bluuebunny/crossref_metadata_2025 huggingface dataset:
Acupuncture for patients with Maigne’s syndrome: A case series
Authors: Lee Hesol , Chae Hyocheong , Ryu Myungseok , Yang Changsop , Kim Sungha
Published: June 2023

Rationale:

Diagnosing the precise etiology of low back pain (LBP) is crucial for facilitating speedy recovery in patients. Maigne's syndrome (MS), commonly referred to as thoracolumbar junction syndrome, is a condition characterized by pain resulting from nerve entrapment, yet its underlying mechanisms remain poorly understood. This study presents a series of six case reports wherein patients diagnosed with MS received acupuncture treatment.

Patient concerns:

Six individuals with LBP were included in the study, and all were diagnosed with MS.

Diagnoses:

The diagnosis was confirmed in all six patients through pinch-roll and thoracic vertebrae compression tests, indicating the presence of thoracolumbar junction syndrome.

Interventions:

Acupuncture treatment was administered to all patients, primarily targeting the T11–L2 facet joints, with additional acupoints selected based on the specific nerve entrapment of MS including the superior cluneal, subcostal, and iliohypogastric nerves.

Outcomes:

Following acupuncture therapy, all patients reported improvements in their LBP symptoms, while four patients also exhibited amelioration in their thoracic vertebrae compression test results.

Lessons:

These findings underscore the significance of promptly diagnosing the underlying cause of LBP and suggest that acupuncture may be an effective approach in alleviating MS-related pain.
Prognostic and clinicopathological significance of TRIM21 in various cancers: A meta and bioinformatic analysis
Authors: Hu Feng , Liu Yan , Wang Feiyang , Fu Xinyi , Liu Xiangjun , Zou Zhenhong , Zhou Bin
Published: June 2023

Background:

Tripartite motif-containing protein 21 (TRIM21), a member of the ubiquitin ligase family, makes a significant contribution to the ubiquitination of multiple tumor marker proteins associated with tumor cell proliferation, metastasis and selective apoptosis. As the research further develops, an increasing number of studies have manifested that the TRIM21 expression level can be considered an indicator of cancer prognosis. However, the interrelationship between TRIM21 and multiple forms of carcinogens has not been demonstrated in a meta-analysis.

Methods:

We performed a systematic literature retrieval in various electronic databases including PubMed, Embase, Web of Science, Wanfang and China National Knowledge Infrastructure. Besides, the hazard ratio (HR) and the pooled relative risk (RR) were integrated in the assessment of cancer incidence and cancer mortality by Stata SE15.1. Additionally, we used an online database based on The Cancer Genome Atlas (TCGA) to further validate our results.

Results:

A total of 17 studies were included, totaling 7239 participants. High expression of TRIM21 was significantly correlated with better OS (HR = 0.74; 95% CI: 0.57–0.91; P < .001) and progression-free survival (PFS) (HR = 0.66; 95% CI: 0.42–0.91; P < .001). We found that high TRIM21 expression predicted significant impact on clinical characteristics like decreased lymph node metastasis (RR = 1.12; 95% CI: 0.97–1.30; P < .001), tumor stage (RR = 1.06; 95% CI: 0.82–1.37; P < .001) and tumor grade (RR = 1.07; 95% CI: 0.56–2.05; P < .001). However, TRIM21 expression had no significant impact on other clinical characteristics such as age (RR = 1.06; 95% CI: 0.91–1.25; P = .068), sex (RR = 1.04; 95% CI: 0.95–1.12; P = .953), or tumor size (RR = 1.14; 95% CI: 0.97–1.33; P = .05). Based on the Gene Expression Profiling Interactive Analysis (GEPIA) online analysis tool, TRIM21 was significantly downregulated in 5 cancers while significantly upregulated in 2 cancers, and the descending expression of TRIM21 predicted shorter OS in 5 cancers, worse PFS in 2 malignancies, while the elevated expression of TRIM21 predicted shorter OS and worse PFS in 2 carcinomas.

Conclusions:

TRIM21 could serve as a new biomarker for patients with solid malignancies and could be a potential therapeutic target for patients.
Diagnosis and treatment of bilateral adrenal pheochromocytoma with RET gene mutation combined with medullary sponge kidney: A case report
Authors: Shen Pengliang , Yin Nan , Sun Libin , Liu Yunfeng , Cao Xiaoming
Published: June 2023

Rationale:

Pheochromocytomas are a group of tumors with high genetic heterogeneity, and the clinical characteristics of rearranged during transfection (RET)-mutated pheochromocytoma with medullary spongiform kidney are rarely studied. The treatment process of 1 patient with bilateral adrenal pheochromocytoma combined with medullary sponge kidney with RET gene mutation in our department was retrospectively analyzed, and the treatment methods for this type of disease were studied and summarized in combination with relevant literature.

