The Nobel Prize in Physiology or Medicine 1994

The Nobel Prize in Physiology or Medicine 1994 was awarded jointly to Alfred G. Gilman and Martin Rodbell "for their discovery of G-proteins and the role of these proteins in signal transduction in cells."

Nobelist	Born	Died	Affiliation at the time of the award
Alfred G. Gilman	1 July 1941, New Haven, CT, USA	23 December 2015, Dallas, TX, USA	University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
Martin Rodbell	1 December 1925, Baltimore, MD, USA	7 December 1998, Chapel Hill, NC, USA	National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

Summary
It has been known for some time that cells communicate with each other by means of hormones and other signal substances, which are released from glands, nerves and other tissues. It is only recently that we have begun to understand how the cell handles this information from the outside and converts it into relevant action – i.e. how signals are transduced in cells.

The discoveries of the G-proteins by the Americans Alfred G. Gilman and Martin Rodbell have been of paramount importance in this context, and have opened up a new and rapidly expanding area of knowledge.

G-proteins have been so named because they bind guanosine triphosphate (GTP). Gilman and Rodbell found that G-proteins act as signal transducers, which transmit and modulate signals in cells. G-proteins have the ability to activate different cellular amplifier systems. They receive multiple signals from the exterior, integrate them and thus control fundamental life processes in the cells.

Disturbances in the function of G-proteins – too much or too little of them, or genetically determined alterations in their composition – can lead to disease. The dramatic loss of salt and water in cholera is a direct consequence of the action of cholera toxin on G-proteins. Some hereditary endocrine disorders and tumours are other examples. Furthermore, some of the symptoms of common diseases such as diabetes or alcoholism may depend on altered transduction of signals through G-proteins.



More detailed information at The Nobel Prize in Physiology or Medicine 1994.

Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses

Content introduction:

• Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses


• Somatic APP gene recombination in Alzheimer’s disease and normal neurons


• Distinct activity-gated pathways mediate attraction and aversion to CO2 in Drosophila


• Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release


• TIC236 links the outer and inner membrane translocons of the chloroplast

1. Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses

Reward drives motivated behaviours and is essential for survival, and therefore there is strong evolutionary pressure to retain contextual information about rewarding stimuli. This drive may be abnormally strong, such as in addiction, or weak, such as in depression, in which anhedonia (loss of pleasure in response to rewarding stimuli) is a prominent symptom. Hippocampal input to the shell of the nucleus accumbens (NAc) is important for driving NAc activity and activity-dependent modulation of the strength of this input may contribute to the proper regulation of goal-directed behaviours. However, there have been few robust descriptions of the mechanisms that underlie the induction or expression of long-term potentiation (LTP) at these synapses, and there is, to our knowledge, no evidence about whether such plasticity contributes to reward-related behaviour. Here Tara A. LeGates at University of Maryland School of Medicine in Baltimore, USA and his colleagues show that high-frequency activity induces LTP at hippocampus–NAc synapses in mice via canonical, but dopamine-independent, mechanisms. The induction of LTP at this synapse in vivo drives conditioned place preference, and activity at this synapse is required for conditioned place preference in response to a natural reward. Conversely, chronic stress, which induces anhedonia, decreases the strength of this synapse and impairs LTP, whereas antidepressant treatment is accompanied by a reversal of these stress-induced changes. They conclude that hippocampus–NAc synapses show activity-dependent plasticity and suggest that their strength may be critical for contextual reward behaviour.



Read more, please click https://www.nature.com/articles/s41586-018-0740-8

2. Somatic APP gene recombination in Alzheimer’s disease and normal neurons

The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here Ming-Hsiang Lee at Sanford Burnham Prebys Medical Discovery Institute in La Jolla, USA and his colleagues describe recombination of the Alzheimer’s disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant ‘genomic cDNAs’ (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal ‘retro-insertion’ of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer’s disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer’s disease that were absent from healthy neurons. Neuronal gene recombination may allow ‘recording’ of neural activity for selective ‘playback’ of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.

Read more, please click https://www.nature.com/articles/s41586-018-0718-6

3. Distinct activity-gated pathways mediate attraction and aversion to CO2 in Drosophila

Carbon dioxide is produced by many organic processes and is a convenient volatile cue for insects that are searching for blood hosts, flowers, communal nests, fruit and wildfires. Although Drosophila melanogaster feed on yeast that produce CO2 and ethanol during fermentation, laboratory experiments suggest that walking flies avoid CO2. Here Floris van Breugel at California Institute of Technology in Pasadena, USA and his colleagues resolve this paradox by showing that both flying and walking Drosophila find CO2 attractive, but only when they are in an active state associated with foraging. Their aversion to CO2 at low-activity levels may be an adaptation to avoid parasites that seek CO2, or to avoid succumbing to respiratory acidosis in the presence of high concentrations of CO2 that exist in nature. In contrast to CO2, flies are attracted to ethanol in all behavioural states, and invest twice the time searching near ethanol compared to CO2. These behavioural differences reflect the fact that ethanol is a unique signature of yeast fermentation, whereas CO2 is generated by many natural processes. Using genetic tools, they determined that the evolutionarily conserved ionotropic co-receptor IR25a is required for CO2 attraction, and that the receptors necessary for CO2 avoidance are not involved in this attraction. Their study lays the foundation for future research to determine the neural circuits that underlie both state- and odorant-dependent decision-making in Drosophila.

Read more, please click https://www.nature.com/articles/s41586-018-0732-8

4. Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release

Development and routine tissue homeostasis require a high turnover of apoptotic cells. These cells are removed by professional and non-professional phagocytes via efferocytosis. How a phagocyte maintains its homeostasis while coordinating corpse uptake, processing ingested materials and secreting anti-inflammatory mediators is incompletely understood. Here, using RNA sequencing to characterize the transcriptional program of phagocytes actively engulfing apoptotic cells, Sho Morioka at University of Virginia in Charlottesville, USA and his colleagues identify a genetic signature involving 33 members of the solute carrier (SLC) family of membrane transport proteins, in which expression is specifically modulated during efferocytosis, but not during antibody-mediated phagocytosis. They assessed the functional relevance of these SLCs in efferocytic phagocytes and observed a robust induction of an aerobic glycolysis program, initiated by SLC2A1-mediated glucose uptake, with concurrent suppression of the oxidative phosphorylation program. The different steps of phagocytosis—that is, ‘smell’ (‘find-me’ signals or sensing factors released by apoptotic cells), ‘taste’ (phagocyte–apoptotic cell contact) and ‘ingestion’ (corpse internalization)—activated distinct and overlapping sets of genes, including several SLC genes, to promote glycolysis. SLC16A1 was upregulated after corpse uptake, increasing the release of lactate, a natural by-product of aerobic glycolysis. Whereas glycolysis within phagocytes contributed to actin polymerization and the continued uptake of corpses, lactate released via SLC16A1 promoted the establishment of an anti-inflammatory tissue environment. Collectively, these data reveal a SLC program that is activated during efferocytosis, identify a previously unknown reliance on aerobic glycolysis during apoptotic cell uptake and show that glycolytic by-products of efferocytosis can influence surrounding cells.

Read more, please click https://www.nature.com/articles/s41586-018-0735-5

5. TIC236 links the outer and inner membrane translocons of the chloroplast

The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries, but how TOC and TIC are assembled together is unknown. Here Yih-Lin Chen at Academia Sinica in Taipei, Taiwan and his colleagues report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC–TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that—unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation—a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB5 and outer-membrane BamA, respectively. Their evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB–BamA protein-secretion system.

Read more, please click https://www.nature.com/articles/s41586-018-0713-y

The Nobel Prize in Physiology or Medicine 1994

The Nobel Prize in Physiology or Medicine 1994 was awarded jointly to Alfred G. Gilman and Martin Rodbell "for their discovery of G-proteins and the role of these proteins in signal transduction in cells."

Nobelist	Born	Died	Affiliation at the time of the award
Alfred G. Gilman	1 July 1941, New Haven, CT, USA	23 December 2015, Dallas, TX, USA	University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
Martin Rodbell	1 December 1925, Baltimore, MD, USA	7 December 1998, Chapel Hill, NC, USA	National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

Summary
It has been known for some time that cells communicate with each other by means of hormones and other signal substances, which are released from glands, nerves and other tissues. It is only recently that we have begun to understand how the cell handles this information from the outside and converts it into relevant action – i.e. how signals are transduced in cells.

