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Survival-Associated Cellular Response Maintained in Pancreatic Ductal Adenocarcinoma (PDAC) Switched Between Soft and Stiff 3D Microgel Culture
Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection prior to metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path toward understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff", elastic modulus, E ≈ 10 kPa) microenvironment even while invading a healthy ("soft", E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in the 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the downregulation of tumor suppressors (LATS1, BCAR3, CDKN2C), as well as the upregulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming
Conserved S/T Residues of the Human Chaperone DNAJB6 Are Required for Effective Inhibition of Aβ42 Amyloid Fibril Formation
The
human molecular chaperone DNAJB6, an oligomeric protein with
a conserved S/T-rich region, is an efficient suppressor of amyloid
fibril formation by highly aggregation-prone peptides such as the
Aβ and polyQ peptides associated with Alzheimer’s and
Huntington’s disease, respectively. We previously showed that
DNAJB6 can inhibit the processes through which amyloid fibrils are
formed via strong interactions with aggregated forms of Aβ42
that become sequestered. Here we report that the concentration-dependent
capability of DNAJB6 to suppress fibril formation in thioflavin T
fluorescence assays decreases progressively with an increasing number
of S/T substitutions, with an almost complete loss of suppression
when 18 S/T residues are substituted. The kinetics of primary nucleation
in particular are affected. No detectable changes in the structure
are caused by the substitutions. Also, the level of binding of DNAJB6
to Aβ42 decreases with the S/T substitutions, as determined
by surface plasmon resonance and microscale thermophoresis. The aggregation
process monitored using nuclear magnetic resonance spectroscopy showed
that DNAJB6, in contrast to a mutational variant with 18 S/T residues
substituted, can keep monomeric Aβ42 soluble for an extended
time. The inhibition of the primary nucleation is likely to depend
on hydroxyl groups in side chains of the S/T residues, and hydrogen
bonding with Aβ42 is one plausible molecular mechanism, although
other possibilities cannot be excluded. The loss of the ability to
suppress fibril formation upon S/T to A substitution was previously
observed also for polyQ peptides, suggesting that the S/T residues
in the DNAJB6-like chaperones have a general ability to inhibit amyloid
fibril formation by different aggregation-prone peptides
Real-Time Metabolomics on Living Microorganisms Using Ambient Electrospray Ionization Flow-Probe
Microorganisms
such as bacteria and fungi produce a variety of
specialized metabolites that are invaluable for agriculture, biological
research, and drug discovery. However, the screening of microbial
metabolic output is usually a time-intensive task. Here, we utilize
a liquid microjunction surface sampling probe for electrospray ionization-mass
spectrometry to extract and ionize metabolite mixtures directly from
living microbial colonies grown on soft nutrient agar in Petri-dishes
without any sample pretreatment. To demonstrate the robustness of
the method, this technique was applied to observe the metabolic output
of more than 30 microorganisms, including yeast, filamentous fungi,
pathogens, and marine-derived bacteria, that were collected worldwide.
Diverse natural products produced from different microbes, including Streptomyces coelicolor, Bacillus
subtilis, and Pseudomonas aeruginosa are further characterized
Real-Time Metabolomics on Living Microorganisms Using Ambient Electrospray Ionization Flow-Probe
Microorganisms
such as bacteria and fungi produce a variety of
specialized metabolites that are invaluable for agriculture, biological
research, and drug discovery. However, the screening of microbial
metabolic output is usually a time-intensive task. Here, we utilize
a liquid microjunction surface sampling probe for electrospray ionization-mass
spectrometry to extract and ionize metabolite mixtures directly from
living microbial colonies grown on soft nutrient agar in Petri-dishes
without any sample pretreatment. To demonstrate the robustness of
the method, this technique was applied to observe the metabolic output
of more than 30 microorganisms, including yeast, filamentous fungi,
pathogens, and marine-derived bacteria, that were collected worldwide.
Diverse natural products produced from different microbes, including Streptomyces coelicolor, Bacillus
subtilis, and Pseudomonas aeruginosa are further characterized