Patient concerns:

In this case, the patient was found to have bilateral adrenal masses for 8 years due to physical examination, and intermittent dizziness and discomfort for 2 years. Imaging and related laboratory examinations suggest bilateral adrenal giant pheochromocytoma with bilateral medullary sponge kidney. RET gene testing was performed on the patient and his descendant after signing the informed consent form.

Diagnoses:

The patient was diagnosed with bilateral adrenal pheochromocytoma with a RET proto-oncogene mutation and a bilateral medullary spongy kidney.

Intervision and outcomes:

After sufficient perioperative preparation, retroperitoneal laparoscopic bilateral adrenal pheochromocytoma resection was performed by stages. The operation was successful, and hormone replacement therapy was performed after the operation, with regular follow-up. Relevant genetic testing revealed that the c.1900T > C: p.C634R mutation was detected in the patient’s RET gene, which was a heterozygous missense mutation, and the mutation was also present in the son of his family. A literature analysis found that pheochromocytoma is a tumor with high genetic heterogeneity, and the RET proto-oncogene is a common pathogenic gene for bilateral adrenal pheochromocytoma. Medullary sponging of kidneys is a rare complication of this disease.

Lessons:

On the basis of adequate perioperative preparation, surgical resection is the most effective and preferred treatment for this type of disease. Laparoscopic surgery is minimally invasive, safe, and effective by stages. Mutations in the RET proto-oncogene may lead to medullary spongy kidneys in multiple endocrine neoplasia 2.
Nasotracheal intubation awake in a patient with multiple fractures of the maxilla and cervical spine: A case report
Authors: Ferreira Luan Oliveira , Vasconcelos Victoria Winkler , de Lima Imaikon Gomes , de Souza Juliana Barbosa , Resende Karina Dias
Published: June 2023

Rationale:

Nasotracheal intubation is an advanced airway modality used in specific contexts, such as limited mouth opening, macroglossia, cervical spine instability. In addition, it can be performed with the patient awake, especially when predictors a difficult airway are unknown.

Patient concerns:

A 41-year-old male with a lesion in the C1 cervical vertebra, associated with a fracture of the right maxilla, was intubated through the nasopharyngeal route while awake. The forms of induction were discussed.

Diagnoses:

Based on the mechanism of trauma and on the report of pain, associated with imaging examination, fracture of the body of the right maxilla and a complex fracture of the anterior arch of the C1 cervical vertebra were diagnosed.

Interventions:

In this case, we present a patient with trauma to the face and spine who was intubated through the nasopharyngeal route while awake and guided by video laryngoscopy and using a rigid cervical collar. The patient was operated on under total general anesthesia (propofol and remifentanil) and plates and screws were placed for maxillary osteosynthesis. The pain was alleviated with a peripheral block of the trigeminal nerve of the maxillary branch with 0.5% levobupivacaine.

Outcomes:

The patient woke up from surgery, was extubated uneventfully and without pain. Cervical spine injuries were followed up by the neurosurgery team for conservative treatment.

Lessons:

Patients with neck injury and facial trauma may need a definitive airway either for emergencies or for elective procedures. Intubating the awake patient may be an option when the anatomy of the cavity is unknown, and inducing the anesthetic act without this knowledge may be a inappropriate option, due to the risk of intubation/ventilation difficulties.
Low Levels of Detectable Urine and Stool GIPs in Children with Celiac Disease on a Gluten-Free Diet
Authors: Horton Maxwell , Olshan Katherine L. , Gleeson Elizabeth , Regis Stephanie , Morson Taylor , Hintze Zackary J. , Leonard Maureen M. , Silvester Jocelyn A.
Published: June 2023

Objectives:

This study examines the prevalence of detectable gluten immunogenic peptides (GIPs) as a proxy for gluten exposure in children with celiac disease on a gluten-free diet in the United States, as estimated by gluten breakdown products excreted in urine and stool.

Methods:

Urine and stool samples were collected in 3 settings (home, gastroenterology clinic, and endoscopy) for pediatric participants (ages 6–21 years old) across 2 medical centers. Commercial ELISA assays were used to quantify the GIPs in each sample.

Results:

GIPs were detected in 4 out of 44 (9.1%) of stool samples and 6 out of 125 (4.8%) of urine samples provided by 84 children. These samples were collected across all settings, and most participants (70%) were asymptomatic at the time of sample collection. For the urine samples collected at the time of endoscopy, all subjects found to have persistent enteropathy had no detectable GIPs (0/12).

Discussion:

GIPs provide an additional method for screening for gluten exposures in individuals with celiac disease on a gluten-free diet, and may be used across multiple settings. We found a low detection rate of GIPs in children. Our finding of undetectable GIPs in individuals with persistent enteropathy may be expected of a single determination under close observation or represent a lack of gluten exposure within the detection window. More research is needed to understand the dynamics of gluten absorption and excretion in the US pediatric population.
Hypocoagulability in Children With Decompensated Chronic Liver Disease and Sepsis: Assessment by Thromboelastography
Authors: Vinayagamoorthy Vignesh , Srivastava Anshu , Das Indranil , Verma Anupam , Mishra Prabhakar , Sen Sarma Moinak , Poddar Ujjal , Yachha Surender Kumar
Published: June 2023

Objective:

To evaluate the coagulation status of children with decompensated chronic liver disease (DCLD) and infection and factors affecting it using thromboelastography (TEG).

