Umber Dube
@umberdube.bsky.social
Physician-scientist at UCSD Dermatology | Building the http://InquiLab.org | Patient-inspired. Patient-informed.
"These findings suggest that RD-induced alterations in basement membrane structure may contribute to melanocyte detachment and loss, which is the cause of skin depigmentation not only in RD-induced vitiligo but also in vitiligo."
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The fate of melanocytes and the disorganization of basement membrane in a guinea pig model of Rhododendrol-induced chemical vitiligo
Background : Rhododendrol (RD) is a phenolic compound that was first developed as a skin-lightening agent that occasionally induces skin depigmentation. Although it has been shown that RD induces mela...
www.biorxiv.org
September 28, 2025 at 3:30 PM
"These findings suggest that RD-induced alterations in basement membrane structure may contribute to melanocyte detachment and loss, which is the cause of skin depigmentation not only in RD-induced vitiligo but also in vitiligo."
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Umber Dube
1/Patient-derived xenografts (PDXs) are used in preclinical testing of cancer therapies, including metabolic therapies. We determined which metabolic properties are retained, and which are lost, when melanomas from patients are implanted and passaged as PDXs in mice.
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Conservation and divergence of metabolic phenotypes between patient tumours and matched xenografts - Nature Metabolism
Rao and Cai et al. perform a detailed metabolic comparison between primary tumours from patients and their matching xenografts, which identify conserved as well as divergent metabolic patterns.
www.nature.com
July 29, 2025 at 2:56 PM
1/Patient-derived xenografts (PDXs) are used in preclinical testing of cancer therapies, including metabolic therapies. We determined which metabolic properties are retained, and which are lost, when melanomas from patients are implanted and passaged as PDXs in mice.
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Umber Dube
Structural variants are significant contributor to autism. But many SVs & TRs are hard to detect with short reads. Long read sequencing with @pacbio.bsky.social and @nanoporetech.com captures and maps out alot of what short reads miss. So what can LR-WGS tell us about autism? 🧵
Long Read Genome Sequencing Elucidates Diverse Functional Consequences of Structural and Repeat Variation in Autism https://www.medrxiv.org/content/10.1101/2025.07.20.25331880v1
July 23, 2025 at 10:53 PM
Structural variants are significant contributor to autism. But many SVs & TRs are hard to detect with short reads. Long read sequencing with @pacbio.bsky.social and @nanoporetech.com captures and maps out alot of what short reads miss. So what can LR-WGS tell us about autism? 🧵
Reposted by Umber Dube
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
June 5, 2025 at 1:37 PM
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Reposted by Umber Dube
A very interesting finding is the robust increase in ancestral diversity in younger participants, suggesting that the US population has become more genetically diverse over time.
🔗link to study: nature.com/articles/s41...
🔗link to study: nature.com/articles/s41...
May 3, 2025 at 6:35 PM
A very interesting finding is the robust increase in ancestral diversity in younger participants, suggesting that the US population has become more genetically diverse over time.
🔗link to study: nature.com/articles/s41...
🔗link to study: nature.com/articles/s41...
Reposted by Umber Dube
Big news for health data research and population diversity: The Mexico City Prospective Study data are now available securely to approved researchers worldwide. www.ndph.ox.ac.uk/news/latin-a...
Cohort description: www.ctsu.ox.ac.uk/research/pro...
Cohort description: www.ctsu.ox.ac.uk/research/pro...
Latin-American genetic data available securely to approved researchers worldwide/Datos genéticos latinoamericanos disponibles para investigadores de todo el mundo
www.ndph.ox.ac.uk
May 2, 2025 at 9:05 AM
Big news for health data research and population diversity: The Mexico City Prospective Study data are now available securely to approved researchers worldwide. www.ndph.ox.ac.uk/news/latin-a...
Cohort description: www.ctsu.ox.ac.uk/research/pro...
Cohort description: www.ctsu.ox.ac.uk/research/pro...