The discoveries of the G-proteins by the Americans Alfred G. Gilman and Martin Rodbell have been of paramount importance in this context, and have opened up a new and rapidly expanding area of knowledge.

G-proteins have been so named because they bind guanosine triphosphate (GTP). Gilman and Rodbell found that G-proteins act as signal transducers, which transmit and modulate signals in cells. G-proteins have the ability to activate different cellular amplifier systems. They receive multiple signals from the exterior, integrate them and thus control fundamental life processes in the cells.

Disturbances in the function of G-proteins – too much or too little of them, or genetically determined alterations in their composition – can lead to disease. The dramatic loss of salt and water in cholera is a direct consequence of the action of cholera toxin on G-proteins. Some hereditary endocrine disorders and tumours are other examples. Furthermore, some of the symptoms of common diseases such as diabetes or alcoholism may depend on altered transduction of signals through G-proteins.



More detailed information at The Nobel Prize in Physiology or Medicine 1994.

Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses

Content introduction:

• Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses


• Somatic APP gene recombination in Alzheimer’s disease and normal neurons


• Distinct activity-gated pathways mediate attraction and aversion to CO2 in Drosophila


• Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release


• TIC236 links the outer and inner membrane translocons of the chloroplast

1. Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses

Reward drives motivated behaviours and is essential for survival, and therefore there is strong evolutionary pressure to retain contextual information about rewarding stimuli. This drive may be abnormally strong, such as in addiction, or weak, such as in depression, in which anhedonia (loss of pleasure in response to rewarding stimuli) is a prominent symptom. Hippocampal input to the shell of the nucleus accumbens (NAc) is important for driving NAc activity and activity-dependent modulation of the strength of this input may contribute to the proper regulation of goal-directed behaviours. However, there have been few robust descriptions of the mechanisms that underlie the induction or expression of long-term potentiation (LTP) at these synapses, and there is, to our knowledge, no evidence about whether such plasticity contributes to reward-related behaviour. Here Tara A. LeGates at University of Maryland School of Medicine in Baltimore, USA and his colleagues show that high-frequency activity induces LTP at hippocampus–NAc synapses in mice via canonical, but dopamine-independent, mechanisms. The induction of LTP at this synapse in vivo drives conditioned place preference, and activity at this synapse is required for conditioned place preference in response to a natural reward. Conversely, chronic stress, which induces anhedonia, decreases the strength of this synapse and impairs LTP, whereas antidepressant treatment is accompanied by a reversal of these stress-induced changes. They conclude that hippocampus–NAc synapses show activity-dependent plasticity and suggest that their strength may be critical for contextual reward behaviour.



Read more, please click https://www.nature.com/articles/s41586-018-0740-8

2. Somatic APP gene recombination in Alzheimer’s disease and normal neurons

The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here Ming-Hsiang Lee at Sanford Burnham Prebys Medical Discovery Institute in La Jolla, USA and his colleagues describe recombination of the Alzheimer’s disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant ‘genomic cDNAs’ (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal ‘retro-insertion’ of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer’s disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer’s disease that were absent from healthy neurons. Neuronal gene recombination may allow ‘recording’ of neural activity for selective ‘playback’ of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.

Read more, please click https://www.nature.com/articles/s41586-018-0718-6

3. Distinct activity-gated pathways mediate attraction and aversion to CO2 in Drosophila

Carbon dioxide is produced by many organic processes and is a convenient volatile cue for insects that are searching for blood hosts, flowers, communal nests, fruit and wildfires. Although Drosophila melanogaster feed on yeast that produce CO2 and ethanol during fermentation, laboratory experiments suggest that walking flies avoid CO2. Here Floris van Breugel at California Institute of Technology in Pasadena, USA and his colleagues resolve this paradox by showing that both flying and walking Drosophila find CO2 attractive, but only when they are in an active state associated with foraging. Their aversion to CO2 at low-activity levels may be an adaptation to avoid parasites that seek CO2, or to avoid succumbing to respiratory acidosis in the presence of high concentrations of CO2 that exist in nature. In contrast to CO2, flies are attracted to ethanol in all behavioural states, and invest twice the time searching near ethanol compared to CO2. These behavioural differences reflect the fact that ethanol is a unique signature of yeast fermentation, whereas CO2 is generated by many natural processes. Using genetic tools, they determined that the evolutionarily conserved ionotropic co-receptor IR25a is required for CO2 attraction, and that the receptors necessary for CO2 avoidance are not involved in this attraction. Their study lays the foundation for future research to determine the neural circuits that underlie both state- and odorant-dependent decision-making in Drosophila.

Read more, please click https://www.nature.com/articles/s41586-018-0732-8

4. Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release

Development and routine tissue homeostasis require a high turnover of apoptotic cells. These cells are removed by professional and non-professional phagocytes via efferocytosis. How a phagocyte maintains its homeostasis while coordinating corpse uptake, processing ingested materials and secreting anti-inflammatory mediators is incompletely understood. Here, using RNA sequencing to characterize the transcriptional program of phagocytes actively engulfing apoptotic cells, Sho Morioka at University of Virginia in Charlottesville, USA and his colleagues identify a genetic signature involving 33 members of the solute carrier (SLC) family of membrane transport proteins, in which expression is specifically modulated during efferocytosis, but not during antibody-mediated phagocytosis. They assessed the functional relevance of these SLCs in efferocytic phagocytes and observed a robust induction of an aerobic glycolysis program, initiated by SLC2A1-mediated glucose uptake, with concurrent suppression of the oxidative phosphorylation program. The different steps of phagocytosis—that is, ‘smell’ (‘find-me’ signals or sensing factors released by apoptotic cells), ‘taste’ (phagocyte–apoptotic cell contact) and ‘ingestion’ (corpse internalization)—activated distinct and overlapping sets of genes, including several SLC genes, to promote glycolysis. SLC16A1 was upregulated after corpse uptake, increasing the release of lactate, a natural by-product of aerobic glycolysis. Whereas glycolysis within phagocytes contributed to actin polymerization and the continued uptake of corpses, lactate released via SLC16A1 promoted the establishment of an anti-inflammatory tissue environment. Collectively, these data reveal a SLC program that is activated during efferocytosis, identify a previously unknown reliance on aerobic glycolysis during apoptotic cell uptake and show that glycolytic by-products of efferocytosis can influence surrounding cells.

Read more, please click https://www.nature.com/articles/s41586-018-0735-5

5. TIC236 links the outer and inner membrane translocons of the chloroplast

The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries, but how TOC and TIC are assembled together is unknown. Here Yih-Lin Chen at Academia Sinica in Taipei, Taiwan and his colleagues report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC–TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that—unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation—a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB5 and outer-membrane BamA, respectively. Their evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB–BamA protein-secretion system.

Read more, please click https://www.nature.com/articles/s41586-018-0713-y

The Nobel Prize in Physiology or Medicine 1995

The Nobel Prize in Physiology or Medicine 1995 was awarded jointly to Edward B. Lewis, Christiane Nüsslein-Volhard and Eric F. Wieschaus "for their discoveries concerning the genetic control of early embryonic development."

Nobelist	Born	Died	Affiliation at the time of the award
Edward B. Lewis	20 May 1918, Wilkes-Barre, PA, USA	21 July 2004, Pasadena, CA, USA	California Institute of Technology (Caltech), Pasadena, CA, USA
Christiane Nüsslein-Volhard	20 October 1942, Magdeburg, Germany		Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Federal Republic of Germany
Eric F. Wieschaus	8 June 1947, South Bend, IN, USA		Princeton University, Princeton, NJ, USA

Summary

The 1995 laureates in physiology or medicine are developmental biologists who have discovered important genetic mechanisms which control early embryonic development. They have used the fruit fly, Drosophila melanogaster, as their experimental system. This organism is classical in genetics. The principles found in the fruit fly, apply also to higher organisms including man.