Methods:

Coagulation status of children admitted with DCLD and infection was assessed by international normalized ratio (INR), platelet count, and TEG [reaction time (R), kinetic time (K), α-angle (AA), maximum amplitude (MA), coagulation index (CI), and lysis index (LY30)] at admission and at 7–14 days after treatment. CI < −3 represents hypocoagulable state. Clinical profile including systemic inflammatory response syndrome (SIRS), infection severity, bleeding, treatment response, and outcome were noted.

Results:

Thirty children (21 boys, median (IQR) age 78 [15.7–180] months) were studied prospectively. At admission, 29 (96.7%) had prolonged INR, 24 (80%) had thrombocytopenia, and 17 (56.6%) were hypocoagulable by TEG. Nine of 30 (30%) had normal TEG but deranged INR and platelets. Nineteen (63.3%) cases had SIRS, 11 (36.6%) had severe sepsis, and 8 (26.6%) had bleeding. Hypocoagulable state was common in severe sepsis than sepsis/infection (81.1% versus 42.1%; P = 0.05) and persistent (n = 4) versus recovered SIRS (n = 15, 100% versus 33%; P = 0.03). Bleeders had prolonged R-time (7.8 versus 5.4 min; P = 0.03), smaller MA (30.2 versus 47 mm; P = 0.05), and α-angle (40.4 versus 62.9; P = 0.03) but similar INR and platelets than nonbleeders. Six patients (20%) had poor in-hospital outcomes; R-time ≥8.5 min predicted mortality with high sensitivity (83%) and specificity (100%).

Conclusions:

Fifth-seven percent of children with DCLD and infection were hypocoagulable by TEG. Severe sepsis and persistent SIRS worsened the coagulation status. TEG identifies bleeders better than INR and platelet count. R-time ≥8.5 min predicts a poor hospital outcome.
Pediatric Acute Liver Failure Secondary to Autoimmune Hepatitis in an Infant With Thrombocytopenia-Absent Radius (TAR) Syndrome: A Case Report
Authors: Mercedes Rebecca , Patel Kalyani , Shiau Henry , Mysore Krupa R. , Ruan Wenly , Leung Daniel H. , Tessier Mary Elizabeth M. , Cerminara Dana , Nicholas Sarah , Fuller Kelby , Faraone Marielle , Galvan N. Thao N. , Goss John , Banc-Husu Anna M.
Published: June 2023

Thrombocytopenia absent radius (TAR) syndrome is a rare genetic disorder that has been associated with food protein–induced allergic proctocolitis and transient leukemoid reactions, among other manifestations. There has been no prior reports of its association with autoimmune disease, more specifically, autoimmune hepatitis (AIH) or the development of pediatric acute liver failure (PALF). We present a case of an 8-month-old infant with TAR syndrome who presented with PALF, secondary to AIH with elevated liver-kidney microsomal antibody (>1:2560). She received a liver transplant and had a very complicated postoperative course including severe T-cell–mediated rejection, infection, biliary stricture, persistently elevated liver-kidney microsomal antibodies, and antibody-mediated rejection. Ultimately, these complications led to graft failure, severe sepsis, and death. This case highlights a new association of TAR syndrome with AIH and PALF and a potentially aggressive nature of AIH both pre- and post-transplant.
Pediatric Colonic Xanthomas, a Previously Unreported Colonoscopic Finding
Authors: Vanderhoof Jon A. , Goldsmith Jeffrey D. , Pauley Rosemary , Fox Victor L.
Published: June 2023

Gastrointestinal xanthomas are benign, usually sessile, polypoid lesions occasionally incidentally seen in adults, usually in the stomach, but have not been reported in the large intestine in children. We identified xanthomas in the sigmoid colon of the 15-year-old girl confirmed histologically. Our findings suggest that colonic xanthomas may occur as an incidental finding in pediatric patients. They have a characteristic visual and histologic appearance but do not appear to be associated with any symptoms or illness and do not require follow-up.
Experience With Establishing a Robotic Donor Hepatectomy Program for Pediatric Liver Transplantation
Authors: Rela Mohamed , Rajalingam Rajesh , Cherukuru Ramkiran , Palaniappan Kumar , Kumar S. Arul , Kanagavelu Rathnavel , Narasimhan Gomathy , Rajakumar Akila , Kaliamoorthy Ilankumaran , Rammohan Ashwin
Published: June 2023

Background.

