to be able to predict those primary tumors that are amenable to this treatment strategy."

About TNBC

The term Triple-Negative Breast Cancer refers to the fact that the cancer cells do not possess estrogen or progesterone receptors and also do not overexpress the protein called HER2. A patient is diagnosed with this form of breast cancer when the cells test "negative" for all three receptors. TNBC differs from other types of invasive breast cancer as they progress faster, have limited targeted treatments, and a generally bleak prognosis. According to the American Cancer Society, TNBC accounts for about 10-15% of all breast cancers and is more common in women younger than the age 40, who are African-American, or women who have a BRCA1 mutation [5].

References

SOURCE Histoindex Pte. Ltd.

Home

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HistoIndex Explores the Clinical Utility of Stain-free AI Digital Pathology Platform in 388 Patients with Triple-Negative Breast Cancer (TNBC) -...

Treating ‘fetus as the patient’ could reduce the incidence of pre-term labor and premature birth – News-Medical.Net

The results of a study by researchers at the University of Texas Medical Branch may pave the way for a new medicine delivery system that could reduce the incidence of pre-term labor and premature birth by allowing physicians to treat the 'fetus as the patient'. The study has been published in Science Advances.

It has long been suspected that pre-term labor is triggered by inflammation caused by a sick fetus. A new study by scientists at UTMB has proved the hypothesis by studying several important assumptions about the relationship between the health of a mother and her unborn child.

According to Dr. Ramkumar Menon, a Professor in UTMB's Department of Obstetrics and Gynecology and Cell Biology, his team worked with ILIAS Biologics, Inc., a South Korean biotechnology company, to test their bioengineered exosomes as a delivery system for anti-inflammatory medicine directly to the fetus.

Exosomes are natural nanoparticles or vesicles in our bodies, and we have trillions of them circulating through us at all times. By packaging the medicine inside a bioengineered exosome and injecting it into the mother intravenously, the exosomes travel through the blood system, cross the placental barrier and arrive in the fetus, where they deliver the medicine."

Dr. Ramkumar Menon, Professor, UTMB's Department of Obstetrics and Gynecology and Cell Biology

In laboratory tests with mice, there were several steps prior to testing the drug delivery. First, Menon said it was important to prove that fetal cells, specifically immune cells, actually migrated through the mother's body to her uterine tissues as well as to her, which can cause inflammation, the leading cause of pre-term labor.

To prove migration of cells, female mice were mated with male mice who had been genetically engineered with a red fluorescent dye called tdtomato. The dye causes cells in the male to turn red, so once mating has occurred, cells in the developing fetus also turn red and can easily be tracked as they migrate through the mother. This model was developed by Dr Sheller-Miller, a post-doctoral fellow in the Menon lab who is also the first author of this report. Development of this model that determined fetal immune cells reaching maternal tissues was also a turning point in this research.

Once scientists had proof of cell migration, they next used the mouse model to determine if bioengineered exosomes could deliver a special anti-inflammatory medicine, an inhibitor of NF-kB, called super repressor (SR) IkB from the mother's bloodstream to the fetus.

The exosomes were created using an innovative approach developed by ILIAS Biologics, Inc. called EXPLOR, or Exosomes engineering for Protein Loading via Optically Reversible protein to protein interaction. The study proved that the exosomes effectively delivered medicine to the fetus, slowed the migration of fetal immune cells, and delayed pre-term labor.

In addition, the study found that: * Sustained effects/delays in labor required repeated dosing * Prolongation of gestation improved pup viability * Mouse models provided valuable information to help understand the mechanisms often seen in humans * Future studies, including human clinical trials are needed to confirm laboratory results

"Pre-term birth rates have not reduced in the past few decades, and this technology (the bioengineered exosomes) could lead the way to other treatments for the delivery of drugs to treat the underlying cause of inflammation in a fetus," said Dr. Menon. This technology can also be used to package other drugs in exosomes to treat other adverse pregnancy complications.