Using Drosophila Nüsslein-Volhard and Wieschaus were able to identify and classify a small number of genes that are of key importance in determining the body plan and the formation of body segments. Lewis investigated how genes could control the further development of individual body segments into specialized organs. He found that the genes were arranged in the same order on the chromosomes as the body segments they controlled. The first genes in a complex of developmental genes controlled the head region, genes in the middle controlled abdominal segments while the last genes controlled the posterior (“tail”) region. Together these three scientists have achieved a breakthrough that will help explain congenital malformations in man.

The fertilized egg is spherical. It divides rapidly to form 2, 4 , 8 cells and so on. Up until the 16-cell stage the early embryo is symmetrical and all cells are equal. Beyond this point, cells begin to specialize and the embryo becomes asymmetrical. Within a week it becomes clear what will form the head and tail regions and what will become the ventral and dorsal sides of the embryo. Somewhat later in development the body of the embryo forms segments and the position of the vertebral column is fixed. The individual segments undergo different development, depending on their position along the “head-tail” axis. Which genes control these events? How many are they? Do they cooperate or do they exert their controlling influence independently of each other?
This year’s laureates have answered several of these questions by identifying a series of important genes and how they function to control the formation of the body axis and body segments. They have also discovered genes that determine which organs that will form in individual segments. Although the fruit fly was used as an experimental system, the principles apply also to higher animals and man. Furthermore, genes analogous to those in the fruit fly have been found in man. An important conclusion is that basic genetic mechanisms controlling early development of multicellular organisms have been conserved during evolution for millions of years.



More detailed information at The Nobel Prize in Physiology or Medicine 1995.

The Nobel Prize in Physiology or Medicine 1995

The Nobel Prize in Physiology or Medicine 1995 was awarded jointly to Edward B. Lewis, Christiane Nüsslein-Volhard and Eric F. Wieschaus "for their discoveries concerning the genetic control of early embryonic development."

Nobelist	Born	Died	Affiliation at the time of the award
Edward B. Lewis	20 May 1918, Wilkes-Barre, PA, USA	21 July 2004, Pasadena, CA, USA	California Institute of Technology (Caltech), Pasadena, CA, USA
Christiane Nüsslein-Volhard	20 October 1942, Magdeburg, Germany		Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Federal Republic of Germany
Eric F. Wieschaus	8 June 1947, South Bend, IN, USA		Princeton University, Princeton, NJ, USA

Summary

The 1995 laureates in physiology or medicine are developmental biologists who have discovered important genetic mechanisms which control early embryonic development. They have used the fruit fly, Drosophila melanogaster, as their experimental system. This organism is classical in genetics. The principles found in the fruit fly, apply also to higher organisms including man.

Using Drosophila Nüsslein-Volhard and Wieschaus were able to identify and classify a small number of genes that are of key importance in determining the body plan and the formation of body segments. Lewis investigated how genes could control the further development of individual body segments into specialized organs. He found that the genes were arranged in the same order on the chromosomes as the body segments they controlled. The first genes in a complex of developmental genes controlled the head region, genes in the middle controlled abdominal segments while the last genes controlled the posterior (“tail”) region. Together these three scientists have achieved a breakthrough that will help explain congenital malformations in man.

The fertilized egg is spherical. It divides rapidly to form 2, 4 , 8 cells and so on. Up until the 16-cell stage the early embryo is symmetrical and all cells are equal. Beyond this point, cells begin to specialize and the embryo becomes asymmetrical. Within a week it becomes clear what will form the head and tail regions and what will become the ventral and dorsal sides of the embryo. Somewhat later in development the body of the embryo forms segments and the position of the vertebral column is fixed. The individual segments undergo different development, depending on their position along the “head-tail” axis. Which genes control these events? How many are they? Do they cooperate or do they exert their controlling influence independently of each other?
This year’s laureates have answered several of these questions by identifying a series of important genes and how they function to control the formation of the body axis and body segments. They have also discovered genes that determine which organs that will form in individual segments. Although the fruit fly was used as an experimental system, the principles apply also to higher animals and man. Furthermore, genes analogous to those in the fruit fly have been found in man. An important conclusion is that basic genetic mechanisms controlling early development of multicellular organisms have been conserved during evolution for millions of years.



More detailed information at The Nobel Prize in Physiology or Medicine 1995.

Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma

Content introduction:

• Two recombinant human monoclonal antibodies that protect against lethal Andes hantavirus infection in vivo


• Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis


• Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma


• IFN-γ–inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5


• The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

1. Two recombinant human monoclonal antibodies that protect against lethal Andes hantavirus infection in vivo

Andes hantavirus (ANDV) is an etiologic agent of hantavirus cardiopulmonary syndrome (HCPS), a severe disease characterized by fever, headache, and gastrointestinal symptoms that may progress to hypotension, pulmonary failure, and cardiac shock that results in a 25 to 40% case-fatality rate. Currently, there is no specific treatment or vaccine; however, several studies have shown that the generation of neutralizing antibody (Ab) responses strongly correlates with survival from HCPS in humans. In this study, Jose L. Garrido at Universidad de Concepción in Concepción, Chile and his colleagues screened 27 ANDV convalescent HCPS patient sera for their capacity to bind and neutralize ANDV in vitro. One patient who showed high neutralizing titer was selected to isolate ANDV–glycoprotein (GP) Abs. ANDV-GP–specific memory B cells were single cell sorted, and recombinant immunoglobulin G antibodies were cloned and produced. Two monoclonal Abs (mAbs), JL16 and MIB22, potently recognized ANDV-GPs and neutralized ANDV. They examined the post-exposure efficacy of these two mAbs as a monotherapy or in combination therapy in a Syrian hamster model of ANDV-induced HCPS, and both mAbs protected 100% of animals from a lethal challenge dose. These data suggest that monotherapy with mAb JL16 or MIB22, or a cocktail of both, could be an effective post-exposure treatment for patients infected with ANDV-induced HCPS.

Read more, please click http://stm.sciencemag.org/content/10/468/eaat6420

2. Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis

Fibrosis is the major determinant of morbidity and mortality in patients with nonalcoholic steatohepatitis (NASH) but has no approved pharmacotherapy in part because of incomplete understanding of its pathogenic mechanisms. Here, Changyu Zhu at Columbia University in New York, USA and his colleagues report that hepatocyte Notch activity tracks with disease severity and treatment response in patients with NASH and is similarly increased in a mouse model of diet-induced NASH and liver fibrosis. Hepatocyte-specific Notch loss-of-function mouse models showed attenuated NASH-associated liver fibrosis, demonstrating causality to obesity-induced liver pathology. Conversely, forced activation of hepatocyte Notch induced fibrosis in both chow- and NASH diet–fed mice by increasing Sox9-dependent Osteopontin (Opn) expression and secretion from hepatocytes, which activate resident hepatic stellate cells. In a cross-sectional study, they found that OPN explains the positive correlation between liver Notch activity and fibrosis stage in patients. Further, they developed a Notch inhibitor [Nicastrin antisense oligonucleotide (Ncst ASO)] that reduced fibrosis in NASH diet–fed mice. In summary, these studies demonstrate the pathological role and therapeutic accessibility of the maladaptive hepatocyte Notch response in NASH-associated liver fibrosis.

Read more, please click http://stm.sciencemag.org/content/10/468/eaat0344

3. Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma

Preclinical and clinical evidence indicates that a subset of asthma is driven by type 2 cytokines such as interleukin-4 (IL-4), IL-5, IL-9, and IL-13. Additional evidence predicts pathogenic roles for IL-6 and type I and type II interferons. Because each of these cytokines depends on Janus kinase 1 (JAK1) for signal transduction, and because many of the asthma-related effects of these cytokines manifest in the lung, Hart S. Dengler at Genentech in South San Francisco, USA and his colleagues hypothesized that lung-restricted JAK1 inhibition may confer therapeutic benefit. To test this idea, they synthesized iJak-381, an inhalable small molecule specifically designed for local JAK1 inhibition in the lung. In pharmacodynamic models, iJak-381 suppressed signal transducer and activator of transcription 6 activation by IL-13. Furthermore, iJak-381 suppressed ovalbumin-induced lung inflammation in both murine and guinea pig asthma models and improved allergen-induced airway hyperresponsiveness in mice. In a model driven by human allergens, iJak-381 had a more potent suppressive effect on neutrophil-driven inflammation compared to systemic corticosteroid administration. The inhibitor iJak-381 reduced lung pathology, without affecting systemic Jak1 activity in rodents. Their data show that local inhibition of Jak1 in the lung can suppress lung inflammation without systemic Jak inhibition in rodents, suggesting that this strategy might be effective for treating asthma.