The benefits of minimal invasive donor hepatectomy, especially for left lateral sectionectomy (LLS) have been unequivocally demonstrated. Moreover, donors in pediatric liver transplantation (LT) are usually parents who need to recover quickly to take care of the child. There are inherent limitations to conventional laparoscopic surgery including surgeon’s experience with advanced laparoscopic surgery and steep learning curve which limits the wide application of minimal invasive donor hepatectomy. We share our experience of establishing a program of robotic donor hepatectomy (RDH) and achieving proficiency in performing RDH for pediatric LT.

Methods.

Data were prospectively collected of consecutive LLS RDH based on a structured learning algorithm. Donor and recipient outcomes were analyzed.

Results.

Seventy-five consecutive cases of LLS RDH were performed. The median primary warm ischemia time was 6 min (interquartile range [IQR]: 5–7 min). No major complications (grade ≥IIIb Clavien-Dindo) were noted in the cohort. There were no emergency conversion to open surgery and neither were there postoperative explorations through a laparotomy. Seven grafts were hyper-reduced and 5 required venoplasty. Two recipients died because of severe sepsis and multiorgan failure. Major complications occurred in 15 children (20%), none of which were attributable to RDH. Median hospital stay of the donors and recipients was 5 d (IQR: 5–6) and 12 d (IQR: 10–18) respectively.

Conclusions.

We share our experience of starting a RDH program for pediatric LT. We highlight the challenges and our learning algorithm to spur teams on the cusp of starting robotic transplant programs.
Circulating Exosomes Mediate Neurodegeneration Following Hepatic Ischemia-Reperfusion Through Inducing Microglial Pyroptosis in the Developing Hippocampus
Authors: Wang Yidan , Jia Lili , Wei Min , Lyu Jingshu , Sheng Mingwei , Sun Ying , Dong Zhonglan , Han Wenhui , Ren Yinghui , Weng Yiqi , Yu Wenli
Published: June 2023

Background.

Poor neurodevelopmental outcomes after pediatric liver transplantation seriously affect the long-term quality of life of recipients, in whom hepatic ischemia reperfusion (HIR) is considered to play a pivotal role. However, the link between HIR and brain injury remains unclear. Because circulating exosomes are considered as the key mediators of information transmission over long distances, we aimed to assess the role of circulating exosomes in HIR-induced hippocampal injury in young rats.

Methods.

We administered exosomes extracted from the sera of HIR model rats to normal young rats via the tail vein. Western blotting, enzyme-linked immunosorbent assay, histological examination, and real-time quantitative polymerase chain reaction were used to evaluate the role of exosomes in neuronal injury and activation of microglial pyroptosis in the developing hippocampus. Primary microglial cells were cocultured with exosomes to further assess the effect of exosomes on microglia. To further explore the potential mechanism, GW4869 or MCC950 was used to block exosome biogenesis or nod-like receptor family protein 3, respectively.

Results.

Serum-derived exosomes played a crucial role in linking HIR with neuronal degeneration in the developing hippocampus. Microglia were found to be the target cells of ischemia-reperfusion derived exosomes (I/R-exosomes). I/R-exosomes were taken up by microglia and promoted the occurrence of microglial pyroptosis in vivo and in vitro. Moreover, the exosome-induced neuronal injury was alleviated by suppressing the occurrence of pyroptosis in the developing hippocampus.

Conclusions.

Microglial pyroptosis induced by circulating exosomes plays a vital role in developing hippocampal neuron injury during HIR in young rats.
The ecology of scale: impact of volume on coalescence and function in methanogenic communities
Authors: Sierocinski Pawel , Stilwell Peter , Padfield Daniel , Bayer Florian , Buckling Angus
Published: June 2023

Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.
Multiscale models driving hypothesis and theory-based research in microbial ecology
Authors: Martinez-Rabert Eloi , Sloan William T. , Gonzalez-Cabaleiro Rebeca
Published: June 2023

Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (
in-silico
bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the
in-silico
bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.
Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions
Authors: Weaver Joseph Earl
Published: June 2023

Both deterministic and stochastic forces shape biofilm communities, but the balance between those forces is variable. Quantifying the balance is both desirable and challenging. For example, drift-driven failure, a stochastic force, can be thought of as an organism experiencing ‘bad luck’ and manipulating ‘luck’ as a factor in real-world systems is difficult. We used an agent-based model to manipulate luck by controlling seed cevalues governing random number generation. We determined which organism among identical competitors experienced the greatest drift-driven failure, gave it a deterministic growth advantage and re-ran the simulation with the same seed. This enabled quantifying the growth advantage required to overcome drift, e.g. a 50% chance to thrive may require a 10–20% improved growth rate. Further, we found that crowding intensity affected that balance. At moderate spacings, there were wide ranges where neither drift nor selection dominated. Those ranges shrank at extreme spacings; close and loose crowding, respectively, favoured drift and selection. We explain how these results may partially illuminate two conundrums: the fact that a stably operating wastewater treatment plant's microbial community can vary greatly over time and the difference between equivalent and total community size in neutral community assembly models.
Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant
Authors: Lin Limin , Ju Feng
Published: June 2023