Reposted by Umber Dube
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA
An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra
github.com
April 29, 2025 at 9:03 PM
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
Reposted by Umber Dube
Massive multi-ancestry GWAS resource for 1,167 clinical traits & diseases in 6 global biobanks (n=1,789,365)
👉29,139 locus-trait pairs
👉2,624 non-overlapping loci across the genome
👉associated with 6 traits each (median)
👉colocalization across traits for 72% of loci [1/3]
👉29,139 locus-trait pairs
👉2,624 non-overlapping loci across the genome
👉associated with 6 traits each (median)
👉colocalization across traits for 72% of loci [1/3]
April 24, 2025 at 7:57 PM
Massive multi-ancestry GWAS resource for 1,167 clinical traits & diseases in 6 global biobanks (n=1,789,365)
👉29,139 locus-trait pairs
👉2,624 non-overlapping loci across the genome
👉associated with 6 traits each (median)
👉colocalization across traits for 72% of loci [1/3]
👉29,139 locus-trait pairs
👉2,624 non-overlapping loci across the genome
👉associated with 6 traits each (median)
👉colocalization across traits for 72% of loci [1/3]
Thanks to @misharosenbach.bsky.social for amplifying NEJM's call for submissions for this collection to #DermSky
A 3-year-old boy presented with a 6-week history of ulcerated plaques with rolled borders and satellite papules on his left lower leg. He had recently immigrated from Venezuela after a long journey by land with his family. Full case details: nej.md/42fwFIm
@ucsandiego.bsky.social #MedSky
@ucsandiego.bsky.social #MedSky
April 25, 2025 at 4:47 AM
Thanks to @misharosenbach.bsky.social for amplifying NEJM's call for submissions for this collection to #DermSky
Reposted by Umber Dube
Why you should know your viral exposure status (i.e CMV) if you're going to undergo immunotherapy for cancer (but almost no one knows)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CMV serostatus is associated with improved survival and delayed toxicity onset following anti-PD-1 checkpoint blockade - Nature Medicine
Analysis of multiple cohorts of patients with melanoma demonstrates a positive association between cytomegalovirus serostatus and overall survival in patients treated with monotherapy but not combinat...
www.nature.com
April 24, 2025 at 12:43 AM
Why you should know your viral exposure status (i.e CMV) if you're going to undergo immunotherapy for cancer (but almost no one knows)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Umber Dube
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
April 23, 2025 at 11:35 AM
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
Methodological issues in visible LED therapy dermatological research and reporting
"... fluences, wavelengths, and solar exposure equivalent differed by orders of magnitude ..., with effective doses often comparable to typical daily solar exposure."
www.medrxiv.org/content/10.1...
"... fluences, wavelengths, and solar exposure equivalent differed by orders of magnitude ..., with effective doses often comparable to typical daily solar exposure."
www.medrxiv.org/content/10.1...
Methodological issues in visible LED therapy dermatological research and reporting
www.medrxiv.org
April 21, 2025 at 11:09 PM
Methodological issues in visible LED therapy dermatological research and reporting
"... fluences, wavelengths, and solar exposure equivalent differed by orders of magnitude ..., with effective doses often comparable to typical daily solar exposure."
www.medrxiv.org/content/10.1...
"... fluences, wavelengths, and solar exposure equivalent differed by orders of magnitude ..., with effective doses often comparable to typical daily solar exposure."
www.medrxiv.org/content/10.1...
Alpha-synuclein regulates nucleolar DNA double-strand break repair in melanoma | Science Advances www.science.org/doi/10.1126/...
Alpha-synuclein regulates nucleolar DNA double-strand break repair in melanoma
Alpha-synuclein, a neurodegeneration-associated protein, functions in nucleolar DNA double-strand break repair in melanoma.
www.science.org
April 10, 2025 at 6:09 PM
Alpha-synuclein regulates nucleolar DNA double-strand break repair in melanoma | Science Advances www.science.org/doi/10.1126/...
Reposted by Umber Dube
This study is a big deal. Is it going to be the one that kicks down the PRS door? Maybe. And that’s saying something.
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
April 9, 2025 at 9:09 PM
This study is a big deal. Is it going to be the one that kicks down the PRS door? Maybe. And that’s saying something.
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Assessment of a Polygenic Risk Score in Screening for Prostate Cancer www.nejm.org/doi/full/10....
Reposted by Umber Dube
Skin injury releases damage-encoded systemic signals that can initiate immunity to novel antigens introduced at distal barrier sites @sciimmunology.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
April 4, 2025 at 6:32 PM
Skin injury releases damage-encoded systemic signals that can initiate immunity to novel antigens introduced at distal barrier sites @sciimmunology.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Umber Dube
I wrote about how population stratification in genetic analyses led to a decade of false findings and almost certainly continues to bias emerging results. But we are starting to have statistical tools to sniff it out. A 🧵:
How population stratification led to a decade of sensationally false genetic findings
Stratification makes environments look like genes
open.substack.com
March 28, 2025 at 9:54 PM
I wrote about how population stratification in genetic analyses led to a decade of false findings and almost certainly continues to bias emerging results. But we are starting to have statistical tools to sniff it out. A 🧵:
Reposted by Umber Dube
Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden https://www.biorxiv.org/content/10.1101/2024.09.30.615839v1
Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden https://www.biorxiv.org/content/10.1101/2024.09.30.615839v1
L-3,4-dihydroxyphenylalanine (L-DOPA), a naturally occurring tyrosine derivative, is prevalent in en
www.biorxiv.org
October 1, 2024 at 3:17 AM
Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden https://www.biorxiv.org/content/10.1101/2024.09.30.615839v1
Reposted by Umber Dube
An interesting paper describing a class of intermediate melanocytic neoplasms driven by MAP2K1 mutations. www.thelancet.com/journals/ebi...