This study result is the second proof of concept that suggests significant anti-inflammatory effects of the same exosomes from ILIAS Biologics. In April 2020, the researchers at Korea Advanced Institute of Science and Technology (KAIST) and the ILIAS team published the same exosomes' substantial efficacy in the septic mouse model in Science Advances.

Source:

Journal reference:

Sheller-Miller, S., et al. (2021) Exosomal delivery of NF-B inhibitor delays LPS-induced preterm birth and modulates fetal immune cell profile in mouse models. Science Advances. doi.org/10.1126/sciadv.abd3865.

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Treating 'fetus as the patient' could reduce the incidence of pre-term labor and premature birth - News-Medical.Net

Using CRISPR Genetic Technology to Catch Cancer in the Act – SciTechDaily

Phylogenetic trees, starting with an individual cancer cell. Each color represents a different location in the body. A very colorful tree shows a highly metastatic phenotype, where a cells descendants jumped many times between different tissues. A tree that is primarily one color represents a less metastatic cell. Credit: Jeffrey Quinn/Whitehead Institute

Using CRISPR technology, researchers are tracking the lineage of individual cancer cells as they proliferate and metastasize in real-time.

When cancer is confined to one spot in the body, doctors can often treat it with surgery or other therapies. Much of the mortality associated with cancer, however, is due to its tendency to metastasize, sending out seeds of itself that may take root throughout the body. The exact moment of metastasis is fleeting, lost in the millions of divisions that take place in a tumor. These events are typically impossible to monitor in real time, says Jonathan Weissman, MIT professor of biology and Whitehead Institute for Biomedical Research member.

Now, researchers led by Weissman, who is also an investigator with the Howard Hughes Medical Institute, have turned a CRISPR tool into a way to do just that. In a paper published on January 21, 2021, in Science, Weissmans lab, in collaboration with Nir Yosef, a computer scientist at the University of California at Berkeley, and Trever Bivona, a cancer biologist at the University of California at San Francisco, treats cancer cells the way evolutionary biologists might look at species, mapping out an intricately detailed family tree. By examining the branches, they can track the cells lineage to find when a single tumor cell went rogue, spreading its progeny to the rest of the body.

With this method, you can ask questions like, How frequently is this tumor metastasizing? Where did the metastases come from? Where do they go? Weissman says. By being able to follow the history of the tumor in vivo, you reveal differences in the biology of the tumor that were otherwise invisible.

Scientists have tracked the lineages of cancer cells in the past by comparing shared mutations and other variations in their DNA blueprints. These methods, however, depend to a certain extent on there being enough naturally occurring mutations or other markers to accurately show relationships between cells.

Thats where Weissman and co-first authors Jeffrey Quinn, then a postdoc in Weissmans lab, and Matthew Jones, a graduate student in Weissmans lab, saw an opportunity to use CRISPR technology specifically, a method developed by Weissman Lab member Michelle Chan to track embryo development to facilitate tracking.

Instead of simply hoping that a cancer lineage contained enough lineage-specific markers to track, the researchers decided to use Chans method to add in markers themselves. Basically, the idea is to engineer a cell that has a genomic scratchpad of DNA, that then can be written on using CRISPR, Weissman says. This writing in the genome is done in such a way that it becomes heritable, meaning a cells grand-offspring would have the writing of its parent cells and grandparent cells recorded in its genome.

To create these special scratchpad cells, Weissman engineered human cancer cells with added genes: one for the bacterial protein Cas9 the famed molecular scissors used in CRISPR genome editing methods others for glowing proteins for microscopy, and a few sequences that would serve as targets for the CRISPR technology.

They then implanted thousands of the modified human cancer cells into mice, mimicking a lung tumor (a model developed by collaborator Bivona). Mice with human lung tumors often exhibit aggressive metastases, so the researchers reasoned they would provide a good model for tracking cancer progression in real time.