High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically evaluated the fitness of different frequently used reference databases (i.e. SILVA 138 SSU, GTDB bact120_r207, Greengenes 13_5 and MiDAS 4.8) and primers of 16S rRNA gene in microbiota profiling of anaerobic digestion and activated sludge collected from a full-scale swine wastewater treatment plant (WWTP). The comparative results showed that MiDAS 4.8 achieved the highest levels of taxonomic diversity and species-level assignment rate. For whichever sample groups, microbiota richness captured by different primers decreased in the following order: V4 > V4-V5 > V3-V4 > V6-V8/V1-V3. Using primer-bias-free metagenomic data results as the judging standard, V4 region also best characterized microbiota structure and well represented typical functional guilds (e.g. methanogens, ammonium oxidizers and denitrifiers), while V6-V8 regions largely overestimated the archaeal methanogens (mainlyMethanosarcina) by over 30 times. Therefore, MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure of the examined swine WWTP.
Characterization of a Helicobacter pylori strain with high biofilm-forming ability
Authors: Wilkinson Daniel , Alsharaf Lolwah , Thompson Stephen , Paulin Andreja , Takor Rhodrick , Zaitoun Abed , Robinson Karen , Thomas Jonathan , McVicker Gareth , Winter Jody
Published: June 2023

Introduction.

Helicobacter pylori

is highly polymorphic, and some strains are much more likely to cause disease than others. Biofilm formation can help bacteria to survive antibiotic treatment, immune attack and other stresses, promoting persistent infection.

Hypothesis/Gap Statement. We hypothesized that

H. pylori

isolates from patients with more severe H. pylori-associated disease would be better at forming biofilms than isolates from patients with less severe disease.

Aim. We initially aimed to determine whether or not the biofilm-forming ability of

H. pylori

isolates was associated with disease in the UK-based patients from whom the bacteria were isolated.

Methodology. Biofilm-forming ability of

H. pylori

isolates was determined using a crystal violet assay on glass coverslips. The complete genome sequence of strain 444A was generated by hybrid assembly of Nanopore MinION and Illumina MiSeq data.

Results. Although we found no associations between biofilm-forming ability of

H. pylori

and disease severity in patients, we discovered that strain 444A had particularly high biofilm-forming ability. This strain had been isolated from a patient with gastric ulcer disease and moderate to severe scores for H. pylori-induced histopathology. Analysis of the genome of the high biofilm-forming

H. pylori

strain 444A revealed that it possesses numerous biofilm- and virulence-associated genes and a small cryptic plasmid encoding a type II toxin–antitoxin system.

Conclusion. There is substantial variation in biofilm-forming ability in H. pylori, but this was not significantly associated with disease severity in our study. We identified and characterized an interesting strain with high biofilm-forming ability, including generation and analysis of the complete genome.
CLEC4A and CLEC12B C-type lectin receptors mediate interactions with Pneumocystis cell wall components
Authors: Kottom Theodore J. , Carmona Eva M. , Schaefbauer Kyle , Limper Andrew H.
Published: June 2023

Introduction. C-type lectin receptors (CLRs) are prominently expressed on myeloid cells where they perform multiple functions including serving as pattern recognition receptors (PRRs) to drive innate as well as adaptive immunity to pathogens. Depending on the presence of a tyrosine-based signalling motif, CLR-microbial pathogen engagement may result in either anti- or pro-inflammatory signalling.

Impact statement. In this manuscript, we report our laboratory study of two novel CLRs that recognize Pneumocystis murina cell wall homogenates (CWH) and a purified Pneumocystis carinii cell wall fraction (CWF).

Aim. To study the potential of newly generated hFc-CLR fusions on binding to Pneumocystis murina CWHs and P. carinii CWFs and subsequent downstream inflammatory signalling analysis.

Methods. Newly generated hFc-CLR fusion CLEC4A and CLEC12B were screened against P. murina CWHs and P. carinii CWFs preparations via modified ELISA. Immunofluorescence assay (IFA) was utilized to visualize hFc-CLR fusion binding against intact fixed fungal life forms to verify results. Quantitative PCR (q-PCR) analysis of lung mRNA from the mouse immunosuppressed Pneumocystis pneumonia (PCP) model versus uninfected mice was employed to detect possible changes in the respective Clec4a and Clec12b transcripts. Lastly, siRNA technology of both CLRs was conducted to determine effects on downstream inflammatory events in mouse macrophages stimulated in the presence of P. carinii CWFs.