Clinical outcomes and genomic profiles of MAP2K1-mutated primary cutaneous melanocytic tumours
Class I MAP2K1 mutations typically occur alongside other MAPK pathway mutations and
may contribute to aggressive melanoma behaviour. In contrast, Class II and III MAP2K1
mutations can independently dr...
www.thelancet.com
March 20, 2025 at 1:27 PM
An interesting paper describing a class of intermediate melanocytic neoplasms driven by MAP2K1 mutations. www.thelancet.com/journals/ebi...
Reposted by Umber Dube
Have a look at our newest commentary in @pnas.org :
"G-quadruplexes and their unexpected ability to fold proteins"
Full text: www.pnas.org/doi/10.1073/...
#G4 #quadruplex #proteins #folding
"G-quadruplexes and their unexpected ability to fold proteins"
Full text: www.pnas.org/doi/10.1073/...
#G4 #quadruplex #proteins #folding
G-quadruplexes and their unexpected ability to fold proteins | PNAS
G-quadruplexes and their unexpected ability to fold proteins
www.pnas.org
March 11, 2025 at 9:18 AM
Have a look at our newest commentary in @pnas.org :
"G-quadruplexes and their unexpected ability to fold proteins"
Full text: www.pnas.org/doi/10.1073/...
#G4 #quadruplex #proteins #folding
"G-quadruplexes and their unexpected ability to fold proteins"
Full text: www.pnas.org/doi/10.1073/...
#G4 #quadruplex #proteins #folding
Reposted by Umber Dube
📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
February 27, 2025 at 2:21 AM
📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
Reposted by Umber Dube
Key reads from last week on human genetics, multiomics, and precision medicine 🧵
1⃣New e/sQTL resource from TOPMed
In 14,324 whole blood & tissue samples the study detects cis- and trans-e/sQTLs and colocalizes them with 10,000 GWAS signals for 164 traits.
🔗 www.medrxiv.org/content/10.1...
1⃣New e/sQTL resource from TOPMed
In 14,324 whole blood & tissue samples the study detects cis- and trans-e/sQTLs and colocalizes them with 10,000 GWAS signals for 164 traits.
🔗 www.medrxiv.org/content/10.1...
February 24, 2025 at 4:09 PM
Key reads from last week on human genetics, multiomics, and precision medicine 🧵
1⃣New e/sQTL resource from TOPMed
In 14,324 whole blood & tissue samples the study detects cis- and trans-e/sQTLs and colocalizes them with 10,000 GWAS signals for 164 traits.
🔗 www.medrxiv.org/content/10.1...
1⃣New e/sQTL resource from TOPMed
In 14,324 whole blood & tissue samples the study detects cis- and trans-e/sQTLs and colocalizes them with 10,000 GWAS signals for 164 traits.
🔗 www.medrxiv.org/content/10.1...
Reposted by Umber Dube
🚨NEW PAPER! Together with Wuno Akingbuwa (@wonuola.bsky.social) we developed a way to estimate non-linear genetic correlations. It didnt sit well with us that known non-linear relations (e.g. BMI and MDD with a famous U shaped ) are poorly captured in statistical genetics. 🧵
www.biorxiv.org
February 14, 2025 at 1:30 PM
🚨NEW PAPER! Together with Wuno Akingbuwa (@wonuola.bsky.social) we developed a way to estimate non-linear genetic correlations. It didnt sit well with us that known non-linear relations (e.g. BMI and MDD with a famous U shaped ) are poorly captured in statistical genetics. 🧵
Reposted by Umber Dube
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
The distribution of highly deleterious variants across human ancestry groups
A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...
www.biorxiv.org
February 2, 2025 at 7:00 PM
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
Reposted by Umber Dube
Multi-ancestry meta-analysis of keloids uncovers novel susceptibility loci in diverse populations https://www.medrxiv.org/content/10.1101/2025.01.28.25321288v1
January 31, 2025 at 5:40 PM
Multi-ancestry meta-analysis of keloids uncovers novel susceptibility loci in diverse populations https://www.medrxiv.org/content/10.1101/2025.01.28.25321288v1
Reposted by Umber Dube
Why scratching makes a rash worse and a potential benefit to scratching--it reduced S. aureus on skin. Andrew Liu's paper from our lab is out now at #science #neuroimmune #immunology www.science.org/doi/10.1126/...
Scratching promotes allergic inflammation and host defense via neurogenic mast cell activation
Itch is a dominant symptom in dermatitis, and scratching promotes cutaneous inflammation, thereby worsening disease. However, the mechanisms through which scratching exacerbates inflammation and wheth...
www.science.org
January 30, 2025 at 8:31 PM
Why scratching makes a rash worse and a potential benefit to scratching--it reduced S. aureus on skin. Andrew Liu's paper from our lab is out now at #science #neuroimmune #immunology www.science.org/doi/10.1126/...