As the cells began to divide, Cas9 made small cuts at these target sites. When the cell repaired the cuts, it patched in or deleted a few random nucleotides, leading to a unique repair sequence called an indel. This cutting and repairing happened randomly in nearly every generation, creating a map of cell divisions that Weissman and the team could then track using special computer models that they created by working with Yosef, a computer scientist.

Tracking cells this way yielded some interesting results. For one thing, individual tumor cells were much different from each other than the researchers expected. The cells the researchers used were from an established human lung cancer cell line called A549. Youd think they would be relatively homogeneous, Weissman says. But in fact, we saw dramatic differences in the propensity of different tumors to metastasize even in the same mouse. Some had a very small number of metastatic events, and others were really rapidly jumping around.

To find out where this heterogeneity was coming from, the team implanted two clones of the same cell in different mice. As the cells proliferated, the researchers found that their descendants metastasized at a remarkably similar rate. This was not the case with the offspring of different cells from the same cell line the original cells had apparently evolved different metastatic potentials as the cell line was maintained over many generations.

The scientists next wondered what genes were responsible for this variability between cancer cells from the same cell line. So they began to look for genes that were expressed differently between nonmetastatic, weakly metastatic, and highly metastatic tumors.

Many genes stood out, some of which were previously known to be associated with metastasis although it was not clear whether they were driving the metastasis or simply a side effect of it. One of them, the gene that codes for the protein Keratin 17, is much more strongly expressed in low metastatic tumors than in highly metastatic tumors. When we knocked down or overexpressed Keratin 17, we showed that this gene was actually controlling the tumors invasiveness, Weissman says.

Being able to identify metastasis-associated genes this way could help researchers answer questions about how tumors evolve and adapt. Its an entirely new way to look at the behavior and evolution of a tumor, Weissman says. We think it can be applied to many different problems in cancer biology.

Weissmans CRISPR method also allowed the researchers to track with more detail where metastasizing cells went in the body, and when. For example, the progeny of one implanted cancer cell underwent metastasis five separate times, spreading each time from the left lung to other tissues such as the right lung and liver. Other cells made a jump to a different area, and then metastasized again from there.

These movements can be mapped neatly in phylogenetic trees (see image), where each color represents a different location in the body. A very colorful tree shows a highly metastatic phenotype, where a cells descendants jumped many times between different tissues. A tree that is primarily one color represents a less metastatic cell.

Mapping tumor progression in this way allowed Weissman and his team to make a few interesting observations about the mechanics of metastasis. For example, some clones seeded in a textbook way, traveling from the left lung, where they started, to distinct areas of the body. Others seeded more erratically, moving first to other tissues before metastasizing again from there.

One such tissue, the mediastinal lymph tissue that sits between the lungs, appears to be a hub of sorts, says co-first author Jeffrey Quinn. It serves as a way station that connects the cancer cells to all of this fertile ground that they can then go and colonize, he says.

Therapeutically, the discovery of metastasis hubs like this could be extremely useful. If you focus cancer therapies on those places, you could then slow down metastasis or prevent it in the first place, Weissman says.

In the future, Weissman hopes to move beyond simply observing the cells and begin to predict their behavior. Its like with Newtonian mechanics if you know the velocity and position and all the forces acting on a ball, you can figure out where the ball is going to go at any time in the future, Weissman says. Were hoping to do the same thing with cells. We want to construct essentially a function of what is driving differentiation of a tumor, and then be able to measure where they are at any given time, and predict where theyre going to be in the future.

The researchers are optimistic that being able to track the family trees of individual cells in real time will prove useful in other settings as well. I think that its going to unlock a whole new dimension to what we think about as a measurable quantity in biology, says co-first author Matthew Jones. Thats whats really cool about this field in general is that were redefining whats invisible and what is visible.

