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opencc-by-4.0May 2023View details →

Processed data and scripts supporting the manuscript "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma"

This submission contains the compiled count table, processed R objects and various scripts and output files accompanying our manuscript "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma" (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-38886-8)

opencc-by-4.0Jun 2023View details →

Relapsed multiple myeloma demonstrates distinct patterns of immune microenvironment and malignant cell-mediated immunosuppression

<table> <tbody> <tr> <td>rowID</td> <td>filename</td> <td>date</td> <td>batch</td> <td>group</td> <td>ID</td> </tr> <tr> <td>1</td> <td>20200121_bm003696_RMM_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>RMM</td> <td>bm003696</td> </tr> <tr> <td>2</td> <td>20200121_bm054122_DRMM_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>DRMM</td> <td>bm054122</td> </tr> <tr> <td>3</td> <td>20200121_bm054496_RMM_tx_02.FCS</td> <td>20200121</td> <td>1</td> <td>RMM</td> <td>bm054496</td> </tr> <tr> <td>4</td> <td>20200121_bm059645_NDMM_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>NDMM</td> <td>bm059645</td> </tr> <tr> <td>5</td> <td>20200121_bm060791_NDMM_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>NDMM</td> <td>bm060791</td> </tr> <tr> <td>6</td> <td>20200121_bm064862_DRMM_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>DRMM</td> <td>bm064862</td> </tr> <tr> <td>7</td> <td>20200121_REF2_tx_01.FCS</td> <td>20200121</td> <td>1</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>8</td> <td>20200124_BM038232_RMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>RMM</td> <td>BM038232</td> </tr> <tr> <td>9</td> <td>20200124_BM051757_NDMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>NDMM</td> <td>BM051757</td> </tr> <tr> <td>10</td> <td>20200124_BM052673_DRMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>DRMM</td> <td>BM052673</td> </tr> <tr> <td>11</td> <td>20200124_BM053393_NDMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>NDMM</td> <td>BM053393</td> </tr> <tr> <td>12</td> <td>20200124_BM053570_RMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>RMM</td> <td>BM053570</td> </tr> <tr> <td>13</td> <td>20200124_BM059775_DRMM_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>DRMM</td> <td>BM059775</td> </tr> <tr> <td>14</td> <td>20200124_REF2_TAX_01.FCS</td> <td>20200124</td> <td>2</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>15</td> <td>20200128_3-1-BM060915-DRMM_TX_01.FCS</td> <td>20200128</td> <td>3</td> <td>DRMM</td> <td>BM060915</td> </tr> <tr> <td>16</td> <td>20200128_3-2-BM064896-DRMM_TX_01.FCS</td> <td>20200128</td> <td>3</td> <td>DRMM</td> <td>BM064896</td> </tr> <tr> <td>17</td> <td>20200128_3-3-BM059424-NDMM_TX_01.FCS</td> <td>20200128</td> <td>3</td> <td>NDMM</td> <td>BM059424</td> </tr> <tr> <td>18</td> <td>20200128_3-4-BM059429-NDMM_TX_02.FCS</td> <td>20200128</td> <td>3</td> <td>NDMM</td> <td>BM059429</td> </tr> <tr> <td>19</td> <td>20200128_3-5-BM043778-RMM_TX_01.FCS</td> <td>20200128</td> <td>3</td> <td>RMM</td> <td>BM043778</td> </tr> <tr> <td>20</td> <td>20200128_3-6-BM008007-RMM_TX_01.FCS</td> <td>20200128</td> <td>3</td> <td>RMM</td> <td>BM008007</td> </tr> <tr> <td>21</td> <td>20200129_3-7-ref2_tax_01.FCS</td> <td>20200129</td> <td>3</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>22</td> <td>20200204_5-1_BM054866-DRMM-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>DRMM</td> <td>BM054866</td> </tr> <tr> <td>23</td> <td