Read more, please click http://stm.sciencemag.org/content/10/468/eaao2151

4. IFN-γ–inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5

It is well established that activation of the transcription factor signal transducer and activator of transcription 1 (STAT1) is required for the interferon-γ (IFN-γ)–mediated antiviral response. Here, Diana Saleiro at Northwestern University in Chicago, USA and her colleagues found that IFN-γ receptor stimulation also activated Unc-51–like kinase 1 (ULK1), an initiator of Beclin-1–mediated autophagy. Furthermore, the interaction between ULK1 and the mitogen-activated protein kinase kinase kinase MLK3 (mixed lineage kinase 3) was necessary for MLK3 phosphorylation and downstream activation of the kinase ERK5. This autophagy-independent activity of ULK1 promoted the transcription of key antiviral IFN-stimulated genes (ISGs) and was essential for IFN-γ–dependent antiviral effects. These findings define a previously unknown IFN-γ pathway that appears to be a key element of the antiviral response.

Read more, please click http://stke.sciencemag.org/content/11/557/eaap9921

5. The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with an unmet clinical need for decades. A single oncogenic fusion gene is associated with treatment resistance and a 40 to 45% decrease in overall survival. Narendra Bharathy at Children’s Cancer Therapy Development Institute in Beaverton, USA and his colleagues previously showed that expression of this PAX3:FOXO1 fusion oncogene in alveolar RMS (aRMS) mediates tolerance to chemotherapy and radiotherapy and that the class I–specific histone deacetylase (HDAC) inhibitor entinostat reduces PAX3:FOXO1 protein abundance. Here, they established the antitumor efficacy of entinostat with chemotherapy in various preclinical cell and mouse models and found that HDAC3 inhibition was the primary mechanism of entinostat-induced suppression of PAX3:FOXO1 abundance. HDAC3 inhibition by entinostat decreased the activity of the chromatin remodeling enzyme SMARCA4, which, in turn, derepressed the microRNA miR-27a. This reexpression of miR-27a led to PAX3:FOXO1 mRNA destabilization and chemotherapy sensitization in aRMS cells in culture and in vivo. Furthermore, a phase 1 clinical trial (ADVL1513) has shown that entinostat is tolerable in children with relapsed or refractory solid tumors and is planned for phase 1B cohort expansion or phase 2 clinical trials. Together, these results implicate an HDAC3–SMARCA4–miR-27a–PAX3:FOXO1 circuit as a driver of chemoresistant aRMS and suggest that targeting this pathway with entinostat may be therapeutically effective in patients.

Read more, please click http://stke.sciencemag.org/content/11/557/eaau7632

Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma

Content introduction:

• Two recombinant human monoclonal antibodies that protect against lethal Andes hantavirus infection in vivo


• Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis


• Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma


• IFN-γ–inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5


• The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

1. Two recombinant human monoclonal antibodies that protect against lethal Andes hantavirus infection in vivo

Andes hantavirus (ANDV) is an etiologic agent of hantavirus cardiopulmonary syndrome (HCPS), a severe disease characterized by fever, headache, and gastrointestinal symptoms that may progress to hypotension, pulmonary failure, and cardiac shock that results in a 25 to 40% case-fatality rate. Currently, there is no specific treatment or vaccine; however, several studies have shown that the generation of neutralizing antibody (Ab) responses strongly correlates with survival from HCPS in humans. In this study, Jose L. Garrido at Universidad de Concepción in Concepción, Chile and his colleagues screened 27 ANDV convalescent HCPS patient sera for their capacity to bind and neutralize ANDV in vitro. One patient who showed high neutralizing titer was selected to isolate ANDV–glycoprotein (GP) Abs. ANDV-GP–specific memory B cells were single cell sorted, and recombinant immunoglobulin G antibodies were cloned and produced. Two monoclonal Abs (mAbs), JL16 and MIB22, potently recognized ANDV-GPs and neutralized ANDV. They examined the post-exposure efficacy of these two mAbs as a monotherapy or in combination therapy in a Syrian hamster model of ANDV-induced HCPS, and both mAbs protected 100% of animals from a lethal challenge dose. These data suggest that monotherapy with mAb JL16 or MIB22, or a cocktail of both, could be an effective post-exposure treatment for patients infected with ANDV-induced HCPS.

Read more, please click http://stm.sciencemag.org/content/10/468/eaat6420

2. Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis

Fibrosis is the major determinant of morbidity and mortality in patients with nonalcoholic steatohepatitis (NASH) but has no approved pharmacotherapy in part because of incomplete understanding of its pathogenic mechanisms. Here, Changyu Zhu at Columbia University in New York, USA and his colleagues report that hepatocyte Notch activity tracks with disease severity and treatment response in patients with NASH and is similarly increased in a mouse model of diet-induced NASH and liver fibrosis. Hepatocyte-specific Notch loss-of-function mouse models showed attenuated NASH-associated liver fibrosis, demonstrating causality to obesity-induced liver pathology. Conversely, forced activation of hepatocyte Notch induced fibrosis in both chow- and NASH diet–fed mice by increasing Sox9-dependent Osteopontin (Opn) expression and secretion from hepatocytes, which activate resident hepatic stellate cells. In a cross-sectional study, they found that OPN explains the positive correlation between liver Notch activity and fibrosis stage in patients. Further, they developed a Notch inhibitor [Nicastrin antisense oligonucleotide (Ncst ASO)] that reduced fibrosis in NASH diet–fed mice. In summary, these studies demonstrate the pathological role and therapeutic accessibility of the maladaptive hepatocyte Notch response in NASH-associated liver fibrosis.

Read more, please click http://stm.sciencemag.org/content/10/468/eaat0344

3. Lung-restricted inhibition of Janus kinase 1 is effective in rodent models of asthma

Preclinical and clinical evidence indicates that a subset of asthma is driven by type 2 cytokines such as interleukin-4 (IL-4), IL-5, IL-9, and IL-13. Additional evidence predicts pathogenic roles for IL-6 and type I and type II interferons. Because each of these cytokines depends on Janus kinase 1 (JAK1) for signal transduction, and because many of the asthma-related effects of these cytokines manifest in the lung, Hart S. Dengler at Genentech in South San Francisco, USA and his colleagues hypothesized that lung-restricted JAK1 inhibition may confer therapeutic benefit. To test this idea, they synthesized iJak-381, an inhalable small molecule specifically designed for local JAK1 inhibition in the lung. In pharmacodynamic models, iJak-381 suppressed signal transducer and activator of transcription 6 activation by IL-13. Furthermore, iJak-381 suppressed ovalbumin-induced lung inflammation in both murine and guinea pig asthma models and improved allergen-induced airway hyperresponsiveness in mice. In a model driven by human allergens, iJak-381 had a more potent suppressive effect on neutrophil-driven inflammation compared to systemic corticosteroid administration. The inhibitor iJak-381 reduced lung pathology, without affecting systemic Jak1 activity in rodents. Their data show that local inhibition of Jak1 in the lung can suppress lung inflammation without systemic Jak inhibition in rodents, suggesting that this strategy might be effective for treating asthma.



Read more, please click http://stm.sciencemag.org/content/10/468/eaao2151

4. IFN-γ–inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5

It is well established that activation of the transcription factor signal transducer and activator of transcription 1 (STAT1) is required for the interferon-γ (IFN-γ)–mediated antiviral response. Here, Diana Saleiro at Northwestern University in Chicago, USA and her colleagues found that IFN-γ receptor stimulation also activated Unc-51–like kinase 1 (ULK1), an initiator of Beclin-1–mediated autophagy. Furthermore, the interaction between ULK1 and the mitogen-activated protein kinase kinase kinase MLK3 (mixed lineage kinase 3) was necessary for MLK3 phosphorylation and downstream activation of the kinase ERK5. This autophagy-independent activity of ULK1 promoted the transcription of key antiviral IFN-stimulated genes (ISGs) and was essential for IFN-γ–dependent antiviral effects. These findings define a previously unknown IFN-γ pathway that appears to be a key element of the antiviral response.