Results. We determined that both CLEC4A and CLEC12B hFc-CLRs displayed significant binding with P. murina CWHs and P. carinii CWFs. Binding events showed significant binding to both curdlan and laminarin, both polysaccharides containing β-(1,3) glucans as well as N-acetylglucosamine (GlcNAc) residues and modest yet non-significant binding to the negative control carbohydrate dextran. IFA with both CLR hFc-fusions against whole P. murina life forms corroborated these findings. Lastly, we surveyed the mRNA expression profiles of both CLRs tested above in the mouse immunosuppressed Pneumocystis pneumonia (PCP) model and determined that both CLRs were significantly up regulated during infection. Lastly, siRNA of both CLRs in the mouse RAW macrophage cell line was conducted and results demonstrated that silencing of Clec4a resulted in no significant changes in TNF-alpha generation in P. carinii CWF stimulated macrophages. On the contrary, silencing of Clec12b CLR resulted in significant decreases in TNF-alpha in RAW cells stimulated with the same CWF.

Conclusion. The data presented here provide new members of the CLRs family recognizing Pneumocystis. Future studies using CLEC4A and/or CLEC12B deficient mice in the PCP mouse model should provide further insights into the host immunological response to Pneumocystis.
A SMART method for efficiently isolating monoclonal antibodies from individual rhesus macaque memory B cells
Authors: Weinfurter Jason T. , Bennett Sarah N. , Reynolds Matthew
Published: June 2023

Characterizing antigen-specific B cells is a critical component of vaccine and infectious disease studies in rhesus macaques (RMs). However, it is challenging to capture immunoglobulin variable (IgV) genes from individual RM B cells using 5’ multiplex (MTPX) primers in nested PCR reactions. In particular, the diversity within RM IgV gene leader sequences necessitates the use of large 5’ MTPX primer sets to amplify IgV genes, decreasing PCR efficiency. To address this problem, we developed a switching mechanism at the 5’ ends of the RNA transcript (SMART)-based method for amplifying IgV genes from single RM B cells, providing unbiased capture of Ig heavy and light chain pairs for cloning antibodies. We demonstrate this technique by isolating simian immunodeficiency virus (SIV) envelope-specific antibodies from single-sorted RM memory B cells. This approach has several advantages over existing methods for PCR cloning antibodies from RMs. First, optimized PCR conditions and SMART 5’ and 3’ rapid amplification of cDNA ends (RACE) reactions generate full-length cDNAs from individual B cells. Second, it appends synthetic primer binding sites to the 5’ and 3’ ends of cDNA during synthesis, allowing for PCR amplification of low-abundance antibody templates. Third, universal 5’ primers are employed to amplify the IgV genes from cDNA, simplifying the primer mixes in the nested PCR reactions and improving the recovery of matched heavy and light chain pairs. We anticipate this method will enhance the isolation of antibodies from individual RM B cells, supporting the genetic and functional characterization of antigen-specific B cells.
A region-resolved proteomic map of the human brain enabled by high-throughput proteomics
Authors: Tüshaus Johanna , Sakhteman Amirhossein , Lechner Severin , The Matthew , Mucha Eike , Krisp Christoph , Schlegel Jürgen , Delbridge Claire , Kuster Bernhard
Published: June 2023

Substantial efforts are underway that aim to deepen our understanding of human brain morphology, structure and function using high-resolution imaging as well has high-content molecular profiling technologies. The current work adds to these efforts by providing a comprehensive and quantitative protein expression map of 13 anatomically distinct brain regions covering more than 10,000 proteins. This was enabled by the optimization, characterization and implementation of a high-sensitivity and high-throughput micro-flow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable of analyzing >2,000 consecutive samples prepared from formalin fixed paraffin embedded (FFPE) material. Analysis of this proteomic resource highlighted e.g. brain region-enriched protein expression patterns and functional protein classes, protein localization differences between brain regions and individual protein markers for specific brain regions. To facilitate access to and ease further mining of the data by the scientific community, all data can be explored online in a purpose-built Shiny App (https://brain-region-atlas.proteomics.ls.tum.de).
56Fe ion exposure increases the incidence of lung and brain tumors at a similar rate in male and female mice
Authors: Finkelstein Sophie R. , Patel Rutulkumar , Deland Katherine , Mercer Joshua , Starr Bryce , Zhu Daniel , Min Hooney , Reinsvold Michael , Campos Lorraine Da Silva , Williams Nerissa , Luo Lixia , Ma Yan , Neff Jadee , Hoenerhoff Mark , Moding Everett J. , Kirsch David G.
Published: June 2023