>20200204_5-2_BM065069-DRMM-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>DRMM</td> <td>BM065069</td> </tr> <tr> <td>24</td> <td>20200204_5-3_BM035491-NDMM-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>NDMM</td> <td>BM035491</td> </tr> <tr> <td>25</td> <td>20200204_5-4_BM0333015-NDMM-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>NDMM</td> <td>BM0333015</td> </tr> <tr> <td>26</td> <td>20200204_5-5_BM0052990-RMM-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>RMM</td> <td>BM0052990</td> </tr> <tr> <td>27</td> <td>20200204_5-5_BM0052990-RMM-Tx_02.FCS</td> <td>20200204</td> <td>5</td> <td>RMM</td> <td>BM0052990</td> </tr> <tr> <td>28</td> <td>20200204_5-5_BM052990-RMM-Tx_02.FCS</td> <td>20200204</td> <td>5</td> <td>RMM</td> <td>BM052990</td> </tr> <tr> <td>29</td> <td>20200204_5-6_BM052692-RMM-Tx_02.FCS</td> <td>20200204</td> <td>5</td> <td>RMM</td> <td>BM052692</td> </tr> <tr> <td>30</td> <td>20200204_5-7 -Ref2-Tx_01.FCS</td> <td>20200204</td> <td>5</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>31</td> <td>20200207_6-1_BM063515_DRMM_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>DRMM</td> <td>BM063515</td> </tr> <tr> <td>32</td> <td>20200207_6-2_BM054226_DRMM_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>DRMM</td> <td>BM054226</td> </tr> <tr> <td>33</td> <td>20200207_6-3_BM008346_NDMM_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>NDMM</td> <td>BM008346</td> </tr> <tr> <td>34</td> <td>20200207_6-4_BM008718_NDMM_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>NDMM</td> <td>BM008718</td> </tr> <tr> <td>35</td> <td>20200207_6-5_BM052764_RMM_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>RMM</td> <td>BM052764</td> </tr> <tr> <td>36</td> <td>20200207_6-6_Ref2_Tax_01.FCS</td> <td>20200207</td> <td>6</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>37</td> <td>20200211_7-1_BM061912_DRMM_TAX_01.FCS</td> <td>20200211</td> <td>7</td> <td>DRMM</td> <td>BM061912</td> </tr> <tr> <td>38</td> <td>20200211_7-2_BM059328_DRMM_TAX_01.FCS</td> <td>20200211</td> <td>7</td> <td>DRMM</td> <td>BM059328</td> </tr> <tr> <td>39</td> <td>20200211_7-3_BM065082_DRMM_TAX_01.FCS</td> <td>20200211</td> <td>7</td> <td>DRMM</td> <td>BM065082</td> </tr> <tr> <td>40</td> <td>20200211_7-4_BM008353_DRMM_TAX_01.FCS</td> <td>20200211</td> <td>7</td> <td>DRMM</td> <td>BM008353</td> </tr> <tr> <td>41</td> <td>20200211_Ref2_Tax_02.FCS</td> <td>20200211</td> <td>7</td> <td>REF</td> <td>REF2</td> </tr> <tr> <td>42</td> <td>20200214_4-1_BM062618_DRMM_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>DRMM</td> <td>BM062618</td> </tr> <tr> <td>43</td> <td>20200214_4-2_BM062255_DRMM_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>DRMM</td> <td>BM062255</td> </tr> <tr> <td>44</td> <td>20200214_4-3_BM032596_NDMM_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>NDMM</td> <td>BM032596</td> </tr> <tr> <td>45</td> <td>20200214_4-4_BM047845_NDMM_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>NDMM</td> <td>BM047845</td> </tr> <tr> <td>46</td> <td>20200214_4-5_BM042666_RMM_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>RMM</td> <td>BM042666</td> </tr> <tr> <td>47</td> <td>20200214_4-6_Ref2_Tax_01.FCS</td> <td>20200214</td> <td>4</td> <td>REF</td> <td>REF2</td> </tr> </tbody> </table>   *files with row ID #26 and #27 need to be concatenated since they represent the same sample acquired over 2 files

opencc-by-4.0Jul 2023View details →

DATASET Skin-Based Vaccination: A Systematic Mapping Review of the Types of Vaccines and Methods Used and Immunity and Protection Elicited in Pigs