Read more, please click http://stke.sciencemag.org/content/11/557/eaap9921

5. The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with an unmet clinical need for decades. A single oncogenic fusion gene is associated with treatment resistance and a 40 to 45% decrease in overall survival. Narendra Bharathy at Children’s Cancer Therapy Development Institute in Beaverton, USA and his colleagues previously showed that expression of this PAX3:FOXO1 fusion oncogene in alveolar RMS (aRMS) mediates tolerance to chemotherapy and radiotherapy and that the class I–specific histone deacetylase (HDAC) inhibitor entinostat reduces PAX3:FOXO1 protein abundance. Here, they established the antitumor efficacy of entinostat with chemotherapy in various preclinical cell and mouse models and found that HDAC3 inhibition was the primary mechanism of entinostat-induced suppression of PAX3:FOXO1 abundance. HDAC3 inhibition by entinostat decreased the activity of the chromatin remodeling enzyme SMARCA4, which, in turn, derepressed the microRNA miR-27a. This reexpression of miR-27a led to PAX3:FOXO1 mRNA destabilization and chemotherapy sensitization in aRMS cells in culture and in vivo. Furthermore, a phase 1 clinical trial (ADVL1513) has shown that entinostat is tolerable in children with relapsed or refractory solid tumors and is planned for phase 1B cohort expansion or phase 2 clinical trials. Together, these results implicate an HDAC3–SMARCA4–miR-27a–PAX3:FOXO1 circuit as a driver of chemoresistant aRMS and suggest that targeting this pathway with entinostat may be therapeutically effective in patients.

Read more, please click http://stke.sciencemag.org/content/11/557/eaau7632

A new method to analyze cell membrane proteins in situ by using mass spectrometry

The cell membrane is a biological membrane that separates the interior of all cells from the outside environment which protects the cell from its environment consisting of a lipid bilayer with embedded proteins. The cell membrane controls the movement of substances in and out of cells and organelles. In this way, it is selectively permeable to ions and organic molecules. In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity and cell signalling and serve as the attachment surface for several extracellular structures, including the cell wall, the carbohydrate layer called the glycocalyx, and the intracellular network of protein fibers called the cytoskeleton.

Membranes protect all of our cells and the organelles inside them, including the mitochondria – the powerhouse of the cell. These membranes are studded with biological machinery made of proteins that enable molecular cargo to pass in and out.

Studying these membrane-embedded machines in their native state is crucial to understanding mechanisms of disease and providing new goals for treatments. However, current methods for studying them involve removing them from the membrane, which can compromise the integrity of membrane proteins and alter their structure and functional properties.

Recently, researchers have developed a new technique to analyse cell membrane proteins in situ which could revolutionise the way in which we study diseases, such as cancer, metabolic and heart diseases. In this work, they ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. This research will enable the development of mass spectrometry in biology to be taken to a new level, enabling new discoveries that would not have been possible before.

The technique could dramatically affect our understanding of both how cell membrane complexes work, and in the process, our approach to healthcare research.
From Escherichia coli outer membranes, scientists identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. They observed efflux pumps bridging inner and outer membranes, and from inner membranes they identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F1FO adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid–bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.

The technique involves vibrating the sample at ultrasonic frequencies so that the cell begins to fall apart. Electrical currents then applied an electric field to eject the protein machines out of the membrane and directly into a mass spectrometer – an instrument that can detect a molecule’s chemical ‘signature’, based on its mass.

Not only did the membrane protein machines survive the ejection; the analysis also revealed how they communicate with each other, are guided to their final location and transport their molecular cargo into the cell. With the development of this method, the application of mass spectrometry in biology will be taken to a new level, using it to make discoveries that would not have been possible before.

“A longstanding question on the structure of one membrane machine from mitochondria has now been solved using this technique.” said Dr Sarah Rouse, from the Department of Life Sciences at Imperial. The results are particularly exciting for mitochondrial membranes—we managed to catch a translocator in action—passing metabolites. Because mitochondrial therapeutics target a wide range of debilitating diseases, we now have a new way of assessing their effects.

Source:
http://www.ox.ac.uk/news/2018-11-16-new-way-look-cell-membranes-could-change-way-we-study-disease

Article:
Title: Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry
Authors: Dror S. Chorev, Lindsay A. Baker, Di Wu, Victoria Beilsten-Edmands, Sarah L. Rouse, Tzviya Zeev-Ben-Mordehai, Chimari Jiko, Firdaus Samsudin, Christoph Gerle, Syma Khalid, Alastair G. Stewart, Stephen J. Matthews, Kay Grünewald, Carol V. Robinson

A new method to analyze cell membrane proteins in situ by using mass spectrometry

The cell membrane is a biological membrane that separates the interior of all cells from the outside environment which protects the cell from its environment consisting of a lipid bilayer with embedded proteins. The cell membrane controls the movement of substances in and out of cells and organelles. In this way, it is selectively permeable to ions and organic molecules. In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity and cell signalling and serve as the attachment surface for several extracellular structures, including the cell wall, the carbohydrate layer called the glycocalyx, and the intracellular network of protein fibers called the cytoskeleton.

Membranes protect all of our cells and the organelles inside them, including the mitochondria – the powerhouse of the cell. These membranes are studded with biological machinery made of proteins that enable molecular cargo to pass in and out.

Studying these membrane-embedded machines in their native state is crucial to understanding mechanisms of disease and providing new goals for treatments. However, current methods for studying them involve removing them from the membrane, which can compromise the integrity of membrane proteins and alter their structure and functional properties.

Recently, researchers have developed a new technique to analyse cell membrane proteins in situ which could revolutionise the way in which we study diseases, such as cancer, metabolic and heart diseases. In this work, they ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. This research will enable the development of mass spectrometry in biology to be taken to a new level, enabling new discoveries that would not have been possible before.

The technique could dramatically affect our understanding of both how cell membrane complexes work, and in the process, our approach to healthcare research.
From Escherichia coli outer membranes, scientists identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. They observed efflux pumps bridging inner and outer membranes, and from inner membranes they identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F1FO adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid–bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.

The technique involves vibrating the sample at ultrasonic frequencies so that the cell begins to fall apart. Electrical currents then applied an electric field to eject the protein machines out of the membrane and directly into a mass spectrometer – an instrument that can detect a molecule’s chemical ‘signature’, based on its mass.

Not only did the membrane protein machines survive the ejection; the analysis also revealed how they communicate with each other, are guided to their final location and transport their molecular cargo into the cell. With the development of this method, the application of mass spectrometry in biology will be taken to a new level, using it to make discoveries that would not have been possible before.

“A longstanding question on the structure of one membrane machine from mitochondria has now been solved using this technique.” said Dr Sarah Rouse, from the Department of Life Sciences at Imperial. The results are particularly exciting for mitochondrial membranes—we managed to catch a translocator in action—passing metabolites. Because mitochondrial therapeutics target a wide range of debilitating diseases, we now have a new way of assessing their effects.

Source:
http://www.ox.ac.uk/news/2018-11-16-new-way-look-cell-membranes-could-change-way-we-study-disease

Article:
Title: Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry
Authors: Dror S. Chorev, Lindsay A. Baker, Di Wu, Victoria Beilsten-Edmands, Sarah L. Rouse, Tzviya Zeev-Ben-Mordehai, Chimari Jiko, Firdaus Samsudin, Christoph Gerle, Syma Khalid, Alastair G. Stewart, Stephen J. Matthews, Kay Grünewald, Carol V. Robinson

The Nobel Prize in Physiology or Medicine 1996

The Nobel Prize in Physiology or Medicine 1996 was awarded jointly to Peter C. Doherty and Rolf M. Zinkernagel "for their discoveries concerning the specificity of the cell mediated immune defence."