Reference: Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts by Jeffrey J. Quinn, Matthew G. Jones, Ross A. Okimoto, Shigeki Nanjo, Michelle M. Chan, Nir Yosef, Trever G. Bivona and Jonathan S. Weissman, 21 January 2021, Science.DOI: 10.1126/science.abc1944

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Using CRISPR Genetic Technology to Catch Cancer in the Act - SciTechDaily

OHIO professors advance international astronaut and space biology research – Ohio University

Ohio University faculty are part of a team of researchers who have published a special compilation of papers that is being described as the largest set of astronaut and space biology data ever produced.

Nathaniel Szewczyk, Ph.D., professor of molecular medicine at the Heritage College of Osteopathic Medicine, and Sarah Wyatt, Ph.D., professor of environmental and plant biology in the College of Arts and Sciences, coauthored six of 29 papers recently published by NASA in a special compilation of Cell Press journal articles called The biology of spaceflight. The OHIO researchers are among more than 200 investigators from dozens of academic, government, aerospace and industry groups to contribute to the articles.

The effort brought together a unique collaboration across the four largest space agencies in the world NASA, JAXA, ESA and ROSCOSMOS with research spanning longitudinal multi-omic profiling, single-cell immune and epitope mapping, novel radiation countermeasures and detailed biochemical profiles of 56 astronauts.

Szewczyk, who also holds the Heritage Endowed Professorship in Molecular Medicine, Osteopathic Heritage Foundation Ralph S. Licklider, D.O., Research Endowment, coauthored the papers, Comparative transcriptomics identifies neuronal and metabolic adaptations to hypergravity and microgravity in Caenorhabditis elegans; A New Era for Space Life Science: International Standards for Space Omics Processing (ISSOP); and Revamping Space-omics in Europe. He and Wyatt coauthored the paper, NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data.

Some of the groundbreaking work reported in these papers used NASAs GeneLab, a repository for all genomics data related to space flight and gravity. The GeneLab is intended to be used by scientists to generate novel discoveries and develop new hypotheses for determining systemic biological responses occurring in spaceflight. Space biologists around the world rely on these omics data to maximize the knowledge gained from spaceflight experiments.

The GeneLab was set up to analyze large data sets of molecules that change in response to space flight, and continues to collect existing data from the past, as well as generates new data from ongoing flights, Szewczyk explained. There is a push to look at whether we can use such data sets to better understand astronaut health and to see what lessons can be learned in similar experiments.

Wyatt learned about the GeneLab after working on her first space flight experiment in 2015 and decided to use her OHIO Faculty Fellowship Leave to work with NASA developing the GeneLab more and helping establish it as a place for accessible data.

Sarah was truly invaluable in setting up GeneLabs agenda, said Sigrid Reinsch, Ph.D., principal investigator and research scientist at NASA-Ames Research Center.

Members of NASA GeneLab and GeneLab-associated analysis working groups have also developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline is all publicly available through the GeneLab database.

The GeneLabs pipeline is a fantastic opportunity for scientists and anyone interested in the data to have easy access to the results and to use this information to compare experiments, Wyatt said. When we looked at the data sets from previous experiments, we knew we needed to integrate and expand them so others could utilize this data. Im excited to see NASA take this on and publish the details and rationale for the construction of this pipeline, as well as to see a former Ph.D. student of mine, Colin Kruse, as an author on this paper.

Kruse graduated with a Ph.D. from OHIOs interdisciplinary graduate program in molecular and cellular biology in 2019, a program which Wyatt also directs. He is currently a post-doc at Los Alamos National Laboratory in New Mexico.

Most of Wyatts research includes her work with gravitational biology and how plants respond to gravity. She has conducted experiments, while at OHIO, sending plants into space to see how genes are regulated in response to spaceflight and will do so again on a flight mission slated for May.

Szewczyk also has a spaceflight experiment slated to launch on the same mission as Wyatts, making it the first time two OHIO professors will have experiments launching on the same mission.

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OHIO professors advance international astronaut and space biology research - Ohio University

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts – Science

1Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.

2Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.

4Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.

5Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA.

6Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.

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Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts - Science