Dataset listing all publications used in systematic mapping review. This file contains the dataset, a dictionary and values worksheets for the following publication:  Skin-Based Vaccination: A Systematic Mapping Review of the Types of Vaccines and Methods Used and Immunity and Protection Elicited in Pigs. Vaccines 2023 <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&size=200&term=C%C3%B3-Rives+I&cauthor_id=36851328">Inés Có-Rives</a> <a href="https://pubmed.ncbi.nlm.nih.gov/36851328/#full-view-affiliation-1">1</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&size=200&term=Chen+AY&cauthor_id=36851328">Ann Ying-An Chen</a> <a href="https://pubmed.ncbi.nlm.nih.gov/36851328/#full-view-affiliation-1">1</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&size=200&term=Moore+AC&cauthor_id=36851328">Anne C Moore</a> <a href="https://pubmed.ncbi.nlm.nih.gov/36851328/#full-view-affiliation-1">1</a> <ul> <li>PMID: 36851328</li> <li>PMCID: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc9962282/">PMC9962282</a></li> <li>DOI: <a href="https://doi.org/10.3390/vaccines11020450">10.3390/vaccines11020450</a></li> </ul> The advantages of skin-based vaccination include induction of strong immunity, dose-sparing, and ease of administration. Several technologies for skin-based immunisation in humans are being developed to maximise these key advantages. This route is more conventionally used in veterinary medicine. Skin-based vaccination of pigs is of high relevance due to their anatomical, physiological, and immunological similarities to humans, as well as being a source of zoonotic diseases and their livestock value. We conducted a systematic mapping review, focusing on vaccine-induced immunity and safety after the skin immunisation of pigs. Veterinary vaccines, specifically anti-viral vaccines, predominated in the literature. The safe and potent skin administration to pigs of adjuvanted vaccines, particularly emulsions, are frequently documented. Multiple methods of skin immunisation exist; however, there is a lack of consistent terminology and accurate descriptions of the route and device. Antibody responses, compared to other immune correlates, are most frequently reported. There is a lack of research on the underlying mechanisms of action and breadth of responses. Nevertheless, encouraging results, both in safety and immunogenicity, were observed after skin vaccination that were often comparable to or superior the intramuscular route. Further research in this area will underlie the development of enhanced skin vaccine strategies for pigs, other animals and humans. Keywords: epicutaneous; epidermal; intradermal; needle-free; percutaneous; pig; skin; transcutaneous; transdermal; vaccine.

opencc-by-4.0Jan 2023View details →

Plantago major effects on the innate immunity of Galleria mellonella

These data have been published for the purpose of better evaluation of the article titled "Immunosuppressive effect of Plantago major on the innate immunity of Galleria mellonella" by the referees. These data have been obtained as a result of experiments and all rights belong to the publishing author and the supporting organization. This study was supported by Çanakkale Onsekiz Mart University The Scientific Research Coordination Unit (Grant number: FBA-2020-325).

opencc-zeroJul 2023View details →

Immune challenge affects reproductive behaviour in the Guppy (Poecilia reticulata)

Immunocompetence and reproductive success are among the most important determinants of fitness in animals. However, energetic and metabolic constraints create conflict between these two priorities. The trade-off between immunity and reproductive fitness has been the subject of great scientific interest over many decades. While a number of studies exploring the relationship between immune activity and reproductive fitness/behaviour have been conducted using birds and mammals inoculated with bacterial endotoxin (LPS), relatively few have focussed on fish. This presents a conspicuous gap in our understanding of how immune activity affects reproduction in vertebrates more generally. Fish have been experimentally neglected in this area due, in part, to the claim that fish are largely resistant to the immune effects of endotoxins, and thus presumably suffer negligible behavioural effects. While the immune response to endotoxins may differ somewhat between fish and terrestrial vertebrates, the findings here suggest that they are nonetheless susceptible to significant behavioural effects with respect to reproduction. In this study, we show that although immune challenge does not suppress general activity in male guppies, it significantly reduces reproductive effort. As such, it is important to expand the examination of these processes to a greater diversity of vertebrate species, including fish.