Nobelist	Born	Affiliation at the time of the award
Peter C. Doherty	15 October 1940, Brisbane, Australia	St. Jude Children's Research Hospital, Memphis, TN, USA
Rolf M. Zinkernagel	6 January 1944, Basel, Switzerland	University of Zurich, Institute of Experimental Immunology, Zurich, Switzerland

Summary

Peter Doherty and Rolf Zinkernagel have been awarded this year’s Nobel Prize in Physiology or Medicine for the discovery of how the immune system recognizes virus-infected cells. Their discovery has, in its turn, laid a foundation for an understanding of general mechanisms used by the cellular immune system to recognize both foreign microorganisms and self molecules. This discovery is therefore highly relevant to clinical medicine. It relates both to efforts to strengthen the immune response against invading microorganisms and certain forms of cancer, and to efforts to diminish the effects of autoimmune reactions in inflammatory diseases, such as rheumatic conditions, multiple sclerosis and diabetes.

The two Nobel Laureates carried out the research for which they have now been awarded the Prize in 1973-75 at the John Curtin School of Medical Research in Canberra, Australia, where Peter Doherty already held his position and to which Rolf Zinkernagel came from Switzerland as a research fellow. During their studies of the response of mice to viruses, they found that white blood cells (lymphocytes) must recognize both the virus and certain self molecules – the so-called major histocompatibility antigens – in order to kill the virus-infected cells. This principle of simultaneous recognition of both self and foreign molecules has since then constituted a foundation for the further understanding of the specificity of the cellular immune system.

The immune system consists of different kinds of white blood cells, including T- and B- lymphocytes whose common function is to protect the individual against infections by means of eliminating invading microorganisms and infected cells. At the same time they must avoid damaging the own organism. What is required is a well developed recognition system that enables lymphocytes to distinguish between on the one hand microorganisms and infected cells, and on the other, the individual´s normal cells. In addition, the recognition system must be able to determine when white blood cells with a capacity to kill should be activated.

In the early 1970s when Peter Doherty and Rolf Zinkernagel had begun their scientific work within immunology, it was possible to distinguish between antibody-mediated and cell- mediated immunity. It was known that antibodies that are produced by B-lymphocytes are able to recognize and eliminate certain microorganisms, particularly bacteria. Far less was known about recognition mechanisms in the cellular immune system, for instance in conjunction with the killing of virus-infected cells by T-lymphocytes. One area where cellular immunity had previously been studied in some detail was, however, transplantation biology. It was known that T-lymphocytes could kill cells from a foreign individual after recognition of certain molecules – the major histocompatibility antigens – in the transplant.



Please click https://www.nobelprize.org/prizes/medicine/1996/press-release/ for more detailed information.

The Nobel Prize in Physiology or Medicine 1996

The Nobel Prize in Physiology or Medicine 1996 was awarded jointly to Peter C. Doherty and Rolf M. Zinkernagel "for their discoveries concerning the specificity of the cell mediated immune defence."

Nobelist	Born	Affiliation at the time of the award
Peter C. Doherty	15 October 1940, Brisbane, Australia	St. Jude Children's Research Hospital, Memphis, TN, USA
Rolf M. Zinkernagel	6 January 1944, Basel, Switzerland	University of Zurich, Institute of Experimental Immunology, Zurich, Switzerland

Summary

Peter Doherty and Rolf Zinkernagel have been awarded this year’s Nobel Prize in Physiology or Medicine for the discovery of how the immune system recognizes virus-infected cells. Their discovery has, in its turn, laid a foundation for an understanding of general mechanisms used by the cellular immune system to recognize both foreign microorganisms and self molecules. This discovery is therefore highly relevant to clinical medicine. It relates both to efforts to strengthen the immune response against invading microorganisms and certain forms of cancer, and to efforts to diminish the effects of autoimmune reactions in inflammatory diseases, such as rheumatic conditions, multiple sclerosis and diabetes.

The two Nobel Laureates carried out the research for which they have now been awarded the Prize in 1973-75 at the John Curtin School of Medical Research in Canberra, Australia, where Peter Doherty already held his position and to which Rolf Zinkernagel came from Switzerland as a research fellow. During their studies of the response of mice to viruses, they found that white blood cells (lymphocytes) must recognize both the virus and certain self molecules – the so-called major histocompatibility antigens – in order to kill the virus-infected cells. This principle of simultaneous recognition of both self and foreign molecules has since then constituted a foundation for the further understanding of the specificity of the cellular immune system.

The immune system consists of different kinds of white blood cells, including T- and B- lymphocytes whose common function is to protect the individual against infections by means of eliminating invading microorganisms and infected cells. At the same time they must avoid damaging the own organism. What is required is a well developed recognition system that enables lymphocytes to distinguish between on the one hand microorganisms and infected cells, and on the other, the individual´s normal cells. In addition, the recognition system must be able to determine when white blood cells with a capacity to kill should be activated.

In the early 1970s when Peter Doherty and Rolf Zinkernagel had begun their scientific work within immunology, it was possible to distinguish between antibody-mediated and cell- mediated immunity. It was known that antibodies that are produced by B-lymphocytes are able to recognize and eliminate certain microorganisms, particularly bacteria. Far less was known about recognition mechanisms in the cellular immune system, for instance in conjunction with the killing of virus-infected cells by T-lymphocytes. One area where cellular immunity had previously been studied in some detail was, however, transplantation biology. It was known that T-lymphocytes could kill cells from a foreign individual after recognition of certain molecules – the major histocompatibility antigens – in the transplant.



Please click https://www.nobelprize.org/prizes/medicine/1996/press-release/ for more detailed information.

Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells

Content introduction:

• Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells


• Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence


• In Vitro Expansion of Primary Human Hepatocytes with Efficient Liver Repopulation Capacity


• A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening


• Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions

1. Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells

Innate immune factors may restrict hematopoietic stem cell (HSC) genetic engineering and contribute to broad individual variability in gene therapy outcomes. Here, Carolina Petrillo at IRCCS San Raffaele Scientific Institute in Milan, Italy and his colleagues show that HSCs harbor an early, constitutively active innate immune block to lentiviral transduction that can be efficiently overcome by cyclosporine H (CsH). CsH potently enhances gene transfer and editing in human long-term repopulating HSCs by inhibiting interferon-induced transmembrane protein 3 (IFITM3), which potently restricts VSV glycoprotein-mediated vector entry. Importantly, individual variability in endogenous IFITM3 levels correlated with permissiveness of HSCs to lentiviral transduction, suggesting that CsH treatment will be useful for improving ex vivo gene therapy and standardizing HSC transduction across patients. Overall, their work unravels the involvement of innate pathogen recognition molecules in immune blocks to gene correction in primary human HSCs and highlights how these roadblocks can be overcome to develop innovative cell and gene therapies.



Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30489-2

2. Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence

Critical features of stem cells include anchoring within a niche and activation upon injury. Notch signaling maintains skeletal muscle satellite (stem) cell quiescence by inhibiting differentiation and inducing expression of extracellular components of the niche. However, the complete spectrum of how Notch safeguards quiescence is not well understood. Here, Meryem B. Baghdadi at Institut Pasteur in Paris, France and his colleagues perform Notch ChIP-sequencing and small RNA sequencing in satellite cells and identify the Notch-induced microRNA-708, which is a mirtron that is highly expressed in quiescent cells and sharply downregulated in activated cells. They employ in vivo and ex vivo functional studies, in addition to live imaging, to show that miR-708 regulates quiescence and self-renewal by antagonizing cell migration through targeting the transcripts of the focal-adhesion-associated protein Tensin3. Therefore, this study identifies a Notch-miR708-Tensin3 axis and suggests that Notch signaling can regulate satellite cell quiescence and transition to the activation state through dynamic regulation of the migratory machinery.

Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30481-8

3. In Vitro Expansion of Primary Human Hepatocytes with Efficient Liver Repopulation Capacity

Transplantation of human hepatocytes (HHs) holds significant potential for treating liver diseases. However, the supply of transplantable HHs is severely constrained by limited donor availability and compromised capacity for in vitro expansion. In response to chronic injury, some HHs are reprogrammed into proliferative cells that express both hepatocyte and progenitor markers, suggesting exploitable strategies for expanding HHs in vitro. Here, Kun Zhang at Tongji University School of Medicine in Shanghai, China and his colleagues report defined medium conditions that allow 10,000-fold expansion of HHs. These proliferating HHs are bi-phenotypic, partially retaining hepatic features while gaining expression of progenitor-associated genes. Importantly, these cells engraft into injured mouse liver at a level comparable to primary HHs, and they undergo maturation following transplantation in vivo or differentiation in vitro. Thus, this study provides a protocol that enables large-scale expansion of transplantable HHs, which could be further developed for modeling and treating human liver disease.

Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30499-5

4. A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening

Gastric cancer displays marked molecular heterogeneity with aggressive behavior and treatment resistance. Therefore, good in vitro models that encompass unique subtypes are urgently needed for precision medicine development. Here, Helen H.N. Yan at The University of Hong Kong in Pokfulam, Hong Kong and his colleagues have established a primary gastric cancer organoid (GCO) biobank that comprises normal, dysplastic, cancer, and lymph node metastases (n = 63) from 34 patients, including detailed whole-exome and transcriptome analysis. The cohort encompasses most known molecular subtypes (including EBV, MSI, intestinal/CIN, and diffuse/GS, with CLDN18-ARHGAP6 or CTNND1-ARHGAP26 fusions or RHOA mutations), capturing regional heterogeneity and subclonal architecture, while their morphology, transcriptome, and genomic profiles remain closely similar to in vivo tumors, even after long-term culture. Large-scale drug screening revealed sensitivity to unexpected drugs that were recently approved or in clinical trials, including Napabucasin, Abemaciclib, and the ATR inhibitor VE-822. Overall, this new GCO biobank, with linked genomic data, provides a useful resource for studying both cancer cell biology and precision cancer therapy.

Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30480-6

5. Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions

Unisexual reproduction is widespread among lower vertebrates, but not in mammals. Deletion of the H19 imprinted region in immature oocytes produced bimaternal mice with defective growth; however, bipaternal reproduction has not been previously achieved in mammals. Zhi-Kun Li at Institute of Zoology, Chinese Academy of Sciences in Beijing, China and his colleagues found that cultured parthenogenetic and androgenetic haploid embryonic stem cells (haESCs) display DNA hypomethylation resembling that of primordial germ cells. Through MII oocyte injection or sperm coinjection with hypomethylated haploid ESCs carrying specific imprinted region deletions, they obtained live bimaternal and bipaternal mice. Deletion of 3 imprinted regions in parthenogenetic haploid ESCs restored normal growth of fertile bimaternal mice, whereas deletion of 7 imprinted regions in androgenetic haploid ESCs enabled production of live bipaternal mice that died shortly after birth. Phenotypic analyses of organ and body size of these mice support the genetic conflict theory of genomic imprinting. Taken together, their results highlight the factors necessary for crossing same-sex reproduction barriers in mammals.

Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30441-7

Abbkine Top Selling Products for Immunology

Abbkine focuses on Immunology and Cytology. Here, we present our top selling products in immunology research, from basic Immunology products such as Protein Extraction and Quantification kits to Tag Antibodies, Primary Antibodies and Secondary Antibodies, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Immunology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Abbkine Top Selling Products for Immunology

Abbkine focuses on Immunology and Cytology. Here, we present our top selling products in immunology research, from basic Immunology products such as Protein Extraction and Quantification kits to Tag Antibodies, Primary Antibodies and Secondary Antibodies, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Immunology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Abbkine Top Selling Products for Immunology

Abbkine focuses on Immunology and Cytology. Here, we present our top selling products in immunology research, from basic Immunology products such as Protein Extraction and Quantification kits to Tag Antibodies, Primary Antibodies and Secondary Antibodies, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Immunology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Abbkine Top Selling Products for Immunology

Abbkine focuses on Immunology and Cytology. Here, we present our top selling products in immunology research, from basic Immunology products such as Protein Extraction and Quantification kits to Tag Antibodies, Primary Antibodies and Secondary Antibodies, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Immunology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Abbkine Top Selling Products for Cytology

Abbkine focuses on Proteomics and Cytology. Here, we present our top selling products in cytology research, from dyes and kits for cell status detection, organelle extraction kits, cell substructure staining and cell metabolism detection products, to cytokine for cell culture and protein detection kits, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Cytology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Abbkine Top Selling Products for Cytology

Abbkine focuses on Proteomics and Cytology. Here, we present our top selling products in cytology research, from dyes and kits for cell status detection, organelle extraction kits, cell substructure staining and cell metabolism detection products, to cytokine for cell culture and protein detection kits, to help your research career.

[pdfjs-viewer url="https%3A%2F%2Fwww.abbkine.com%2Fwp-content%2Fuploads%2F2018%2F11%2FAbbkine-Top-Selling-Products-for-Cytology.pdf" viewer_width=100% viewer_height=1360px fullscreen=true download=true print=true]

Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells

Content introduction:

• Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells


• Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence


• In Vitro Expansion of Primary Human Hepatocytes with Efficient Liver Repopulation Capacity


• A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening


• Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions

1. Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells

Innate immune factors may restrict hematopoietic stem cell (HSC) genetic engineering and contribute to broad individual variability in gene therapy outcomes. Here, Carolina Petrillo at IRCCS San Raffaele Scientific Institute in Milan, Italy and his colleagues show that HSCs harbor an early, constitutively active innate immune block to lentiviral transduction that can be efficiently overcome by cyclosporine H (CsH). CsH potently enhances gene transfer and editing in human long-term repopulating HSCs by inhibiting interferon-induced transmembrane protein 3 (IFITM3), which potently restricts VSV glycoprotein-mediated vector entry. Importantly, individual variability in endogenous IFITM3 levels correlated with permissiveness of HSCs to lentiviral transduction, suggesting that CsH treatment will be useful for improving ex vivo gene therapy and standardizing HSC transduction across patients. Overall, their work unravels the involvement of innate pathogen recognition molecules in immune blocks to gene correction in primary human HSCs and highlights how these roadblocks can be overcome to develop innovative cell and gene therapies.



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2. Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence

Critical features of stem cells include anchoring within a niche and activation upon injury. Notch signaling maintains skeletal muscle satellite (stem) cell quiescence by inhibiting differentiation and inducing expression of extracellular components of the niche. However, the complete spectrum of how Notch safeguards quiescence is not well understood. Here, Meryem B. Baghdadi at Institut Pasteur in Paris, France and his colleagues perform Notch ChIP-sequencing and small RNA sequencing in satellite cells and identify the Notch-induced microRNA-708, which is a mirtron that is highly expressed in quiescent cells and sharply downregulated in activated cells. They employ in vivo and ex vivo functional studies, in addition to live imaging, to show that miR-708 regulates quiescence and self-renewal by antagonizing cell migration through targeting the transcripts of the focal-adhesion-associated protein Tensin3. Therefore, this study identifies a Notch-miR708-Tensin3 axis and suggests that Notch signaling can regulate satellite cell quiescence and transition to the activation state through dynamic regulation of the migratory machinery.

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3. In Vitro Expansion of Primary Human Hepatocytes with Efficient Liver Repopulation Capacity

Transplantation of human hepatocytes (HHs) holds significant potential for treating liver diseases. However, the supply of transplantable HHs is severely constrained by limited donor availability and compromised capacity for in vitro expansion. In response to chronic injury, some HHs are reprogrammed into proliferative cells that express both hepatocyte and progenitor markers, suggesting exploitable strategies for expanding HHs in vitro. Here, Kun Zhang at Tongji University School of Medicine in Shanghai, China and his colleagues report defined medium conditions that allow 10,000-fold expansion of HHs. These proliferating HHs are bi-phenotypic, partially retaining hepatic features while gaining expression of progenitor-associated genes. Importantly, these cells engraft into injured mouse liver at a level comparable to primary HHs, and they undergo maturation following transplantation in vivo or differentiation in vitro. Thus, this study provides a protocol that enables large-scale expansion of transplantable HHs, which could be further developed for modeling and treating human liver disease.

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4. A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening

Gastric cancer displays marked molecular heterogeneity with aggressive behavior and treatment resistance. Therefore, good in vitro models that encompass unique subtypes are urgently needed for precision medicine development. Here, Helen H.N. Yan at The University of Hong Kong in Pokfulam, Hong Kong and his colleagues have established a primary gastric cancer organoid (GCO) biobank that comprises normal, dysplastic, cancer, and lymph node metastases (n = 63) from 34 patients, including detailed whole-exome and transcriptome analysis. The cohort encompasses most known molecular subtypes (including EBV, MSI, intestinal/CIN, and diffuse/GS, with CLDN18-ARHGAP6 or CTNND1-ARHGAP26 fusions or RHOA mutations), capturing regional heterogeneity and subclonal architecture, while their morphology, transcriptome, and genomic profiles remain closely similar to in vivo tumors, even after long-term culture. Large-scale drug screening revealed sensitivity to unexpected drugs that were recently approved or in clinical trials, including Napabucasin, Abemaciclib, and the ATR inhibitor VE-822. Overall, this new GCO biobank, with linked genomic data, provides a useful resource for studying both cancer cell biology and precision cancer therapy.