The main deterrent to long-term space travel is the risk of Radiation Exposure Induced Death (REID). The National Aeronautics and Space Administration (NASA) has adopted Permissible Exposure Levels (PELs) to limit the probability of REID to 3% for the risk of death due to radiation-induced carcinogenesis. The most significant contributor to current REID estimates for astronauts is the risk of lung cancer. Recently updated lung cancer estimates from Japan’s atomic bomb survivors showed that the excess relative risk of lung cancer by age 70 is roughly four-fold higher in females compared to males. However, whether sex differences may impact the risk of lung cancer due to exposure to high charge and energy (HZE) radiation is not well studied. Thus, to evaluate the impact of sex differences on the risk of solid cancer development post-HZE radiation exposure, we irradiatedRbfl/fl; Trp53fl/+male and female mice infected with Adeno-Cre with various doses of 320 kVp X-rays or 600 MeV/n56Fe ions and monitored them for any radiation-induced malignancies. We observed that lung adenomas/carcinomas and esthesioneuroblastomas (ENBs) were the most common primary malignancies in X-ray and56Fe ion-exposed mice, respectively. In addition, 1 Gy56Fe ion exposure compared to X-rays led to a significantly higher incidence of lung adenomas/carcinomas (p=0.02) and ENBs (p<0.0001). However, we did not find a significantly higher incidence of any solid malignancies in female mice as compared to male mice, regardless of radiation quality. Furthermore, gene expression analysis of ENBs suggested a distinct gene expression pattern with similar hallmark pathways altered, such as MYC targets and MTORC1 signaling, in X-ray and56Fe ion-induced ENBs. Thus, our data revealed that56Fe ion exposure significantly accelerated the development of lung adenomas/carcinomas and ENBs compared to X-rays, but the rate of solid malignancies was similar between male and female mice, regardless of radiation quality.
Evaluation of population structure inferred by principal component analysis or the admixture model
Authors: van Waaij Jan , Li Song , Garcia-Erill Genís , Albrechtsen Anders , Wiuf Carsten
Published: June 2023

Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.
A CD24+CD271+Melanoma Cancer Stem Cell Possesses Hybrid Characteristics of its Single Marker Counterparts and Promotes Invasion and Therapeutic Resistance
Authors: Knowles Olivia , Doldan Patricio , Hillier-Richardson Isabella , Lunt Stephanie , Youssef Gehad , Gammon Luke , Mackenzie Ian C. , Philpott Michael P. , Rizvi Hasan , Bergamaschi Daniele , Harwood Catherine A. , Biddle Adrian
Published: June 2023

An important role for phenotype switching has been demonstrated in metastasis and therapeutic resistance of both melanoma and epithelial tumours. Phenotype switching in epithelial tumours is driven by a minority cancer stem cell sub-population with lineage plasticity, but such a sub-population has not been identified in melanoma. We investigated whether cell surface markers used to identify cancer stem cells in epithelial tumours could identify a cancer stem cell sub-population with lineage plasticity in melanoma. We identified a CD24+CD271+minority sub-population in melanoma that possesses the stem cell characteristics of lineage plasticity and self-renewal. This population displayed hybrid characteristics, combining the attributes of discrete CD24+and CD271+cellular sub-populations but with heightened sphere formation, lineage plasticity, migratory ability and drug resistance over its single-marker counterparts. CD24+and CD24+CD271+stem cell sub-populations were observed in 10% of human melanomas, mainly at the invasive front. The lack of CD24+and CD24+CD271+stem cells in the majority of human melanoma specimens led us to conclude that they may be dispensable for melanoma progression. Nevertheless, the enhanced sphere formation, lineage plasticity, migratory ability and drug resistance of the CD24+CD271+sub-population may signal a contextual requirement for these stem cells when melanomas face challenging environments both clinically and in experimental systems.
Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology
Authors: Phan Tin , Brozak Samantha , Pell Bruce , Ciupe Stanca M. , Ke Ruian , Ribeiro Ruy M. , Gitter Anna , Mena Kristina D. , Perelson Alan S. , Kuang Yang , Wu Fuqing
Published: June 2023

Wastewater surveillance has been widely used to track and estimate SARS-CoV-2 incidence. While both infectious and recovered individuals shed virus into wastewater, epidemiological inferences using wastewater often only consider the viral contribution from the former group. Yet, the persistent shedding in the latter group could confound wastewater-based epidemiological inference, especially during the late stage of an outbreak when the recovered population outnumbers the infectious population. To determine the impact of recovered individuals’ viral shedding on the utility of wastewater surveillance, we develop a quantitative framework that incorporates population-level viral shedding dynamics, measured viral RNA in wastewater, and an epidemic dynamic model. We find that the viral shedding from the recovered population can become higher than the infectious population after the transmission peak, which leads to a decrease in the correlation between wastewater viral RNA and case report data. Furthermore, the inclusion of recovered individuals’ viral shedding into the model predicts earlier transmission dynamics and slower decreasing trends in wastewater viral RNA. The prolonged viral shedding also induces a potential delay in the detection of new variants due to the time needed to generate enough new cases for a significant viral signal in an environment dominated by virus shed by the recovered population. This effect is most prominent toward the end of an outbreak and is greatly affected by both the recovered individuals’ shedding rate and shedding duration. Our results suggest that the inclusion of viral shedding from non-infectious recovered individuals into wastewater surveillance research is important for precision epidemiology.
A multi-organ map of the human immune system across age, sex and ethnicity
Authors: Mangiola S , Milton M , Ranathunga N , Li-Wai-Suen CSN , Odainic A , Yang E , Hutchison W , Garnham A , Iskander J , Pal B , Yadav V , Rossello JFJ , Carey VJ , Morgan M , Bedoui S , Kallies A , Papenfuss AT
Published: June 2023