opencc-by-4.0Jul 2023View details →

Data and code for Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba

This repository contains data and code to do the analyses in the paper "Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba" published in Royal Society Open Science. The paper investigates how infection by Paraburkholderia symbionts affects host Dictyostelium discoideum's immune function.

opencc-zeroAug 2023View details →

Adaptive immune response selects for postponed maturation and increased body size

<ol> <li>The Major Histocompatibility Complex (MHC) genes encode proteins that initiate the adaptive immune response by presenting pathogen-derived antigenic peptides to T lymphocytes. Host-pathogen coevolution drives MHC polymorphism, introducing intraspecific variation in host life expectancy. This variation interacts with optimal growth strategy, as growth increases reproductive potential. While mortality rate and body size-dependent fecundity are major factors shaping life histories, the effect of intraspecific variation in MHC-based immunity on the evolution of growth strategies and host body size remains unknown.</li> <li>Here, we model how host MHC–pathogen coevolution—and its concomitant impact on host mortality—can affect the evolution of host life-histories, as represented by age at maturation and body size. Life histories were compared in scenarios with and without adaptive immune response under equal population-level mortality rates.</li> <li>We show that host-pathogen coevolutionary dynamics select for postponed maturation and increased body size. Although MHC genes and genes that determine body size were physically unlinked, selection imposed by the Red Queen process generated linkage disequilibrium between immunocompetent MHC alleles and the maturation-postponing alleles that prolong growth phase and increase body size. Particularly large body size was attained when pathogens mutated slowly, thus allowing the advantage of resistant MHC alleles to persist over multiple generations.</li> <li>The emergence of adaptive immunity, which is pathogen-specific and enables immunological memory, is considered a major evolutionary innovation of vertebrates. Our work suggests that the adaptive immune response, mediated by polymorphic MHC genes, may drive the evolution of host body size. This form of adaptive immunity may have thus predisposed vertebrates to evolve large body sizes and exhibit the macroevolutionary patterns of increasing body size over time that have been detected in comparative studies. </li> </ol>

opencc-zeroAug 2023View details →

A simulated natural heatwave perturbs bumble bee immunity and resistance to infection

As a consequence of ongoing climate change, heatwaves are predicted to increase in frequency, intensity, and duration in many regions. Such extreme events can shift organisms from thermal optima for physiology and behavior, with the thermal stress hypothesis predicting reduced performance at temperatures where the maintenance of biological functions is energetically costly. Performance includes the ability to resist biotic stressors, such as infectious diseases. Climate change is a proposed threat to native bee pollinators, directly and through indirect effects on floral resources, but the thermal stress hypothesis, particularly pertaining to disease resistance, has received limited attention. We exposed adult Bombus impatiens bumble bee workers to simulated, ecologically relevant heatwave or control thermal regimes and assessed longevity, immunity, and resistance to concurrent or future parasite infections. We demonstrate that survival and induced antibacterial immunity are reduced following heatwaves. Supporting that heatwave exposure compromised immunity, the cost of immune activation by a non-pathogenic elicitor was thermal regime dependent, with costs to long-term survival in control but not heatwave exposed bees. However, in the face of real infections, an inability to mount an optimal immune response will be detrimental, which was reflected by higher infections from trypanosome parasite exposure following the heatwave, relative to the control regime. These results demonstrate interactions between heatwave exposure and bumble bee performance, including immune and infection outcomes. Thus, the health of bumble bee pollinator populations may be affected through altered interactions with parasites and pathogens, in addition to other effects of extreme manifestations of climate change.

opencc-by-4.0Sep 2023View details →

Malaria drives unique regulatory responses across multiple immune cells during human infection