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5. Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions

Unisexual reproduction is widespread among lower vertebrates, but not in mammals. Deletion of the H19 imprinted region in immature oocytes produced bimaternal mice with defective growth; however, bipaternal reproduction has not been previously achieved in mammals. Zhi-Kun Li at Institute of Zoology, Chinese Academy of Sciences in Beijing, China and his colleagues found that cultured parthenogenetic and androgenetic haploid embryonic stem cells (haESCs) display DNA hypomethylation resembling that of primordial germ cells. Through MII oocyte injection or sperm coinjection with hypomethylated haploid ESCs carrying specific imprinted region deletions, they obtained live bimaternal and bipaternal mice. Deletion of 3 imprinted regions in parthenogenetic haploid ESCs restored normal growth of fertile bimaternal mice, whereas deletion of 7 imprinted regions in androgenetic haploid ESCs enabled production of live bipaternal mice that died shortly after birth. Phenotypic analyses of organ and body size of these mice support the genetic conflict theory of genomic imprinting. Taken together, their results highlight the factors necessary for crossing same-sex reproduction barriers in mammals.

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The Nobel Prize in Physiology or Medicine 1997

The Nobel Prize in Physiology or Medicine 1997 was awarded to Stanley B. Prusiner "for his discovery of Prions - a new biological principle of infection."

Stanley B. Prusiner

Born: 28 May 1942, Des Moines, IA, USA

Affiliation at the time of the award: University of California School of Medicine, San Francisco, CA, USA

Summary

The 1997 Nobel Prize in Physiology or Medicine is awarded to the American Stanley Prusiner for his pioneering discovery of an entirely new genre of disease-causing agents and the elucidation of the underlying principles of their mode of action. Stanley Prusiner has added prions to the list of well known infectious agents including bacteria, viruses, fungi and parasites. Prions exist normally as innocuous cellular proteins, however, prions possess an innate capacity to convert their structures into highly stabile conformations that ultimately result in the formation of harmful particles, the causative agents of several deadly brain diseases of the dementia type in humans and animals. Prion diseases may be inherited, laterally transmitted, or occur spontaneously. Regions within diseased brains have a characteristic porous and spongy appearance, evidence of extensive nerve cell death, and affected individuals exhibit neurological symptoms including impaired muscle control, loss of mental acuity, memory loss and insomnia. Stanley Prusiner’s discovery provides important insights that may furnish the basis to understand the biological mechanisms underlying other types of dementia-related diseases, for example Alzheimer’s disease, and establishes a foundation for drug development and new types of medical treatment strategies.

In 1972 Stanley Prusiner began his work after one of his patients died of dementia resulting from Creutzfeldt-Jakob disease (CJD). It had previously been shown that CJD, kuru, and scrapie, a similar disease affecting sheep, could be transmitted through extracts of diseased brains. There were many theories regarding the nature of the infectious agent, including one that postulated that the infectious agent lacked nucleic acid, a sensational hypothesis since at the time all known infectious agents contained the hereditary material DNA or RNA. Prusiner took up the challenge to precisely identify the infectious agent and ten years later in 1982 he and his colleagues successfully produced a preparation derived from diseased hamster brains that contained a single infectious agent. All experimental evidence indicated that the infectious agent was comprised of a single protein, and Prusiner named this protein a prion, an acronym derived from “proteinaceous infectious particle.” It should be noted that the scientific community greeted this discovery with great skepticism, however, an unwavering Prusiner continued the arduous task to define the precise nature of this novel infectious agent.



Please click https://www.nobelprize.org/prizes/medicine/1997/press-release/ for more detailed information.

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

Content introduction:

• Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites


• Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data


• De novo assembly of haplotype-resolved genomes with trio binning


• An integrative tissue-network approach to identify and test human disease genes


• High-quality genome sequences of uncultured microbes by assembly of read clouds

1. Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

The functions of many long noncoding RNAs (lncRNAs) in the human genome remain unknown owing to the lack of scalable loss-of-function screening tools. Ying Liu at Peking University in Beijing, China and her colleagues previously used pairs of CRISPR–Cas9 single guide RNAs (sgRNAs) for small-scale functional screening of lncRNAs4. Here they demonstrate genome-wide screening of lncRNA function using sgRNAs to target splice sites and achieve exon skipping or intron retention. Splice-site targeting outperformed a conventional CRISPR library in a negative selection screen targeting 79 ribosomal genes. Using a genome-scale library of splicing-targeting sgRNAs, they performed a screen covering 10,996 lncRNAs and identified 230 that are essential for cellular growth of chronic myeloid leukemia K562 cells. Screening GM12878 lymphoblastoid cells and HeLa cells with the same library identified cell-type-specific differences in lncRNA essentiality. Extensive validation confirmed the robustness of our approach.

Read more, please click https://www.nature.com/articles/nbt.4283

2. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

How intrinsic gene-regulatory networks interact with a cell's spatial environment to define its identity remains poorly understood. Qian Zhu at Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health in Massachusetts, USA and his colleagues developed an approach to distinguish between intrinsic and extrinsic effects on global gene expression by integrating analysis of sequencing-based and imaging-based single-cell transcriptomic profiles, using cross-platform cell type mapping combined with a hidden Markov random field model. They applied this approach to dissect the cell-type- and spatial-domain-associated heterogeneity in the mouse visual cortex region. Their analysis identified distinct spatially associated, cell-type-independent signatures in the glutamatergic and astrocyte cell compartments. Using these signatures to analyze single-cell RNA sequencing data, they identified previously unknown spatially associated subpopulations, which were validated by comparison with anatomical structures and Allen Brain Atlas images.



Read more, please click https://www.nature.com/articles/nbt.4260

3. De novo assembly of haplotype-resolved genomes with trio binning

Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. Sergey Koren at National Human Genome Research Institute in Maryland, USA and his colleagues developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly. In contrast with prior approaches, the effectiveness of their method improved with increasing heterozygosity. Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. They used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches. They sequenced an F1 cross between the cattle subspecies Bos taurus taurus and Bos taurus indicus and completely assembled both parental haplotypes with NG50 haplotig sizes of >20 Mb and 99.998% accuracy, surpassing the quality of current cattle reference genomes. They suggest that trio binning improves diploid genome assembly and will facilitate new studies of haplotype variation and inheritance.

Read more, please click https://www.nature.com/articles/nbt.4277

4. An integrative tissue-network approach to identify and test human disease genes

Effective discovery of causal disease genes must overcome the statistical challenges of quantitative genetics studies and the practical limitations of human biology experiments. Here Victoria Yao at Princeton University in New Jersey, USA and his colleagues developed diseaseQUEST, an integrative approach that combines data from human genome-wide disease studies with in silico network models of tissue- and cell-type-specific function in model organisms to prioritize candidates within functionally conserved processes and pathways. They used diseaseQUEST to predict candidate genes for 25 different diseases and traits, including cancer, longevity, and neurodegenerative diseases. Focusing on Parkinson's disease (PD), a diseaseQUEST-directed Caenhorhabditis elegans behavioral screen identified several candidate genes, which they experimentally verified and found to be associated with age-dependent motility defects mirroring PD clinical symptoms. Furthermore, knockdown of the top candidate gene, bcat-1, encoding a branched chain amino acid transferase, caused spasm-like 'curling' and neurodegeneration in C. elegans, paralleling decreased BCAT1 expression in PD patient brains. diseaseQUEST is modular and generalizable to other model organisms and human diseases of interest.

Read more, please click https://www.nature.com/articles/nbt.4246

5. High-quality genome sequences of uncultured microbes by assembly of read clouds

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, Alex Bishara at Stanford University in California, USA and his colleagues present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. They present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. They applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. They also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Their approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.

Read more, please click https://www.nature.com/articles/nbt.4266