Understanding tissue biology’s heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.
OMA1 protease eliminates arrested protein import intermediates upon depolarization of the inner mitochondrial membrane
Authors: Krakowczyk Magda , Lenkiewicz Anna M. , Sitarz Tomasz , Marins Mussulini Ben Hur , Linke Vanessa , Malinska Dominika , Szczepankiewicz Andrzej , Wydrych Agata , Nieznanska Hanna , Serwa Remigiusz A. , Chacinska Agnieszka , Bragoszewski Piotr
Published: June 2023

Most mitochondrial proteins originate from the cytosol and require active transport into the organelle. Such precursor proteins must be largely unfolded to pass through translocation channels in mitochondrial membranes. Misfolding of transported proteins can result in their arrest and translocation failure. Arrested proteins block further import, disturbing mitochondrial functions and cellular proteostasis. Cellular responses to translocation failure have been defined in yeast. To discover molecular mechanisms that resolve failed import events in human cells, we developed the translocase clogging model using a fusion protein with a rigid domain. The mechanism we uncover differs significantly from these described in fungi, where ATPase-driven extraction of blocked protein is directly coupled with proteasomal processing. We found human cells to rely primarily on mitochondrial factors to clear translocation channel blockage. The mitochondrial membrane depolarization triggered proteolytic cleavage of the stalled protein, which involved mitochondrial protease OMA1. The cleavage allowed releasing the protein fragment that blocked the translocase. The released fragment was further cleared in the cytosol by the valosin containing protein (VCP)/p97 and proteasome.
Molecular basis of VEGFR1 autoinhibition at the plasma membrane
Authors: Chakraborty Manas Pratim , Das Diptatanu , Mondal Purav , Kaul Pragya , Bhattacharyya Soumi , Das Prosad Kumar , Das Rahul
Published: June 2023

Ligand-independent activation of VEGFR is a hallmark in diabetes and several cancers. Like most RTKs, the VEGFR2, the primary VEGF receptor, is activated spontaneously at higher receptor concentrations. An exception is VEGFR1, which remains constitutively inactive in the basal state. Ligand stimulation transiently phosphorylates VEGFR1 and induces weak kinase activation in endothelial cells. Recent studies, however, suggest that VEGFR1 signaling is indispensable in regulating various physiological or pathological events, which is puzzling. Why VEGFR1 is differentially regulated is an open question. Here we elucidate a mechanism of juxtamembrane inhibition that shifts the equilibrium more to the inactive state, rendering VEGFR1 an inefficient kinase. Our data suggest that a combination of tyrosine phosphatase activity and JM inhibition suppress the basal phosphorylation of VEGFR1. We conclude that a subtle imbalance in phosphatase activation or removing juxtamembrane inhibition is sufficient to induce basal activation of VEGFR1 and remodel tyrosine phosphorylation to be sustained.
Setdb1 safeguards genome integrity in muscle stem cells to allow for regenerative myogenesis and inflammation
Authors: Garcia Pauline , Jarassier William , Brun Caroline , Giordani Lorenzo , Agostini Fany , Kung Wai Hing , Peccate Cécile , Ravent Jade , Fall Sidy , Petit Valentin , Cheung Tom H , Ait-Si-Ali Slimane , Le Grand Fabien
Published: June 2023

Modulations in chromatin structure orchestrate gene expression and direct stem cell fate. More specifically, the histone 3 lysine 9 Methyltransferase Setdb1 controls transcriptional repression to regulate pluripotency and self-renewal. While Setdb1 functions have been extensively studied in embryonic stem cells and in cancer cells, less is known on its role in adult stem cellsin vivo. Here, we show that Setdb1 expression by adult muscle stem cells (MuSCs) is required for muscle tissue regeneration following acute injury. We find that SETDB1 represses the expression of the endogenous retroviruses (ERVs) family of transposable elements in MuSCs. ERV de-expression inSetdb1-nullMuSCs prevents their amplification following exit from quiescence and promotes cell death. Multi-omics profiling further shows that the absence of SETDB1 in MuSCs leads to the activation of the DNA-sensing cGAS-STING pathway, entailing increased cytokine expression.In vivo, conditional disruption ofSetdb1in MuSCs provokes aberrant infiltration of inflammatory cells including the appearance of a pathological macrophage lineage. The ensuing histiocytosis is accompanied by necrosis of the newly formed muscle fibers which, in addition with the progressive loss of MuSCs, completely abolish skeletal muscle tissue repair. In contrast, disruption ofSetdb1gene in another muscle-resident cell type, the fibro-adipogenic progenitors (FAPs), does not impact regenerative inflammation. In conclusion, the control of genome stability by SETDB1 in an adult somatic stem cell is necessary for both its regenerative potential and an adequate inflammation regulating tissue repair.