To investigate malaria driven transcriptional changes in specific immune cell subsets, we sorted live PBMCs from 6 malaria infected donors (day 0), and two subsequent time points after drug treatment (day 7 and 28), along with PBMCs from 2 healthy controls. We performed scRNAseq of these cells, and used clustering and sub-clustering to identify specific immune cell subsets. Differential gene analysis between day 0 and day 28 was performed for each cell cluster and sub-cluster. Key transcriptional changes were confirmed at the protein level with additional donor samples.

opencc-zeroMar 2023View details →

Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies

Research on COVID-19 vaccination in immune-deficient/disordered people (IDP) has primarily focused on cancer and organ transplantation populations. In a prospective cohort of 195 IDP and 35 healthy volunteers, anti-spike IgG was detected in 88% of IDP post-dose 2, increasing to 93% by six months post-dose 3. Despite high seroconversion, median IgG levels for IDP never surpassed 1/3 that of healthy volunteers. IgG binding to Omicron BA.1 was lower than all other variants. Angiotensin-converting enzyme 2 pseudo-neutralization (% inhibition) was only modestly correlated with anti-spike IgG concentration. IgG levels were not significantly altered by participants' use of different mRNA-based vaccines, immunomodulating treatments, and prior SARS-CoV-2 infections. While our data show that three doses of COVID-19 vaccinations induce anti-spike IgG in most IDP, additional doses are needed to achieve the levels of protection in healthy volunteers. Due to the strikingly reduced IgG response to Omicron BA.1, the efficacy of additional vaccinations, including bivalent vaccines, should be studied in this population.

opencc-by-4.0Oct 2023View details →

A biobank of patients with Primary Immune Deficiencies (PID)

<pre>A biobank of patients with Primary Immune Deficiencies (PID).</pre>

opencc-by-4.0Dec 2022View details →

Targeted social immunity is associated with a pathogen-specific erosion of individual immune function in ants - dataset

Complete dataset of quantitative data and R scripts used to generate the figures and statistics of the publication, sorted by figure panel number. Information about data structure are including in the scripts.

Exploring the Immune Response to SARS-CoV-2 modRNA Vaccines in Patients With Secondary Progressive Multiple Sclerosis (AMA-VACC)

ClinicalTrials.gov study NCT04792567. IPD Sharing: YES. Countries: 1. Publications: 1.

A Study of Rilzabrutinib in Adult Patients With Immune Thrombocytopenia (ITP)

ClinicalTrials.gov study NCT03395210. IPD Sharing: YES. Countries: 8. Publications: 4.

A Study of TAK-981 in People With Advanced Solid Tumors or Cancers in the Immune System

ClinicalTrials.gov study NCT03648372. IPD Sharing: YES. Countries: 1. Publications: 1.

Study of Japanese Encephalitis Chimeric Virus Vaccine (JE-CV) in Children Previously Immunized With JE-CV

ClinicalTrials.gov study NCT01190228. IPD Sharing: YES. Countries: 1. Publications: 1.

A Study to Evaluate Efficacy of rFVIIIFc for Immune Tolerance Induction (ITI) in Severe Hemophilia A Participants With Inhibitors Undergoing the First ITI Treatment (verITI-8 Study)

ClinicalTrials.gov study NCT03093480. IPD Sharing: YES. Countries: 10. Publications: 1.

Immunogenicity and Safety of Tetravalent Dengue Vaccine Candidate (TDV) in Flavivirus-Naïve and Dengue-Immune Adults

ClinicalTrials.gov study NCT03746015. IPD Sharing: YES. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Long Term Immune Memory Responses to HPV Vaccination Following 2 vs 3 Doses of Quad-HPV Vaccine

ClinicalTrials.gov study NCT02968420. IPD Sharing: NO. Countries: 1. Publications: 2.

Study to Evaluate Rilzabrutinib in Adults and Adolescents With Persistent or Chronic Immune Thrombocytopenia (ITP)

ClinicalTrials.gov study NCT04562766. IPD Sharing: YES. Countries: 26. Publications: 3.